As you walk through the streets, you often come across construction sites where roads are being repaired or collapsed walls are being restored. But did you know that within our bodies, DNA is constantly undergoing repair work to restore genetic information? This article by the Center for Genomic Integrity within the Institute for Basic Science, which studies the molecular mechanisms of DNA damage repair, explains the process that quietly safeguards your health at this very moment—DNA damage repair.

The genetic information that makes up our bodies is encoded in DNA. Stored like a barcode, this genetic information is expressed as nucleic acids (such as RNA) and proteins through transcription and translation processes, and the complex actions of these nucleic acids and proteins form the foundation of life phenomena at the organism level, such as in humans. Therefore, maintaining the integrity of our genetic information is crucial.

However, our genetic information faces numerous threats every day. The cells in our body (at least some of them) must constantly divide, and during the DNA replication stage necessary to create new cells, unavoidable mutations can occur. While DNA replication proteins in our bodies work with very high accuracy, they are not 100% error-free. Additionally, various substances we encounter in daily life, particularly those classified as "carcinogens," often cause direct or indirect damage to DNA. This damage leaves behind mutations, and the accumulation of these mutations can lead to various diseases, including cancer and degenerative disorders.

Fortunately, our cells possess a variety of DNA damage repair mechanisms that have evolved since the days of single-celled organisms. By using the appropriate repair processes tailored to the type of DNA damage, our genetic information is kept relatively safe over time, providing the foundation for humans to live long lives. In a sense, the process of DNA damage and DNA repair can be thought of as an ongoing battle between offense and defense happening within our bodies even now.

[Figure 1] DNA Damage Repair Mechanism
Various types of damage repair mechanisms exist, each employing an appropriate repair process depending on the specific DNA lesion.
(Source: Dall'Agnese, Giuseppe et al. “Role of condensates in modulating DNA repair pathways and its implication for chemoresistance.” The Journal of Biological Chemistry, vol. 299, no. 6, 2023, 104800. doi:10.1016/j.jbc.2023.104800)

When Both Strands of DNA Are Broken

Reactive oxygen species, radiation, and other powerful DNA-damaging agents can break the chemical bonds in DNA molecules, leading to what is known as a "DNA double-strand break." In a single cell, approximately 10 to 50 DNA double-strand breaks occur each day. Although these breaks are less frequent compared to other types of DNA damage, if not properly repaired, they can lead to severe mutations or cell death.

Another concerning aspect of DNA double-strand breaks is that even when the broken DNA is rejoined, side effects such as point mutations or chromosomal rearrangements can frequently occur. These side effects are often associated with the "nonhomologous end joining (NHEJ)" repair mechanism, one of the primary methods for repairing DNA double-strand breaks. Due to the high risk posed by DNA double-strand breaks, this repair method can be seen as a trade-off, resolving immediate issues at the expense of future genomic stability.

Homologous Recombination Process

The homologous recombination process is a DNA double-strand break repair mechanism used in dividing cells. Unlike the aforementioned nonhomologous end joining, homologous recombination repairs damage by copying intact genetic information from the replicated homologous chromosome after the synthesis phase (S phase) of the cell cycle. This makes it a safer repair process, as it does not introduce mutations during the repair.

Homologous recombination requires a sophisticated molecular mechanism involving various repair proteins in a sequential manner. The first step, known as end resection, involves removing proteins and complex structures around the damaged site and trimming the DNA double strand into single strands. The exposed single-stranded DNA then invades the corresponding normal DNA sequence on the homologous chromosome, using the complementary sequence as a template to synthesize and restore the damaged genetic information.

Since the DNA damage repair process like homologous recombination follows a precise sequence of molecular mechanisms, any issues during the repair can actually lead to greater genomic instability.

Discovery of a New Phenomenon in the Homologous Recombination Process

Various types of repair proteins participate in the initial step of homologous recombination, the end resection process. Our research team has discovered that the ring-shaped PCNA protein, which is involved in DNA replication, also plays a role in the end resection process. We found that as the end resection process is initiated by the MRN (MRE11-RAD50-NBS1) protein complex, PCNA moves to the DNA double-strand break site, and the tumor suppressor protein ATAD5 detaches PCNA from the end resection site.

When PCNA interferes with the end resection process, it inhibits the activity of the MRN complex. Notably, when ATAD5 is deficient and PCNA remains at the end resection site, not only is the end resection process hindered, but the entire homologous recombination process is also obstructed. In situations where homologous recombination repair becomes difficult, cells may switch to an error-prone repair system, such as polymerase theta-mediated end joining (TMEJ), as an alternative to survive, but this leads to an increase in mutations.

[Figure 2] Mechanism by which PCNA Accumulation at DNA Double-Strand Break Sites Causes Homologous Recombination Repair Defects

In normal cells (left illustration), PCNA, which has moved to the double-strand break site, is removed by the ATAD5 protein, allowing subsequent homologous recombination processes, including the removal of end-binding proteins KU70/80, to proceed. In ATAD5-deficient cells (right illustration), PCNA remains at the double-strand break site, obstructing short-range end resection and hindering subsequent homologous recombination repair processes.

Understanding the DNA damage repair process forms the foundation for technologies aimed at treating cancer and genetic diseases. Based on our research team's findings on the importance of the ATAD5 protein within the homologous recombination process, we hope to deepen our understanding of this process and eventually apply it as a molecular mechanism for clinical treatments.

Paper Title: Short-range end resection requires ATAD5-mediated PCNA unloading for faithful homologous recombination, Nucleic Acid Research, 2023

Is Stable DNA Damage Repair Always Beneficial?

DNA damage repair is often likened to a guardian of genomic stability in living organisms. Stable DNA damage repair ensures the safety of the organism’s life and the genetic information passed on to future generations. However, there are cases where stable DNA damage repair can be detrimental, particularly in the context of cancer.

Although it varies by cancer type, when cancer cells possess a stable DNA damage repair system, they may exhibit poor responsiveness to chemotherapy compared to cancer cells with unstable repair systems, leading to worse patient outcomes. Traditional chemotherapy often works by directly damaging the DNA of cancer cells, but those with stable DNA repair processes can easily develop resistance to these treatments.

Recent studies have revealed that lactate accumulation, resulting from the Warburg Effect* commonly seen in cancer cells, can promote homologous recombination within these cells. High homologous recombination activity, driven by elevated lactate levels, has been associated with poor prognosis in cancer patients. Conversely, inhibiting homologous recombination by disrupting the lactylation of key proteins involved in the process (such as the MRN protein complex) through lactate can enhance the cancer cells' responsiveness to chemotherapy.

*The Warburg Effect: This refers to the phenomenon where, even in the presence of oxygen, cancer cells prefer to generate energy (ATP) by converting glucose to pyruvate without using oxygen, rather than through oxidative phosphorylation in the mitochondria. Pyruvate is then fermented into the byproduct, lactate.

References:
•NBS1 lactylation is required for efficient DNA repair and chemotherapy resistance, Nature,

2024
•Metabolic regulation of homologous recombination repair by MRE11 lactylation, Cell, 2024
As shown, while the DNA damage repair process is crucial for our well-being, there are times when inhibiting or exploiting vulnerabilities within this process becomes a critical starting point for disease treatment. Even now, many researchers are diligently working to uncover the secrets within the DNA damage repair process. We hope that a deeper understanding of DNA repair will lead to the conquest of more diseases in the future.