Adductome: Difference between revisions
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{{Short description|Study of DNA adducts}} |
{{Short description|Study of DNA adducts}} |
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'''Adductomics''' is the study of the totality of [[ |
'''Adductomics''' is the study of the totality of [[adduct]]s arising from modification of either nucleic acids, such as [[DNA]], and [[RNA]], or [[protein]]s, the context of the totality of the adducts e.g., all the different DNA adducts that are present in the genome of a particular sample. [[DNA adducts]] arise from [[Chemical compound|compounds]] that bind to [[DNA]], that covalently modify the DNA, resulting in damage. This damage can result in [[mutations]]. These mutations can result in a variety of adverse health effects, including [[cancer]] and [[birth defects]] in [[multicellular organisms]]. The science of adductomics seeks to identify and measure all DNA, RNA or protein adducts, identify their origins, and determine their role in health and disease. |
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The term "adductome" first appeared in a journal article in 2005.<ref>{{cite journal | vauthors = Tomonari M, Kanaly RA, Tomoyuki H, Haruhiko S, Hirokazu T, Saber M | date = 2005 | title = DNA adductome strategy for detection of multiple DNA adducts. | journal = Nippon Kankyo Hen'igen Gakkai Taikai Puroguramu | location = Yoshishu | volume = 34 | page = 77 | trans-journal = Program of the Annual Meeting of the Japanese Society of Mutagenesis }}</ref> Although originally the term related to adducts of DNA, the adductomic approach has now been adopted by [[protein]] chemists in their attempts to identify [[protein adducts]]. More recently, this has been extended by Kanaly's group to include RNA adducts.<ref>{{cite journal | vauthors = Takeshita T, Kanaly RA | title = <i>In vitro</i> DNA/RNA Adductomics to Confirm DNA Damage Caused by Benzo[<i>a</i>]pyrene in the Hep G2 Cell Line | journal = Frontiers in Chemistry | volume = 7 | pages = 491 | date = 2019 | pmid = 31338364 | doi = 10.3389/fchem.2019.00491 | pmc = 6629907 | bibcode = 2019FrCh....7..491T | doi-access = free }}</ref> Most recently, nucleic acid adductomics has been reported, which has to potential to study a range of DNA and RNA adducts.<ref name=" |
The term "adductome" first appeared in a journal article in 2005.<ref>{{cite journal | vauthors = Tomonari M, Kanaly RA, Tomoyuki H, Haruhiko S, Hirokazu T, Saber M | date = 2005 | title = DNA adductome strategy for detection of multiple DNA adducts. | journal = Nippon Kankyo Hen'igen Gakkai Taikai Puroguramu | location = Yoshishu | volume = 34 | page = 77 | trans-journal = Program of the Annual Meeting of the Japanese Society of Mutagenesis }}</ref> Although originally the term related to adducts of DNA, the adductomic approach has now been adopted by [[protein]] chemists in their attempts to identify [[protein adducts]]. More recently, this has been extended by Kanaly's group to include RNA adducts.<ref>{{cite journal | vauthors = Takeshita T, Kanaly RA | title = <i>In vitro</i> DNA/RNA Adductomics to Confirm DNA Damage Caused by Benzo[<i>a</i>]pyrene in the Hep G2 Cell Line | journal = Frontiers in Chemistry | volume = 7 | pages = 491 | date = 2019 | pmid = 31338364 | doi = 10.3389/fchem.2019.00491 | pmc = 6629907 | bibcode = 2019FrCh....7..491T | doi-access = free }}</ref> Most recently, nucleic acid adductomics has been reported, which has to potential to study a range of DNA and RNA adducts.<ref name="Cooke_2023">{{cite journal | vauthors = Cooke MS, Chang YJ, Chen YR, Hu CW, Chao MR | title = Nucleic acid adductomics - The next generation of adductomics towards assessing environmental health risks | journal = The Science of the Total Environment | volume = 856 | issue = Pt 2 | pages = 159192 | date = January 2023 | pmid = 36195140 | doi = 10.1016/j.scitotenv.2022.159192 | bibcode = 2023ScTEn.856o9192C }}</ref> |
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== DNA and RNA == |
== DNA and RNA == |
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== Nucleic acid == |
== Nucleic acid == |
