Each of the hundreds of trillions of cells that make up the human body suffers more than 10,000 DNA damage every day . These would be catastrophic if cells were not able to repair them, for which they set in motion a very delicate machinery that allows detecting and correcting these damages and avoiding diseases such as cancer .
Thanks to machine learning and high-performance fluorescence microscopy, the DNA repair machinery has been visualized in a detail never seen before
Using the machine learning ( machine learning , English) -a branch of artificial intelligence that allows the system to identify patterns in the data to make predictions – applied to fluorescence microscopy high performance, researchers at the National Cancer Research Center ( CNIO ) and the Massachusetts General Hospital (USA) have managed to visualize this DNA repair machinery in a detail never seen before and to identify new repair proteins . These results, published in the journal Cell Reports , could help the development of new cancer therapies.
As soon as there is damage to the genetic material, for example a break in the DNA double strand , the cell activates response mechanisms that function as “an emergency call”, exemplifies Bárbara Martínez , lead author of the study and researcher at the CNIO. Quickly, proteins bind to this molecular lesion to send alarm signals, which will be recognized by other proteins specialized in correcting the damage.
In search of better cancer therapies
The goal of chemotherapy is precisely to kill tumor cells by inducing DNA damage, which causes the cells to collapse and die. “By knowing how DNA damage occurs and how it is repaired, we will better understand how cancer develops and how to fight it. Any new discovery in DNA repair will help develop better therapies against cancer, while protecting our healthy cells ”, the expert details.
The researchers have created a new methodology that, with the help of a machine learning analysis method designed by the CNIO’s Confocal Unit , allows this process to be analyzed with a degree of detail and precision never before achieved. “To date, a limiting factor for tracking DNA repair time was the inability to analyze the amount of data generated from microscopic images.”
By knowing how DNA damage occurs and how it is repaired, we will better understand how cancer develops and how we can fight it.Bárbara Martínez, CNIO researcher
To do this, researchers have used high-performance fluorescence microscopy to take thousands of photographs of cells after inducing genetic damage. In a first phase, they introduced more than 300 different proteins into cells and evaluated in a single experiment whether they interfered with DNA repair over time. This technique has facilitated the discovery of nine unpublished proteins that participate in this process.
Photographs of human cells with damaged DNA using a laser beam in the laboratory. In green, the classic H2AX repair protein bound to the breaks generated by the laser; in red, the RNF166 protein discovered in this study bound to DNA breaks, coinciding with H2AX; in blue, cellular DNA. / Bárbara Martínez-Pastor (CNIO) and Giorgia G. Silveira (MGH)
Subsequently, the authors decided to go one step further and visually monitor all 300 proteins after generating the genetic damage. To do this, they adapted a classic DNA microirradiation technique – which damages it with the help of an ultraviolet laser – to use it on a large scale for the first time.
“We saw that many proteins stuck to damaged DNA and others did just the opposite: they moved away from the lesions. Attaching to or detaching from damaged DNA to make way for other repair proteins is a common feature of DNA repair proteins. The two phenomena are relevant ”, explains Martínez.
Cells without PHF20 – one of the proteins discovered in this study – cannot properly repair their DNA and are more sensitive to irradiation than normal cells
Among the proteins discovered is PHF20 . The authors have shown that this protein is detached from lesions seconds after they are formed to facilitate the binding of 53BP1 , a very important protein for repair of tears. Cells without PHF20 cannot properly repair their DNA and are more sensitive to irradiation than normal cells, which indicates that it plays a fundamental role in this important process for the survival of cells.
These new technologies offer new opportunities to study DNA repair and manipulation. “The advantage is that they are very versatile methods that can be used to discover new genes or chemical compounds that affect DNA repair, and that they use direct techniques to visualize intracellular repair phenomena”, concludes the researcher.
Martínez-Pastor et al . “Assessing kinetics and recruitment of DNA repair factors using high content screens”. Cell Reports , 2021. DOI: 10.1016 / j.celrep.2021.110176
Rights: Creative Commons.