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Diaz AH, Duque-Noreña M, Rincón E, Chamorro E. Explainable no-code OECD-compliant machine learning models to predict the mutagenic activity of polycyclic aromatic hydrocarbons and their radical cation metabolites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 972:179133. [PMID: 40101616 DOI: 10.1016/j.scitotenv.2025.179133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 03/10/2025] [Accepted: 03/11/2025] [Indexed: 03/20/2025]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are persistent pollutants with well-known genotoxic and mutagenic effects, posing risks to ecosystems and human health. Their hydrophobic nature promotes accumulation in soils and aquatic environments, increasing exposure risks. Upon metabolic activation, PAHs generate reactive species that form DNA adducts, driving their mutagenic potential. This study presents an OECD-compliant methodology that integrates conceptual density functional theory (CDFT) calculations at the GFN2-xTB level with machine learning models to predict PAH mutagenicity. Using quantum chemical descriptors of procarcinogens and radical cation metabolites alongside Ames test data, key electronic properties linked to mutagenicity were identified. Feature selection consistently highlighted radical cation descriptors as key indicators of metabolic activation pathways. Machine learning models - including SPAARC, Random Tree, and JCHAID - achieved validation accuracies exceeding 89 %, with minimal false-negative rates, ensuring conservative predictions for environmental risk assessment. The PSL and CDP electrophilicity frameworks proved particularly effective in modeling DNA damage-related processes. This no-code, freeware-based methodology provides a scalable and cost-effective tool for assessing mutagenic risks in environmentally relevant conditions. The findings reinforce the importance of metabolic activation, validate the radical cation as a reliable proxy for this process, and demonstrate the predictive value of electronic properties in QSAR modeling. These insights support advances in environmental toxicology and contribute to improved strategies for regulatory risk assessment.
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Affiliation(s)
- Andrés Halabi Diaz
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Avenida Republica 275, Santiago 8370146, Chile; Departamento de Investigación y Desarrollo, Good Global Research and Science (GGRS), Avenida Ramón Picarte 780, Valdivia 5090000, Chile; Departamento de I+D+i, CatchPredict SpA, Avenida Ramón Picarte 780, Valdivia 5090000, Chile.
| | - Mario Duque-Noreña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Avenida Republica 275, Santiago 8370146, Chile; Centro de Investigación para el Diseño de Materiales (CEDEM), Facultad de Ciencias Exactas, Universidad Andrés Bello, Avenida Republica 275, 8370146 Santiago, Chile.
| | - Elizabeth Rincón
- Facultad de Ciencias, Instituto de Ciencias Químicas, Universidad Austral de Chile, Independencia 631, Valdivia 5090000, Chile.
| | - Eduardo Chamorro
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Campus Universitario, Ciudad Empresarial, Avenida del Condor 720, 8580704 Huechuraba, Santiago, Chile.
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Chen KM, Krebs NM, Sun YW, Sun D, Liao J, Reinhart L, Krzeminski J, Amin S, Stoner G, Mallery SR, El-Bayoumy K. Inhibition of benzo[a]pyrene-induced DNA adduct in buccal cells of smokers by black raspberry lozenges. Carcinogenesis 2025; 46:bgae067. [PMID: 39367810 PMCID: PMC11886790 DOI: 10.1093/carcin/bgae067] [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] [Received: 06/28/2024] [Revised: 09/18/2024] [Accepted: 10/03/2024] [Indexed: 10/07/2024] Open
Abstract
Using LC-MS/MS analysis we previously showed for the first time (Carcinogenesis 43:746-753, 2022) that levels of DNA damage induced by benzo[a]pyrene (B[a]P), an oral carcinogen and tobacco smoke (TS) constituent, were significantly higher in buccal cells of smokers than those in nonsmokers; these results suggest the potential contribution of B[a]P in the development of oral squamous cell carcinoma (OSCC) in humans. Treating cancers, including OSCC, at late stages, even with improved targeted therapies, continues to be a major challenge. Thus interception/prevention remains a preferable approach for OSCC management and control. In previous preclinical studies, we and others demonstrated the protective effects of black raspberry (BRB) against carcinogen-induced DNA damage and OSCC. Thus, to translate preclinical findings, we tested the hypothesis in a Phase 0 clinical study that BRB administration reduces DNA damage induced by B[a]P in the buccal cells of smokers. After enrolling 27 smokers, baseline buccal cells were collected before the administration of BRB lozenges (5/day for 8 weeks, 1 gm BRB powder/lozenge) at baseline, at the middle and the end of BRB administration. The last samples were collected 4 weeks after BRB cessation (washout period). B[a]P-induced DNA damage (BPDE-N2-dG) was evaluated by LC-MS/MS. BRB administration resulted in a significant reduction in DNA damage: 26.3% at the midpoint (P = .01506) compared to baseline, 36.1% at the end of BRB administration (P = .00355), and 16.6% after BRB cessation (P = .007586). Our results suggest the potential benefits of BRB as a chemopreventive agent against the development of TS-initiated OSCC.