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Nucleic acid (NA) adductomics brings together DNA-, RNA- and, to some extent, protein adductomics to provide a more comprehensive view of the adduct burden to these molecules. NA adductomics builds upon previous DNA adductomics and DNA crosslinkomics <ref>{{cite journal | vauthors = Hu CW, Chang YJ, Cooke MS, Chao MR | title = DNA Crosslinkomics: A Tool for the Comprehensive Assessment of Interstrand Crosslinks Using High Resolution Mass Spectrometry | journal = Analytical Chemistry | volume = 91 | issue = 23 | pages = 15193–15203 | date = December 2019 | pmid = 31670503 | pmc = 6891145 | doi = 10.1021/acs.analchem.9b04068 }}</ref> (which aims to analyze the totality of DNA-DNA crosslinks <ref>{{cite journal | vauthors = Noll DM, Mason TM, Miller PS | title = Formation and repair of interstrand cross-links in DNA | journal = Chemical Reviews | volume = 106 | issue = 2 | pages = 277–301 | date = February 2006 | pmid = 16464006 | pmc = 2505341 | doi = 10.1021/cr040478b }}</ref>) assays <ref>{{cite journal | vauthors = Stornetta A, Villalta PW, Hecht SS, Sturla SJ, Balbo S | title = Screening for DNA Alkylation Mono and Cross-Linked Adducts with a Comprehensive LC-MS(3) Adductomic Approach | journal = Analytical Chemistry | volume = 87 | issue = 23 | pages = 11706–11713 | date = December 2015 | pmid = 26509677 | pmc = 5126974 | doi = 10.1021/acs.analchem.5b02759 }}</ref> and encompasses the analysis of modified (2′-deoxy)ribonucleosides (2′-dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks.<ref name=" |
Nucleic acid (NA) adductomics brings together DNA-, RNA- and, to some extent, protein adductomics to provide a more comprehensive view of the adduct burden to these molecules. NA adductomics builds upon previous DNA adductomics and DNA crosslinkomics <ref>{{cite journal | vauthors = Hu CW, Chang YJ, Cooke MS, Chao MR | title = DNA Crosslinkomics: A Tool for the Comprehensive Assessment of Interstrand Crosslinks Using High Resolution Mass Spectrometry | journal = Analytical Chemistry | volume = 91 | issue = 23 | pages = 15193–15203 | date = December 2019 | pmid = 31670503 | pmc = 6891145 | doi = 10.1021/acs.analchem.9b04068 }}</ref> (which aims to analyze the totality of DNA-DNA crosslinks <ref>{{cite journal | vauthors = Noll DM, Mason TM, Miller PS | title = Formation and repair of interstrand cross-links in DNA | journal = Chemical Reviews | volume = 106 | issue = 2 | pages = 277–301 | date = February 2006 | pmid = 16464006 | pmc = 2505341 | doi = 10.1021/cr040478b }}</ref>) assays <ref>{{cite journal | vauthors = Stornetta A, Villalta PW, Hecht SS, Sturla SJ, Balbo S | title = Screening for DNA Alkylation Mono and Cross-Linked Adducts with a Comprehensive LC-MS(3) Adductomic Approach | journal = Analytical Chemistry | volume = 87 | issue = 23 | pages = 11706–11713 | date = December 2015 | pmid = 26509677 | pmc = 5126974 | doi = 10.1021/acs.analchem.5b02759 }}</ref> and encompasses the analysis of modified (2′-deoxy)ribonucleosides (2′-dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks.<ref name="Cooke_2023" /> Interestingly, many of these types of adducts are seen in urine from healthy humans, using ''urinary NA adductomics''.<ref name="Cooke_2023" /> Confirmation of the presence of DNA-RNA crosslinks in urine came from a recent study that demonstrated the presence of cellular DNA-RNA crosslinks, arising from [[formaldehyde]] exposure.<ref>{{cite journal | vauthors = Dator RP, Murray KJ, Luedtke MW, Jacobs FC, Kassie F, Nguyen HD, Villalta PW, Balbo S | display-authors = 6 | title = Identification of Formaldehyde-Induced DNA-RNA Cross-Links in the A/J Mouse Lung Tumorigenesis Model | journal = Chemical Research in Toxicology | volume = 35 | issue = 11 | pages = 2025–2036 | date = November 2022 | pmid = 36356054 | pmc = 10336729 | doi = 10.1021/acs.chemrestox.2c00206 | pmc-embargo-date = November 21, 2023 }}</ref> |
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== References == |
== References == |
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Revision as of 06:58, 19 August 2023
Adductomics is the study of the totality of adducts arising from modification of either nucleic acids, such as DNA, and RNA, or proteins, the context of the totality of the adducts e.g., all the different DNA adducts that are present in the genome of a particular sample. DNA adducts arise from compounds that bind to DNA, that covalently modify the DNA, resulting in damage. This damage can result in mutations. These mutations can result in a variety of adverse health effects, including cancer and birth defects in multicellular organisms. The science of adductomics seeks to identify and measure all DNA, RNA or protein adducts, identify their origins, and determine their role in health and disease.
