Development of an untargeted DNA adductomics method by ultra-high performance liquid chromatography coupled to
Giorgia La Barbera1, Marshal Spenser Shuler1, Søren Hammershøj Beck2
1Department of Nutrition Exercise and Sports, University of Copenhagen, Frederiksberg, DK-1985, Denmark.
Abstract:
Genotoxicants originating from inflammation, diet, and environment can covalently modify DNA, possibly initiating the process of carcinogenesis. DNA adducts have been known for long, but the old methods allowed to target only a few known DNA adducts at a time, not providing a global picture of the "DNA adductome". DNA adductomics is a new research field, aiming to screen for unknown DNA adducts by high resolution mass spectrometry (HRMS). However, DNA adductomics presents several analytical challenges such as the need for high sensitivity and for the development of effective screening approaches to identify novel DNA adducts. In this work, a sensitive untargeted DNA adductomics method was developed by using ultra-high performance liquid chromatography (UHPLC) coupled via an ESI source to a quadrupole-time of flight mass spectrometric instrumentation. Mobile phases with ammonium bicarbonate gave the best signal enhancement. The MS capillary voltage, cone voltage, and detector voltage had most effect on the response of the DNA adducts. A low adsorption vial was selected for reducing analyte loss. Hybrid surface-coated analytical columns were tested for reducing adsorption of the DNA adducts. The optimized method was applied to analyse DNA adducts in calf thymus, cat colon, and human colon DNA by performing a MSE acquisition (all-ion fragmentation acquisition) and screening for the loss of deoxyribose and the nucleobase fragment ions. Fifty-four DNA adducts were tentatively identified, hereof 38 never reported before. This is the first untargeted DNA adductomics study on human colon tissue, and one of the few untargeted DNA adductomics studies in the literature reporting the identification of such a high number of unknowns. This demonstrates promising results for the application of this sensitive method in future human studies for investigating novel potential cancer-causing factors.
Insights
Researchers developed a new, sensitive method to detect unknown DNA adducts, identifying 38 novel compounds. This DNA adductomics approach advances cancer research by revealing potential environmental carcinogens.
Area of Science:
- Environmental chemistry
- Molecular toxicology
- Analytical chemistry
Background:
- Genotoxicants from various sources can damage DNA, potentially leading to cancer.
- Traditional methods for DNA adduct analysis are limited, hindering a comprehensive understanding of the 'DNA adductome'.
- DNA adductomics, using high-resolution mass spectrometry (HRMS), aims to screen for unknown DNA adducts but faces sensitivity and screening challenges.
Purpose of the Study:
- To develop a sensitive, untargeted DNA adductomics method for identifying novel DNA adducts.
- To overcome analytical challenges in DNA adductomics, including sensitivity and effective screening approaches.
- To apply the developed method to analyze DNA adducts in various biological samples, including human colon tissue.
Main Methods:
- Ultra-high performance liquid chromatography (UHPLC) coupled with electrospray ionization (ESI) and quadrupole-time of flight mass spectrometry (Q-TOF MS) was employed.
- Optimization of mobile phases (ammonium bicarbonate), MS parameters (capillary voltage, cone voltage, detector voltage), low-adsorption vials, and hybrid surface-coated columns.
- MSE (all-ion fragmentation) acquisition was used for screening DNA adducts by analyzing the loss of deoxyribose and nucleobase fragment ions.
Main Results:
- A sensitive, untargeted DNA adductomics method was successfully developed and optimized.
- Fifty-four DNA adducts were tentatively identified in calf thymus, cat colon, and human colon DNA.
- Of the identified adducts, 38 were novel, representing a significant advancement in adduct discovery.
Conclusions:
- The developed method offers high sensitivity and effectiveness for untargeted DNA adductomics.
- This study represents the first untargeted DNA adductomics analysis of human colon tissue, identifying numerous novel adducts.
- The method shows great promise for future human studies investigating novel environmental carcinogens and their role in cancer.
More Related Videos
11:00Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry UPLC-HRMS
Published on: May 20, 2013
05:52Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF
Published on: January 12, 2024
Related Concept Videos
01:21Mass Spectrometry: Complex Analysis
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
01:33Peptide Identification Using Tandem Mass Spectrometry
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
01:15High-Performance Liquid Chromatography: Types of Detectors