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Affiliation(s)
- Kun-Ming Chen
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, United States
| | - Nicolle M Krebs
- Department of Public Health Sciences, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, United States
| | - Yuan-Wan Sun
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, United States
| | - Dongxiao Sun
- Department of Pharmacology, Mass Spectrometry Core Facilities, 500 University Drive, Penn State College of Medicine, Hershey, PA 17033, United States
| | - Jiangang Liao
- Department of Public Health Sciences, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, United States
| | - Lisa Reinhart
- Department of Public Health Sciences, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, United States
| | - Jacek Krzeminski
- Department of Pharmacology, Mass Spectrometry Core Facilities, 500 University Drive, Penn State College of Medicine, Hershey, PA 17033, United States
| | - Shantu Amin
- Department of Pharmacology, Mass Spectrometry Core Facilities, 500 University Drive, Penn State College of Medicine, Hershey, PA 17033, United States
| | - Gary Stoner
- Department of Medicine, College of Medicine, The Ohio State University, 1645 Neil Avenue, Columbus, OH 43210, United States
| | - Susan R Mallery
- Division of Oral Maxillofacial Pathology, College of Dentistry, 305 West 12th Avenue, The Ohio State University, Columbus, OH 43210, United States
| | - Karam El-Bayoumy
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, United States
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Chen KM, Sun YW, Krebs NM, Reinhart L, Sun D, Liao J, Cook R, Elizabeth PB, Mallery SR, El-Bayoumy K. The Effects of Black Raspberry as a Whole Food-Based Approach on Biomarkers of Oxidative Stress in Buccal Cells and Urine of Smokers. Cancer Prev Res (Phila) 2024; 17:157-167. [PMID: 38286439 PMCID: PMC10987264 DOI: 10.1158/1940-6207.capr-23-0153] [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] [Received: 04/21/2023] [Revised: 12/12/2023] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
Cigarette smoke is a rich source of free radicals that can promote oxidative stress and carcinogenesis, including head and neck squamous cell carcinoma (HNSCC) development; importantly, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-iso-prostaglandin F2α (8-isoprostane) are biomarkers of oxidative stress. Several mechanisms, including the antioxidant properties of black raspberry (BRB), account for their chemopreventive effects. In the present clinical trial, we tested the hypothesis that BRB administration reduces biomarkers levels of oxidative stress in buccal cells and urine of smokers. One week after enrolling 21 smokers, baseline buccal cells and urine samples were collected before the administration of BRB lozenges for 8 weeks (5/day, 1 gm BRB/lozenge). Buccal cells and urine samples were collected at the middle and the end of BRB administration. The last samples were collected after the BRB cessation (washout period). We analyzed levels of 8-oxodG and 8-isoprostane (LC/MS-MS), urinary cotinine (ELISA), and creatinine (spectrophotometry). BRB significantly reduced the levels of 8-oxodG by 17.08% (P = 0.00079) in buccal cells and 12.44% (P = 0.034) in urine at the middle of BRB administration as compared with baseline; the corresponding values at the end of BRB administration were 16.46% (P = 0.026) in buccal cells and 25.72% (P = 0.202) in urine. BRB had no significant effect on the levels of urinary 8-isoprostane. BRB's capacity to inhibit 8-oxodG formation of smokers' buccal cells and urine is clearly evident and the reduction in 8-oxodG suggests that antioxidant abilities are central to BRB's HNSCC chemopreventive properties. PREVENTION RELEVANCE Cigarette smoke contains highly active components namely free radicals that can promote oxidative stress and oral cancer. We found that black raspberry (BRB) inhibited the formation of oxidative stress markers in the oral cavity and urine of smokers suggesting the antioxidant abilities of BRB in preventing oral cancer.