The term "adductome" first appeared in a journal article in 2005.[1] Although originally the term related to adducts of DNA, the adductomic approach has now been adopted by protein chemists in their attempts to identify protein adducts. More recently, this has been extended by Kanaly's group to include RNA adducts.[2] Most recently, nucleic acid adductomics has been reported, which has to potential to study a range of DNA and RNA adducts.[3]
DNA and RNA
Cellular DNA and/or RNA adductomics is performed after the target nucleic acid has been extracted from the cells [4] (e.g., from cultured cells, or tissues). Urinary DNA adductomics non-invasively evaluates DNA adducts that are present in urine,[5] following their DNA repair.[6]
Nucleic acid
Nucleic acid (NA) adductomics brings together DNA-, RNA- and, to some extent, protein adductomics to provide a more comprehensive view of the adduct burden to these molecules. NA adductomics builds upon previous DNA adductomics and DNA crosslinkomics [7] (which aims to analyze the totality of DNA-DNA crosslinks [8]) assays [9] and encompasses the analysis of modified (2′-deoxy)ribonucleosides (2′-dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks.[3] Interestingly, many of these types of adducts are seen in urine from healthy humans, using urinary NA adductomics.[3] Confirmation of the presence of DNA-RNA crosslinks in urine came from a recent study that demonstrated the presence of cellular DNA-RNA crosslinks, arising from formaldehyde exposure.[10]
References
- ^ Tomonari M, Kanaly RA, Tomoyuki H, Haruhiko S, Hirokazu T, Saber M (2005). "DNA adductome strategy for detection of multiple DNA adducts". Nippon Kankyo Hen'igen Gakkai Taikai Puroguramu [Program of the Annual Meeting of the Japanese Society of Mutagenesis]. 34. Yoshishu: 77.
- ^ Takeshita T, Kanaly RA (2019). "In vitro DNA/RNA Adductomics to Confirm DNA Damage Caused by Benzo[a]pyrene in the Hep G2 Cell Line". Frontiers in Chemistry. 7: 491. Bibcode:2019FrCh....7..491T. doi:10.3389/fchem.2019.00491. PMC 6629907. PMID 31338364.
- ^ a b c Cooke MS, Chang YJ, Chen YR, Hu CW, Chao MR (January 2023). "Nucleic acid adductomics - The next generation of adductomics towards assessing environmental health risks". The Science of the Total Environment. 856 (Pt 2): 159192. Bibcode:2023ScTEn.856o9192C. doi:10.1016/j.scitotenv.2022.159192. PMID 36195140.
- ^ Balbo S, Turesky RJ, Villalta PW (March 2014). "DNA adductomics". Chemical Research in Toxicology. 27 (3): 356–366. doi:10.1021/tx4004352. PMC 3997222. PMID 24437709.
- ^ Cooke MS, Hu CW, Chang YJ, Chao MR (December 2018). "Urinary DNA adductomics - A novel approach for exposomics". Environment International. 121 (Pt 2): 1033–1038. doi:10.1016/j.envint.2018.10.041. PMC 6279464. PMID 30392940.
- ^ Evans MD, Saparbaev M, Cooke MS (September 2010). "DNA repair and the origins of urinary oxidized 2'-deoxyribonucleosides". Mutagenesis. 25 (5): 433–442. doi:10.1093/mutage/geq031. PMID 20522520.
- ^ Hu CW, Chang YJ, Cooke MS, Chao MR (December 2019). "DNA Crosslinkomics: A Tool for the Comprehensive Assessment of Interstrand Crosslinks Using High Resolution Mass Spectrometry". Analytical Chemistry. 91 (23): 15193–15203. doi:10.1021/acs.analchem.9b04068. PMC 6891145. PMID 31670503.
- ^ Noll DM, Mason TM, Miller PS (February 2006). "Formation and repair of interstrand cross-links in DNA". Chemical Reviews. 106 (2): 277–301. doi:10.1021/cr040478b. PMC 2505341. PMID 16464006.
- ^ Stornetta A, Villalta PW, Hecht SS, Sturla SJ, Balbo S (December 2015). "Screening for DNA Alkylation Mono and Cross-Linked Adducts with a Comprehensive LC-MS(3) Adductomic Approach". Analytical Chemistry. 87 (23): 11706–11713. doi:10.1021/acs.analchem.5b02759. PMC 5126974. PMID 26509677.
- ^ Dator RP, Murray KJ, Luedtke MW, Jacobs FC, Kassie F, Nguyen HD, et al. (November 2022). "Identification of Formaldehyde-Induced DNA-RNA Cross-Links in the A/J Mouse Lung Tumorigenesis Model". Chemical Research in Toxicology. 35 (11): 2025–2036. doi:10.1021/acs.chemrestox.2c00206. PMC 10336729. PMID 36356054.
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