Chemotherapy could be more effective if it were combined with the inhibition of a newly discovered form of DNA repair, a mechanism that cells activate to fix exactly the sort of damage that many chemotherapy drugs cause—or are supposed to cause. The relevant chemotherapy drugs are alkylating agents, which try to kill cancer cells by adding alkyl groups to DNA. These debilitating accretions, however, can be removed by an alkylation repair complex.
This repair complex is recruited to damage sites via a signaling pathway, one that has recently been described by scientists based at the Washington University School of Medicine in St. Louis. The scientists reported their findings November 8 in the journal Nature, in an article entitled “A Ubiquitin-Dependent Signalling Axis Specific for ALKBH-Mediated DNA Dealkylation Repair.”
The article notes that although biochemical mechanisms for repairing several forms of genomic insults are well understood, important gaps in our knowledge remain. Although we are familiar with the upstream signaling pathways that account for certain kinds of DNA damage—double-stranded breaks and interstrand cross-links—we are less certain about other kinds of DNA damage, including the damage wrought by alkylating agents.
Alkylation can happen naturally, which is why cells have this repair system in the first place. Also, certain chemotherapy drugs force it to happen. Busulfan, used to treat leukemia, and temozolomide, prescribed for brain tumors, alkylate many spots along DNA. It is difficult for the genetic blueprint to be copied accurately where DNA has been alkylated, so such alkylation damage kills the cells.
By inflicting a great degree of alkylation damage, chemo attempts to overwhelms the cells' ability to heal themselves. Yet chemo may fail to inflict sufficient lasting damage, unless the cells' DNA dealkylation repair mechanism is somehow thwarted. As it happens, some tumors are abnormally dependent on the proteins involved in this form of DNA repair, such that knocking out those proteins kills the tumor cells.
“We found that human cells can sense alkylation damage and mobilize a repair complex specifically suited to repair this kind of injury,” said the Nature article's senior author Nima Mosammaparast, M.D., Ph.D., an assistant professor of pathology and immunology. “Knocking out this complex may be a way to increase the potency of certain chemotherapy drugs, or to specifically target tumor cells that have become dependent on the repair complex.”
Studying cells treated with alkylating chemotherapy drugs or with drugs that lead to other kinds of DNA damage, the researchers determined how cells try to mend DNA damage caused specifically by alkylating agents. They identified a group of proteins that clustered near the spots on the DNA that had been alkylated.
“We find that the alkylation repair complex ASCC (activating signal cointegrator complex) relocalizes to distinct nuclear foci specifically upon exposure of cells to alkylating agents,” wrote the article's authors. “These foci associate with alkylated nucleotides, and coincide spatially with elongating RNA polymerase II and splicing components.”
Cells that lacked a key member of this protein complex were more likely to die if they were treated with alkylating drugs than cells that had the protein, indicating the importance of the protein complex in repairing DNA. Lacking the key protein made no difference when the DNA was damaged in other ways.
“Proper recruitment of the repair complex requires recognition of K63-linked polyubiquitin by the CUE (coupling of ubiquitin conjugation to ER degradation) domain of the subunit ASCC2,” the article continued. “Loss of this subunit impedes alkylation adduct repair kinetics and increases sensitivity to alkylating agents, but not other forms of DNA damage.” 
These findings suggest that sensing alkylation damage is a major primary defense against chemotherapy drugs such as busulfan and other alkylating agents. Interfering with this repair complex could amplify the killing power of such drugs and potentially even avert or undermine drug resistance. After a successful course of chemotherapy, tumors sometimes recur tougher than before, having become resistant to the drugs from the first round of treatment.
“There's some evidence now that overexpressing components of this signaling pathway may be how some tumors become resistant to chemotherapy,” Mosammaparast said. “Blocking this pathway could be a way to make resistant tumors sensitive again.”
Recurrent tumors are not the only ones that may have high levels of DNA repair proteins. Some tumors that have never encountered alkylating chemotherapy drugs have high levels of key alkylation-repair proteins. And when they do, it portends poorly for the patients.
“In some kinds of pancreatic, prostate, and lung cancer, overexpressing components of this pathway indicates a significantly worse prognosis,” Mosammaparast noted.
There is a possible silver lining, though. Tumors that have high levels of key alkylation repair proteins are often dependent on them, meaning that if those proteins were somehow inhibited, the cells would die. Normal cells are not dependent on this alkylation repair pathway to the same degree. Other repair systems can handle the level of alkylating DNA damage typically encountered by a healthy cell.
“That could be an opening for a chemotherapy drug,” Mosammaparast said. “We may be able to design a drug that is toxic to tumors but not to normal cells by targeting this alkylation repair pathway.”
The drug olaparib, approved in 2014 to treat hereditary ovarian cancer, exploits a similar vulnerability. It targets tumors that are unusually dependent on a repair pathway that stitches DNA back together after it has been cut into pieces. Olaparib blocks that pathway, and without it the cancerous cells die.


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