The phosphodiesterase tyrosyl-DNA phosphodiesterase 1 (TDP1) is a protein involved in DNA repair from DNA topoisomerase IB (TOP1)-DNA break crosslinks. TDP1's major job is to repair the bonded bond between TOP1 (topoisomerase I) and DNA in DNA, created by topoisomerase inhibitors like carmastine. TDP1 over-expressing or malfunctioning might prevent DNA damage repair, and so toxically act on the tumor cells. TDP1 inhibitors and TOP1 inhibitors are potently synergistic with cancer cells, and overcome TOP1 inhibitor resistance, and have tumor targets. So this would seem to offer an opportunity to reverse tumour resistance to TOP1 inhibitors.
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Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Structure and Function
The phosphodiesterase tyrosyl-DNA phosphodiesterase 1 (TDP1) is a nuclease that mostly participates in DNA repair. Its primary role is to cut the phosphodiester bonds on the DNA of tyrosine residues so that cells can repair damage caused by single-strand breaks or other types of DNA damage. TDP1 physiological function is to enable the repair of DNA damage that maintains the genome's integrity and contributes to the cell's defense against oxidative stress and other noxious forces.
Structure of Tyrosyl-DNA Phosphodiesterase 1 (TDP1)
TDP1 is a polydomain protein. The catalytic region of TDP1 contains the important amino acid residues that catalytic enzymes need to work and interact with DNA substrates to catalyze reactions. The DNA-binding part of TDP1's structure also includes a site that binds DNA to specifically bind damaged DNA.
Physiological Activity of Tyrosyl-DNA Phosphodiesterase 1 (TDP1)
TDP1 is used to take up and resorb tyrosine-DNA breaks, which then repair cell DNA damage and stabilize the genome. TDP1 allows cells to survive when exposed to oxidative stress or other extreme damage because it repairs DNA. Because TDP1 repairs DNA, it is one of the potential targets for anti-cancer drug discovery, as certain cancer cells turn resistant to chemotherapies like topoisomerase inhibitors.
Tyrosyl-DNA Phosphodiesterase 1 (TDP1) and DSBs Are Both Co-inhibited Better Tolerant of CPT
The TOP1cc converts into DSBs only after CPT administration with MUS81. TDP1-KO cells accumulate TOP1cc which amplifies this function. Replication loss can turn RAW SSBs generated by TOP1 poisons into one-ended DSBs, turning on ATM. The proteolysis of TOP1 covalently bonded makes the ends of SSBs with TOP1cc available to other repair elements. Overproduction of DSBs in TDP1-KO cells aids HR repair of TOP1-induced damage and in some sense repairs the defect left by TDP1 loss.
Fig. 1 Pathways uncoupled by TDP1 involved in TOP1-induced DNA repair (Zhang, H., et al. 2022).
Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Promotes TOP1-Mediated DNA Repair
One intermediate of TOP1 activity involves cleavage complex where DNA is cut, and the enzyme is attached to the 3' end of DNA by a phosphotyrosine bond. TOP1 cleavage complexes (TOP1ccs) are usually transient, because the topoisomerase closes the break down when its catalytic process is complete. But DNA metabolism or presence of topoisomerase poisons in the form of antitumor medications can stabilize TOP1ccs, making this intermediate more half-life sustaining. The TOP1 peptide that is proteolytically removed is still bound by a 3' end of the break, but opens a 5'-hydroxyl moiety to induce break signaling by PARP1 and recruitment of XRCC1 and related SSB repair factors. Tyrosyl DNA phosphodiesterase 1 (TDP1) is an exceptionally conserved eukaryotic enzyme that hydrolyses the phosphotyrosine bond between the TOP1 adduct and DNA.
TOP1-related DSBs might be an unacknowledged source of neurodegenerative diseases linked to defective SSB repair. TDP1-deficient (lunatic) lung cancer cells are reduced in repair of DSBs using TOP1, and TDP1 signalling appears redundant for HR. Further, DNAPKcs - a regulatory element of the canonical non-homologous end joining repair pathway (cNHEJ) - is hyperactivated when TDP1 is missing. Most basic cellular processes are dependent on the replication and transcription of DNA. The double-stranded DNA needed to be strand separated, with one strand acting as a template, for replication and transcription. To reduce the topological stress on DNA, TOP1 snips the 3' end of single-stranded DNA.
TDP1 Cells Overloaded With DSBs Caused by TOP1cc
TOP1cc might meet replication forks and split into single-ended DSBs to call ATM. ATM activation is induced right after CPT treatment, without the need for proteolysis of covalently bound TOP1. CPT-induced and replication-related DSBs are likely to be one-ended DSBs and should be generated mainly in the S phase. CPT poisons TOP1 by replicating and transcribing and DNA is damaged. Since inhibition of DNA replication or transcription also has other effects that can influence TOP1cc proteolysis, we can't say that DNA replication and transcription convert TOP1cc directly into overly large DSBs.
Contribution of TOP1cc Excision Pathway to TDP1
Top1cc can also be broken down by nucleases that cut the DNA strip on which TOP1 is glued. ERCC1-XPF structure-specific nuclease and its yeast homolog Rad10-Rad1 are 3' flap endonuclease complexes of the nucleotide excision repair mechanism; they were reported to be involved in the repair of TOP1-mediated DNA damage, perhaps by breaking off oligonucleotides with tyrosyl-phosphodiester bonds at their 3' end or directly breaking the 3'-phosphotyrosine bond. TDP1 and XPF were together deleted, and cellular sensitivity was slightly increased when TDP1 was eliminated.
Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Is an Important Target for Cancer
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an enzyme that is a tyrosyl-DNA phosphodiesterase evolved to remove the covalent bond between TOP1-enzyme tyrosine and the 3' end of DNA. Repair of DNA damage through TOP1 works in tandem with and without TDP1. TDP1 amplification on tumor cells results in cancer cell survival and proliferation. This is why TDP1 has been identified as an anti-tumor therapeutic. TDP1 inhibitors could be used to make the tumor cells more susceptible to DNA damage and hence better able to deal with the treatment.
When damaged with TOP1 induction, additional DSBs, and activated DSB-induced DDR signals were seen in TDP1-KO cells (perhaps repair intermediates of different repair mechanisms in TDP1-deficient cells). TDP1 belongs to the superfamily of phospholipases D. It can hydrolyze the 3'-phosphotyrosine linkage of TOP1ccs, participate in DNA repair, and perhaps overcome by anticancer and antiviral chain-termination analogs via overexpression of TDP1. Moreover, TDP1 inhibitors combined with anticancer drugs could be very therapeutically promising in cancer therapy. So TDP1 inhibitors can turn the tumor on its head.
References
- Zhang, H., et al. TDP1-independent pathways in the process and repair of TOP1-induced DNA damage. Nature communications. 2022, 13(1): 4240.
- Zhang, ., et al. TDP1 represents a promising therapeutic target for overcoming tumor resistance to chemotherapeutic agents: Progress and potential. Bioorganic Chemistry. 2024, 154: 108072.
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