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Möller C, Virzi J, Chang YJ, Keidel A, Chao MR, Hu CW, Cooke MS. DNA modifications: Biomarkers for the exposome? ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 108:104449. [PMID: 38636743 DOI: 10.1016/j.etap.2024.104449] [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: 02/12/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
The concept of the exposome is the encompassing of all the environmental exposures, both exogenous and endogenous, across the life course. Many, if not all, of these exposures can result in the generation of reactive species, and/or the modulation of cellular processes, that can lead to a breadth of modifications of DNA, the nature of which may be used to infer their origin. Because of their role in cell function, such modifications have been associated with various major human diseases, including cancer, and so their assessment is crucial. Historically, most methods have been able to only measure one or a few DNA modifications at a time, limiting the information available. With the development of DNA adductomics, which aims to determine the totality of DNA modifications, a far more comprehensive picture of the DNA adduct burden can be gained. Importantly, DNA adductomics can facilitate a "top-down" investigative approach whereby patterns of adducts may be used to trace and identify the originating exposure source. This, together with other 'omic approaches, represents a major tool for unraveling the complexities of the exposome and hence allow a better a understanding of the environmental origins of disease.
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Affiliation(s)
- Carolina Möller
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
| | - Jazmine Virzi
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Alexandra Keidel
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA; College of Public Health, University of South Florida, Tampa, FL 33620, USA; Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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Hojo M, Maeno A, Sakamoto Y, Yamamoto Y, Taquahashi Y, Hirose A, Suzuki J, Inomata A, Nakae D. Time-Course of Transcriptomic Change in the Lungs of F344 Rats Repeatedly Exposed to a Multiwalled Carbon Nanotube in a 2-Year Test. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2105. [PMID: 37513116 PMCID: PMC10383707 DOI: 10.3390/nano13142105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Despite intensive toxicological studies of carbon nanotubes (CNTs) over the last two decades, only a few studies have demonstrated their pulmonary carcinogenicities in chronic animal experiments, and the underlying molecular mechanisms are still unclear. To obtain molecular insights into CNT-induced lung carcinogenicity, we performed a transcriptomic analysis using a set of lung tissues collected from rats in a 2-year study, in which lung tumors were induced by repeated intratracheal instillations of a multiwalled carbon nanotube, MWNT-7. The RNA-seq-based transcriptome identified a large number of significantly differentially expressed genes at Year 0.5, Year 1, and Year 2. Ingenuity Pathway Analysis revealed that macrophage-elicited signaling pathways such as phagocytosis, acute phase response, and Toll-like receptor signaling were activated throughout the experimental period. At Year 2, cancer-related pathways including ERBB signaling and some axonal guidance signaling pathways such as EphB4 signaling were perturbed. qRT-PCR and immunohistochemistry indicated that several key molecules such as Osteopontin/Spp1, Hmox1, Mmp12, and ERBB2 were markedly altered and/or localized in the preneoplastic lesions, suggesting their participation in the induction of lung cancer. Our findings support a scenario of inflammation-induced carcinogenesis and contribute to a better understanding of the molecular mechanism of MWCNT carcinogenicity.
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Affiliation(s)
- Motoki Hojo
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Ai Maeno
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Yoshimitsu Sakamoto
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Yukio Yamamoto
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Yuhji Taquahashi
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences, 3-25-26 Tono-machi, Kawasaki-ku, Kawasaki 210-9501, Kanagawa, Japan
| | - Akihiko Hirose
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan, 1-4-25 Koraku, Bunkyo-ku, Tokyo 112-0004, Japan
| | - Jin Suzuki
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Akiko Inomata
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Dai Nakae
- Department of Medical Sports, Faculty of Health Care and Medical Sports, Teikyo Heisei University, 4-1 Uruido-Minami, Ichihara 290-0193, Chiba, Japan
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4
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Natsume H, Szczepaniak K, Yamada H, Iwashita Y, Gędek M, Šuto J, Ishino K, Kasajima R, Matsuda T, Manirakiza F, Nzitakera A, Wu Y, Xiao N, He Q, Guo W, Cai Z, Ohta T, Szekely T, Kadar Z, Sekiyama A, Oshima T, Yoshikawa T, Tsuburaya A, Kurono N, Wang Y, Miyagi Y, Gurzu S, Sugimura H. Non-CpG sites preference in G:C > A:T transition of TP53 in gastric cancer of Eastern Europe (Poland, Romania and Hungary) compared to East Asian countries (China and Japan). Genes Environ 2023; 45:1. [PMID: 36600315 DOI: 10.1186/s41021-022-00257-y] [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: 07/07/2022] [Accepted: 11/23/2022] [Indexed: 01/05/2023] Open
