Novel DNA adductomics methodological developments for research in colon cancer

Project Information

Adductomics

Grant agreement ID: 843892

DOI

10.3030/843892

Project closed

EC signature date 5 April 2019

Start date 1 May 2019

End date 30 September 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 207 312,00

EU contribution

€ 207 312,00

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 1 - Adductomics (Novel DNA adductomics methodological developments for research in colon cancer)

Reporting period: 2019-05-01 to 2021-04-30

Summary of the context and overall objectives of the project

Colorectal cancer (CRC) is the third most common cancer worldwide. It develops as a result of multiple genetic changes that can be can be caused by environmental mutagens. Genotoxic carcinogenic compounds coming from pollution, diet, alcohol and cigarette smoke, come in contact with DNA of the gut epithelial cells and they form DNA-adducts that can lead to mutation and cancer development. However, the associations of CRC with meat intake, alcohol intake, and smoking, among others, have not yet been completely elucidated. Identifying the DNA adduct associated with CRC will give important information on the source of these DNA adducts, and therefore on the real causes of CRC. Knowing the causes of CRC and the mechanisms of action of specific genotoxicants on DNA damage would give the basis for the development of preventive and therapeutical approaches towards CRC. The overall objective of the project is to identify the DNA adducts associated to CRC. Therefore, a human DNA adductomics approach was developed by means of the latest high-resolution mass spectrometry (HRMS) instrumentation for the investigation of CRC.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In the first months of the project, I optimized the instrumental conditions of a HRMS for the analysis of 25 standard reference compounds, improving the sensitivity of up to 2 orders of magnitude. I reached the detection levels needed for detecting 1 modified nucleoside over 100000000 unmodified nucleosides (levels generally present in nature). Once improved the sensitivity of the instrumentation, I focused on the sample preparation and I optimized the method for the analysis of DNA adducts in colon tissues. This led to the identification of 13 DNA adducts from DNA of calf thymus and cat. In the following months, I created a database of DNA adducts related to CRC including more than 275 compounds. These results are summarized in a paper archived in ChemRxiv (doi: 10.33774/chemrxiv-2021-pvr0m) pending submission to Analytical Chemistry and an online databse. In the second year of the project, I have started the optimization of a method for analyzing the DNA adducts in surrogate samples rather than on human colon. In the meantime, I carried out a human pilot case-control study where 20 subjects with or without CRC were included and samples were collected. The analysis and identification of DNA adducts was performed in colon tissues and gave the first results on the DNA adducts possibly associated to CRC. Due to the Covid-19 pandemics it was difficult to participate to public events and conferences since most of them were canceled. Therefore, the results of the projects were presented at several small online meetings and seminars, enhancing my network possibilities and establishing new collaborations. I plan of presenting the results next year at one or two international congresses.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

An untargeted method for the identification of DNA adducts from colon tissues was developed for the first time in the literature. This will have a great impact on the research community, since several research groups will be able to perform reliable clinical studies for studying CRC and other pathologies. A new comprehensive database (including DNA adduct .cdxml files, .mol files, INCHI and SMILE code) was reported for the first time and it can be used from other research group for supporting the identification of DNA adducts in other studies. I performed the first human study where untargeted DNA adductomics was applied for elucidating CRC causes. The identification of the DNA adducts possibly related to CRC is the starting point of further studies on the molecular mechanisms of those DNA adducts on CRC. In a long-term perspective this could be used for designing new preventive and therapeutical approaches and promoting health in the society.
The interest towards the developed method and the performed human study is demonstrated by the collaborations that I established during the whole course of the project with: the group of animal biotechnology at the Technical University of Munich, the group of DNA adductomics at the University of Minnesota led by Prof Silvia Balbo, the group of chemometrics of Federico Marini. These collaborations open new perspectives for my future career both giving me the opportunity of visiting or working in these research groups and of developing new projects and applications on DNA adductomics.

DNA modifications and carcinogenesis mechanism