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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] [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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Urinary Measurement of Epigenetic DNA Modifications and 8-oxodG as Possible Noninvasive Markers of Colon Cancer Evolution. Int J Mol Sci 2022; 23:ijms232213826. [PMID: 36430302 PMCID: PMC9693012 DOI: 10.3390/ijms232213826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
The active DNA demethylation mechanism involves 5-methylcytosine (5-mCyt) enzymatic oxidation with the subsequent formation of 5-hydroxymethylcytosine (5-hmCyt), which can be further oxidized to 5-formylcytosine (5-fCyt) and 5-carboxylcytosine (5-caCyt). The products of active DNA demethylation are released into the bloodstream and eventually also appear in urine. We used online two-dimensional ultraperformance liquid chromatography with tandem mass spectrometry (2D-UPLC-MS/MS) to compare DNA methylation marks and 8-oxo-2'-deoxyguanosine (8-oxodG) in colorectal cancer and pre-cancerous condition in urine. The study included four groups of subjects: healthy controls, patients with inflammatory bowel disease (IBD), persons with adenomatous polyps (AD), and individuals with colorectal cancer (CRC). We have found that the level of 5-fCyt in urine was significantly lower for CRC and polyp groups than in the control group. The level of 5-hmCyt was significantly higher only in the CRC group compared to the control (2.3 vs. 2.1 nmol/mmol creatinine). Interestingly, we have found highly statistically significant correlation of 5-hydroxymethyluracil with 5-hydroxymethylcytosine, 5-(hydroxymethyl)-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxyuridine, and 5-methyl-2'-deoxycytidine in the CRC patients' group.
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Skalska-Bugala A, Starczak M, Szukalski Ł, Gawronski M, Siomek-Gorecka A, Szpotan J, Labejszo A, Zarakowska E, Szpila A, Jachalska A, Szukalska A, Kruszewski M, Sadowska A, Wasilow A, Baginska P, Czyz J, Olinski R, Rozalski R, Gackowski D. Diagnostic and Prognostic Power of Active DNA Demethylation Pathway Intermediates in Acute Myelogenous Leukemia and Myelodysplastic Syndromes. Cells 2022; 11:cells11050888. [PMID: 35269510 PMCID: PMC8909098 DOI: 10.3390/cells11050888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
Acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are characterized by genomic instability, which may arise from the global hypomethylation of the DNA. The active DNA demethylation process may be linked with aberrant methylation and can be involved in leukemogenesis. The levels of 5-methylcytosine oxidation products were analyzed in minimally invasive material: the cellular DNA from peripheral blood cells and urine of patients with AML and MDS along with the control group, using isotope-dilution two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. The receiver operating characteristic curve analysis was used for the assessment of the ability to discriminate patients’ groups from the control group, and AML from MDS. The most diagnostically useful for discriminating AML patients from the control group was the urinary excretion of 5-hydroxymethylcytosine (AUC = 0.918, sensitivity: 85%, and specificity: 97%), and 5-(hydroxymethyl)-2′-deoxyuridine (0.873, 74%, and 92%), while for MDS patients 5-(hydroxymethyl)-2′-deoxycytidine in DNA (0.905, 82%, and 98%) and urinary 5-hydroxymethylcytosine (0.746, 66%, and 92%). Multi-factor models of classification trees allowed the correct classification of patients with AML and MDS in 95.7% and 94.7% of cases. The highest prognostic value of the analyzed parameters in predicting the transformation of MDS into AML was observed for 5-carboxy-2′-deoxycytidine (0.823, 80%, and 97%) and 5-(hydroxymethyl)-2′-deoxyuridine (0.872, 100%, and 75%) in DNA. The presented research proves that the intermediates of the active DNA demethylation pathway determined in the completely non-invasive (urine) or minimally invasive (blood) material can be useful in supporting the diagnostic process of patients with MDS and AML. The possibility of an early identification of a group of MDS patients with an increased risk of transformation into AML is of particular importance.
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Affiliation(s)
- Aleksandra Skalska-Bugala
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Łukasz Szukalski
- Department of Hematology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-168 Bydgoszcz, Poland; (Ł.S.); (A.J.); (J.C.)
| | - Maciej Gawronski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Agnieszka Siomek-Gorecka
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Justyna Szpotan
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
| | - Anna Labejszo
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Anna Szpila
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Anna Jachalska
- Department of Hematology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-168 Bydgoszcz, Poland; (Ł.S.); (A.J.); (J.C.)
| | - Adriana Szukalska
- Clinic of Hematology, University Hospital No. 2—Jan Biziel Memorial Hospital, 85-168 Bydgoszcz, Poland; (A.S.); (M.K.)
| | - Marcin Kruszewski
- Clinic of Hematology, University Hospital No. 2—Jan Biziel Memorial Hospital, 85-168 Bydgoszcz, Poland; (A.S.); (M.K.)
| | - Anna Sadowska
- Department of Hematology, Nicolaus Copernicus Hospital, 87-100 Toruń, Poland;
| | - Aleksandra Wasilow
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Patrycja Baginska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Jaroslaw Czyz
- Department of Hematology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-168 Bydgoszcz, Poland; (Ł.S.); (A.J.); (J.C.)
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Rafal Rozalski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
- Correspondence: (R.R.); (D.G.); Tel.: +48-525-853-749 (D.G & R.R)
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
- Correspondence: (R.R.); (D.G.); Tel.: +48-525-853-749 (D.G & R.R)
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