DNA topoisomerase 1 is anenzyme that in humans is encoded by theTOP1gene. It is aDNA topoisomerase, an enzyme that catalyzes the transient breaking and rejoining of a single strand ofDNA.
This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This enzyme catalyzes the transient breaking and rejoining of a single strand of DNA which lets the broken strand rotate around the intact strand,[5] thus altering the topology of DNA. This gene is localized to chromosome 20 and has pseudogenes which reside on chromosomes 1 and 22.[6]
As reviewed by Champoux,[7] the type IB topoisomerases, including TOP1, form a covalent intermediate in which the active site tyrosine becomes attached to the 3' phosphate end of the cleaved strand rather than the 5' phosphate end.
The eukaryotictopoisomerases I were found to nick the DNA with a preference for a sequence of nucleotides that extends from positions -4 to -1 from the nick. The preferred nucleotides in the strand to be cut are 5'-(A/T)(G/C)(A/T)T-3' with the enzyme covalently attached to the -1 T residue, though sometimes a C residue is found at the -1 position.
The TOP1 protein of humans has been subdivided into four regions. TheN-terminal 214 amino acids are dispensable for relaxation ofsupercoiling activityin vitro and there are fournuclear localization signals and sites forinteraction with other cellular proteins within the N-terminal domain. The N-terminal domain is followed by a highly conserved, 421 amino acid core domain containing all of the catalytic residues except the active sitetyrosine. This is followed by a poorly conserved linker domain of 77 amino acids. Finally there is a 53 amino acid C-terminal domain. Theactive siteTyr723 is found within the C-terminal domain.
As further summarized by Pommier and by Seol et al.,[5][8] TOP1 breaks the DNA by atransesterification reaction using the active site tyrosine as thenucleophile that attacks the DNA phosphodiester backbone. After the TOP1 covalently attaches to the 3' end of the broken strand,supercoiling of the DNA is relaxed by controlled rotation of DNA about the intact strand. Then the 5' hydroxyl end of the broken DNA strand can reverse the phosphotyrosyl bond, enabling the release of TOP1 andreligation of the DNA. The nicking and closing reactions are fast, and about 100 cycles can occur per second.
The briefly attached, covalently bonded TOP1-DNA structure at the 3' end of a cleaved DNA single strand is called a TOP1-DNA cleavage complex, or TOP1cc. The TOP1cc is a specific target of TOP1inhibitors. One of the first inhibitors shown to target TOP1 isirinotecan. Irinotecan is an analogue of the cytotoxic natural alkaloidcamptothecin, obtained from the Chinese treeCamptotheca acuminata.[9] Irinotecan is especially effective through itsmetabolic productSN-38. Irinotecan andSN-38 act by trapping a subset of TOP1-DNA cleavage complexes, those with a guanine +1 in the DNA sequence.[5] One irinotecan or SN-38 molecule stacks against the base pairs flanking the topoisomerase-induced cleavage site and poisons (inactivates) the TOP1 enzyme.[5] The articleCamptothecin lists other analogues of camptothecin and the articleTopoisomerase inhibitor lists other compounds which inhibit TOP1.
Since 1985, TOP1 has been known as a target for the treatment of human cancers.[9] Camptothecin analogues irinotecan andtopotecan, which inhibit TOP1, are among the most effective FDA-approved anticancer chemotherapeutic agents used in clinical practice. Higher expression of TOP1 in KRAS mutant non-small cell lung cancer and correlation to survival suggests that TOP1 inhibitors might have increased benefit when administered to treat patients with a KRAS mutant tumor.[10]
Synthetic lethality arises when a combination of deficiencies in the expression of two or more genes leads to cell death, whereas a deficiency in only one of these genes does not. The deficiencies can arise throughmutation,epigenetic alteration or by inhibition of a gene's expression.
Irinotecan inactivation of TOP1 appears to be synthetically lethal in combination with deficiencies in expression of some specific DNA repair genes.
Irinotecan inactivation of TOP1 was synthetically lethal with deficient expression of the DNA repairWRN gene in patients with colon cancer.[11] In a 2006 study, 45 patients had colonic tumors withhypermethylatedWRN genepromoters (silencedWRN expression), and 43 patients had tumors with unmethylatedWRN gene promoters, so that WRN protein expression was high.[11] Irinotecan was more strongly beneficial for patients with hypermethylatedWRN promoters (39.4 months survival) than for those with unmethylatedWRN promoters (20.7 months survival). TheWRN gene promoter is hypermethylated in about 38% ofcolorectal cancers.[11]
Irinotecan inactivation of TOP1 may be synthetically lethal with deficient expression of DNA repair geneMRE11. A recent study was carried out with 1,264 patients with stage III colon cancer.[12] The patients were treated with a postoperative weeklyadjuvantbolus of 5-fluorouracil/leucovorin (FU/LV) or else with irinotecan+FU/LV and were followed up for 8 years. Eleven percent of the tumors were deficient for DNA repair enzymeMRE11 due to a deletion of a string of thymidines in the DNA sequence of theMRE11 gene. The addition of irinotecan to FU/LV in the treatment protocol resulted inMRE11-deficient patients having better long-term disease free survival than patients with wild-typeMRE11 (though the effect was small), indicating some degree of synthetic lethality between irinotecan-induced TOP1 inactivation andMRE11 deficiency.[12]
There are a number ofpre-clinical studies indicating synthetic lethality of irinotecan with other genetic orepigenetic DNA repair deficiencies common in cancers. For instance, the DNA repair geneATM is frequentlyhypermethylated (silenced) in many cancers (seehypermethylation of ATM in cancers). A 2016 study showed that low expression of the ATM protein in gastric cancer cellsin vitro and in a mouse model caused increased sensitivity to inactivation by irinotecan compared to cells with high expression of ATM.[13] This indicates synthetic lethality of ATM deficiency with irinotecan-mediated TOP1 deficiency.[13]
Another pre-clinical effort was a screening study to find a compound that would be synthetically lethal with a deficiency of N-myc downstream regulated gene 1 (NDRG1) expression.NDRG1 is a metastasis-suppressor gene in prostate cancer,[14] and appears to have a role in DNA repair.[15] Screening of 3360 compounds revealed that irinotecan-mediated TOP1 deficiency (and one other compound, cetrimonium bromide) exhibit synthetic lethality with NDRG1 deficiency in prostate cancer cells.[14]
Exposure of human HeLA cells toUVB irradiation specifically stimulates the formation of covalent complexes between topoisomerase I andDNA.[16] Topoisomerase I appears to have a direct role innucleotide excision repair, a process that removes UVB-induced, and other, DNA damages.[16]
^abSubramanian, D.; Rosenstein, B. S.; Muller, M. T. (1998). "Ultraviolet-induced DNA damage stimulates topoisomerase I-DNA complex formation in vivo: Possible relationship with DNA repair".Cancer Research.58 (5):976–84.PMID9500459.