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Affiliation(s)
- Kun-Ming Chen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Yuan-Wan Sun
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Nicolle M. Krebs
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Lisa Reinhart
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Dongxiao Sun
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Jiangang Liao
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Rachel Cook
- Undergraduate Student, Pennsylvania State University, University Park, PA 16802
| | - Paige Bond Elizabeth
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Susan R. Mallery
- College of Dentistry, Division of Oral Maxillofacial Pathology, Ohio State University, Columbus, Ohio
| | - Karam El-Bayoumy
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033
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Wang G, Su H, Guo Z, Li H, Jiang Z, Cao Y, Li C. Rubus Occidentalis and its bioactive compounds against cancer: From molecular mechanisms to translational advances. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 126:155029. [PMID: 38417241 DOI: 10.1016/j.phymed.2023.155029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/05/2023] [Accepted: 08/15/2023] [Indexed: 03/01/2024]
Abstract
BACKGROUND Cancer ranks as the second leading cause of death globally, imposing a significant public health burden. The rise in cancer resistance to current therapeutic agents underscores the potential role of phytotherapy. Black raspberry (BRB, Rubus Occidentalis) is a fruit rich in anthocyanins, ellagic acid, and ellagitannins. Accumulating evidence suggests that BRB exhibits promising anticancer effects, positioning it as a viable candidate for phytotherapy. PURPOSE This article aims to review the existing research on BRB regarding its role in cancer prevention and treatment. It further analyzes the effective components of BRB, their metabolic pathways, and the potential mechanisms underlying the fruit's anticancer effects. METHODS Ovid MEDLINE, EMBASE, Web of Science, and CENTRAL were searched through the terms of Black Raspberry, Raspberry, and Rubus Occidentali up to January 2023. Two reviewers performed the study selection by screening the title and abstract. Full texts of potentially eligible studies were retrieved to access the details. RESULTS Out of the 767 articles assessed, 73 papers met the inclusion criteria. Among them, 63 papers investigated the anticancer mechanisms, while 10 conducted clinical trials focusing on cancer treatment or prevention. BRB was found to influence multiple cancer hallmarks by targeting various pathways. Decomposition of free radicals and regulation of estrogen metabolism, BRB can reduce DNA damage caused by reactive oxygen species. BRB can also enhance the function of nucleotide excision repair to repair DNA lesions. Through regulation of epigenetics, BRB can enhance the expression of tumor suppressor genes, inducing cell cycle arrest, and promoting apoptosis and pyroptosis. BRB can reduce the energy and nutrients supply to the cancer nest by inhibiting glycolysis and reducing angiogenesis. The immune and inflammatory microenvironment surrounding cancer cells can also be ameliorated by BRB, inhibiting cancer initiation and progression. However, the limited bioavailability of BRB diminishes its anticancer efficacy. Notably, topical applications of BRB, such as gels and suppositories, have demonstrated significant clinical benefits. CONCLUSION BRB inhibits cancer initiation, progression, and metastasis through diverse anticancer mechanisms while exhibiting minimal side effects. Given its potential, BRB emerges as a promising phototherapeutic agent for cancer treatment.
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Affiliation(s)
- Guanru Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China; Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China
| | - Hengpei Su
- College of Materials Science and Engineering, Sichuan University, No.29, Jiuyanqiao Wangjiang Rd., Chengdu 610064, China
| | - Zijian Guo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China; Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China
| | - Honglin Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China; Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China
| | - Zhishen Jiang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China
| | - Yubin Cao
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China; Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China.
| | - Chunjie Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China; Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section of Ren Min Nan Rd., Chengdu 610041, China.
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