During a widespread DNA damage, the nucleus utilizing mitochondrial machinery for urgent repairs that threatens the genome’s integrity.
A typical human cell exhibits metabolic activity, with chemical reactions occurring that convert nutrients into energy and useful products to sustain life. These reactions also give rise to reactive oxygen species, perilous by-products such as hydrogen peroxide that harm the fundamental components of DNA, much like how metal corrodes due to exposure to oxygen and water, forming rust. The genome’s integrity is imperiled by reactive oxygen species in a manner akin to how the cumulative effect of rust can lead to the collapse of buildings.
It is believed that cells delicately manage their energy requirements and endeavor to safeguard DNA from damage by confining metabolic activity outside the nucleus, primarily within the cytoplasm and mitochondria. Antioxidant enzymes are deployed to eliminate reactive oxygen species at their origin, preempting their arrival at DNA. This defensive strategy shields the approximately 3 billion nucleotides from potentially catastrophic mutations. In the event of DNA damage, cells momentarily halt and initiate repair processes, synthesizing fresh building blocks and filling in gaps.
Despite the pivotal role of cellular metabolism in preserving genome integrity, no systematic, unbiased investigation into the impact of metabolic disturbances on the DNA damage and repair process has been conducted. This holds particular significance for diseases like cancer, known for their ability to exploit metabolic processes to foster unbridled growth.
The challenge of understanding this aspect was addressed by a research team 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. Various experiments were carried out to identify the metabolic enzymes and processes crucial for a cell’s response to DNA damage. The findings have been published today in the journal Molecular Systems Biology.
DNA damage was intentionally induced in human cell lines through the use of a common chemotherapy drug called etoposide by the researchers. Etoposide operates by breaking DNA strands and inhibiting an enzyme responsible for repairing the damage. Surprisingly, the induction of DNA damage resulted in the generation and accumulation of reactive oxygen species within the nucleus. The researchers observed that cellular respiratory enzymes, which serve as a significant source of reactive oxygen species, relocated from the mitochondria to the nucleus in response to DNA damage.
These findings mark a paradigm shift in the field of cellular biology, as they suggest that the nucleus is indeed metabolically active.
“Where there’s smoke there’s fire, and where there’s reactive oxygen species there are metabolic enzymes at work. Historically, we’ve thought of the nucleus as a metabolically inert organelle that imports all its needs from the cytoplasm, but our study demonstrates that another type of metabolism exists in cells and is found in the nucleus.”
Dr. Sara Sdelci, corresponding author of the study and Group Leader at the Centre for Genomic Regulation
The metabolic genes crucial for cell survival in this scenario were also identified by CRISPR-Cas9 in the experiments conducted by the researchers. In these experiments, it was unveiled that the enzyme PRDX1 was instructed by cells to move to the nucleus, where it would scavenge reactive oxygen species to prevent further damage. PRDX1 was also discovered to be involved in repairing the damage by regulating the cellular availability of aspartate, a critical raw material necessary for the synthesis of nucleotides, the building blocks of DNA.
“All in all, PRDX1 functions akin to a robotic pool cleaner. It’s a tool cells employ to maintain their internal ‘cleanliness’ and thwart the accumulation of reactive oxygen species, but it’s never been observed at the nuclear level before. This evidence indicates that, during a crisis, the nucleus reacts by seizing mitochondrial machinery and enacts an emergency rapid-industrialization policy.”
Dr. Sdelci
The discoveries have the potential to direct future avenues of cancer research. Certain anti-cancer drugs, like etoposide employed in this investigation, eliminate tumor cells by damaging their DNA and hindering the repair process. When enough damage accumulates, the cancer cell triggers a process where it self-destructs.
Throughout their experiments, it was noticed by the researchers that disabling metabolic genes vital for cellular respiration – the process responsible for generating energy from oxygen and nutrients – rendered normal healthy cells resistant to etoposide. This observation holds significance because many cancer cells rely on glycolysis, a process enabling them to produce energy without engaging in cellular respiration, even in the presence of oxygen. Consequently, etoposide, along with other chemotherapies sharing a similar mechanism, is likely to have a limited impact when treating glycolytic tumors.
The study’s authors advocate for the exploration of novel strategies, such as a dual treatment approach that combines etoposide with medications designed to enhance the generation of reactive oxygen species. This combination could potentially overcome drug resistance and expedite the demise of cancer cells. Furthermore, they hypothesize that pairing etoposide with inhibitors targeting nucleotide synthesis processes could amplify the drug’s effectiveness by obstructing DNA damage repair and ensuring the proper self-destruction of cancer cells.
Dr. Joanna Loizou, the corresponding author and Group Leader at the Centre for Molecular Medicine and the Medical University of Vienna, underscores the significance of adopting data-driven methodologies for uncovering new biological processes. “
By employing unbiased technologies like CRISPR-Cas9 screening and metabolomics, we have gained insights into the intricate interplay between the two fundamental cellular processes of DNA repair and metabolism. Our findings provide insights into how targeting these two pathways in cancer may enhance therapeutic outcomes for patients.”
Dr. Joanna Loizou
https://www.embopress.org/doi/full/10.15252/msb.202211267
Abstract
While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential for the resolution of DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Further analysis identified that Peroxiredoxin 1, PRDX1, contributes to the DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it reduces DNA damage-induced nuclear reactive oxygen species. Moreover, PRDX1 loss lowers aspartate availability, which is required for the DNA damage-induced upregulation of de novo nucleotide synthesis. In the absence of PRDX1, cells accumulate replication stress and DNA damage, leading to proliferation defects that are exacerbated in the presence of etoposide, thus revealing a role for PRDX1 as a DNA damage surveillance factor.