Abstract
AIM Mutation spectrum of TP53 in gastric cancer (GC) has been investigated world-widely, but a comparison of mutation spectrum among GCs from various regions in the world are still sparsely documented. In order to identify the difference of TP53 mutation spectrum in GCs in Eastern Europe and in East Asia, we sequenced TP53 in GCs from Eastern Europe, Lujiang (China), and Yokohama, Kanagawa (Japan) and identified the feature of TP53 mutations of GC in these regions. SUBJECTS AND METHOD In total, 689 tissue samples of GC were analyzed: 288 samples from East European populations (25 from Hungary, 71 from Poland and 192 from Romania), 268 from Yokohama, Kanagawa, Japan and 133 from Lujiang, Anhui province, China. DNA was extracted from FFPE tissue of Chinese, East European cases; and from frozen tissue of Japanese GCs. PCR products were direct-sequenced by Sanger method, and in ambiguous cases, PCR product was cloned and up to 8 clones were sequenced. We used No. NC_000017.11(hg38) as the reference sequence of TP53. Mutation patterns were categorized into nine groups: six base substitutions, insertion, deletion and deletion-insertion. Within G:C > A:T mutations the mutations in CpG and non-CpG sites were divided. The Cancer Genome Atlas data (TCGA, ver.R20, July, 2019) having somatic mutation list of GCs from Whites, Asians, and other ethnicities were used as a reference for our data. RESULTS The most frequent base substitutions were G:C > A:T transition in all the areas investigated. The G:C > A:T transition in non-CpG sites were prominent in East European GCs, compared with Asian ones. Mutation pattern from TCGA data revealed the same trend between GCs from White (TCGA category) vs Asian countries. Chinese and Japanese GCs showed higher ratio of G:C > A:T transition in CpG sites and A:T > G:C mutation was more prevalent in Asian countries. CONCLUSION The divergence in mutation spectrum of GC in different areas in the world may reflect various pathogeneses and etiologies of GC, region to region. Diversified mutation spectrum in GC in Eastern Europe may suggest GC in Europe has different carcinogenic pathway of those from Asia.
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Affiliation(s)
- Hiroko Natsume
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Kinga Szczepaniak
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Medical University of Warsaw, 1B Banacha Street, Warsaw, Poland
| | - Hidetaka Yamada
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
| | - Yuji Iwashita
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Marta Gędek
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Medical University of Lublin, ul. Radziwiłłowska 11, wew, 5647, Lublin, Poland
| | - Jelena Šuto
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Department of Oncology, Clinical Hospital Centre Split, Split, Croatia
| | - Keiko Ishino
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Rika Kasajima
- The Center for Cancer Genome Medicine, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi-ku, Yokohama, Kanagawa, 241-8515, Japan.,Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Felix Manirakiza
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Augustin Nzitakera
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Yijia Wu
- Lujiang People Hospital, 32 Wenmingzhong Road, Lujiang, Hefei, 231501, China
| | - Nong Xiao
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Qiong He
- Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Wenwen Guo
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China.,Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Zhenming Cai
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China.,Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjing, 211166, China
| | - Tsutomu Ohta
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Department of Physical Therapy, Faculty of Health and Medical Sciences, Tokoha University, 1230 Miyakoda-cho, Kita-ku, Hamamatsu, Shizuoka, 431-2102, Japan
| | - Tıberiu Szekely
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, Targu Mures, Ghe Marinescu 38 Street, 540139, Targu Mures, Romania.,Department of Oncology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, Targu Mures, Ghe Marinescu 38 Street, 540139, Targu Mures, Romania
| | - Zoltan Kadar
- Department of Oncology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, Targu Mures, Ghe Marinescu 38 Street, 540139, Targu Mures, Romania
| | - Akiko Sekiyama
- Department of Clinical Laboratory, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi-ku, Yokohama, Kanagawa, 241-8515, Japan
| | - Takashi Oshima
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi-ku, Yokohama, Kanagawa, 241-8515, Japan
| | - Takaki Yoshikawa
- Department of Gastric Surgery, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akira Tsuburaya
- Department of Surgery, Ozawa Hospital, 1-1-17, Honcho, Odawara, Kanagawa, 250-0012, Japan
| | - Nobuhito Kurono
- Department of Chemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Yaping Wang
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China.
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Asahi-ku, Yokohama, 241-8515, Japan.
| | - Simona Gurzu
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, Targu Mures, Ghe Marinescu 38 Street, 540139, Targu Mures, Romania.
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higasi-ku, Hamamatsu, Shizuoka, 431-3192, Japan. .,Sasaki Foundation Sasaki Institute, 2-2, KandaSurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan.
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