Study examines how DNA damage is repaired by antioxidant enzymes

The metabolic activity of a normal human cell is rife with chemical processes that transform food into energy and valuable compounds that support life. Reactive oxygen species, which are harmful byproducts like hydrogen peroxide that harm DNA's building blocks in a similar manner to how oxygen and water erode metal and cause rust, are also produced by these reactions. Reactive oxygen species put a genome's integrity at danger, much as how rust causes structures to crumble over time.

It is assumed that by limiting metabolic activity to the cytoplasm, mitochondria, and regions outside the nucleus, cells can finely balance their energy requirements and prevent DNA damage. Antioxidant enzymes are used as a defense mechanism to mop up reactive oxygen species at their source before they reach DNA. This prevents the approximately 3 billion nucleotides from experiencing potentially disastrous alterations. Cells briefly halt and perform repairs, synthesising new building blocks and filling in the gaps, if DNA damage nonetheless occurs.

Despite the crucial function of cellular metabolism in preserving genome integrity, the impact of metabolic disturbances on the DNA damage and repair process has not been well investigated. This is crucial for illnesses like cancer, which are known for their capacity to seize control of metabolic systems and drive unchecked development.

This problem has been addressed by a team of researchers led by Sara Sdelci at the Centre for Genomic Regulation (CRG) in Barcelona and Joanna Loizou at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna and the Medical University of Vienna. They have conducted a number of experiments to determine which metabolic enzymes and processes are crucial for a cell's DNA damage response. The results were released in the journal Molecular Systems Biology today.

The researchers used the standard chemotherapeutic drug etoposide to experimentally cause DNA damage in human cell lines. Breaking DNA strands and inhibiting an enzyme that aids in damage repair are how etoposide functions. Unexpectedly, causing DNA damage caused reactive oxygen species to be produced and to build up inside the nucleus. The scientists discovered that in reaction to DNA damage, cellular respiratory enzymes, a significant source of reactive oxygen species, moved from the mitochondria to the nucleus.

The findings imply the nucleus is metabolically active, which represents a paradigm change in cellular biology. "Fire starts where there is smoke, and metabolic enzymes are active where there are reactive oxygen species. Our study disproves the conventional wisdom that the nucleus is a metabolically inert organelle that imports all of its requirements from the cytoplasm and that another type of metabolism occurs in cells and is located in the nucleus, according to Dr. Sdelci, the study's corresponding author and Group Leader at the Centre for Genomic Regulation.

All of the metabolic genes critical for cell survival in this situation were found by the researchers using CRISPR-Cas9. These studies showed that cells direct the antioxidant enzyme PRDX1, which is typically located in mitochondria, to go to the nucleus and scavenge any reactive oxygen species there in order to stop additional damage. Additionally, PRDX1 was discovered to reverse the damage by controlling the cellular availability of aspartate, a necessary raw material for the synthesis of nucleotides, the DNA's building blocks.

"PRDX1 is similar to an automated pool cleaning. It has never been used at the nuclear level, despite the fact that cells are known to employ it to maintain their interiors "clean" and avoid the buildup of reactive oxygen species. This demonstrates how the nucleus adopts mitochondrial machinery in times of stress and implements an emergency quick industrialization program, claims Dr. Sdelci.

The results can direct future cancer research directions. Some anti-cancer medications, like the experimental drug etoposide, kill tumor cells by disrupting their DNA and impeding the process of repair. The cancer cell starts an autodestructive process if enough damage builds up.

In their tests, the scientists discovered that normal, healthy cells were resistant to etoposide when metabolic genes crucial for cellular respiration—the mechanism that converts oxygen and nutrients into energy—were knocked off. The discovery is significant since many cancer cells are glycolytic, which means that they produce energy even in the presence of oxygen without engaging in cellular respiration. As a result, it is anticipated that etoposide and other chemotherapy drugs with a comparable mechanism will only have a modest impact on the treatment of glycolytic cancers.

The study's authors urge more research into novel approaches like dual therapy, which combines etoposide with medications that also increase the production of ROS, in order to combat drug resistance and hasten the death of cancer cells. Additionally, they propose that combining etoposide with inhibitors of nucleotide synthesis might increase the drug's effectiveness by blocking DNA damage repair and guaranteeing that cancer cells properly self-destruct.

Dr. Loizou, the group leader at the Centre for Molecular Medicine and the Medical University of Vienna and the corresponding author, emphasizes the need of using data-driven methods to identify novel biological processes. "We have discovered how the two essential biological processes of DNA repair and metabolism are connected by employing unbiased technologies such as CRISPR-Cas9 screening and metabolomics. Our research clarifies how focusing on these two cancer-related pathways might help patients receive more effective treatment.