TDP2 unglues trapped topoisomerase II from the KMT2A locus - it suppresses translocations overall and manufactures one rare junction class
also called tyrosyl-DNA phosphodiesterase 2 · TTRAP · 5'-tyrosyl DNA phosphodiesterase · TOP2cc reversal
When topoisomerase II gets stuck on DNA, an enzyme called TDP2 snips it off so the two clean ends can be glued straight back together. Losing TDP2 makes cells break KMT2A more and swap chromosomes more - but one unusual kind of scar found in therapy-related leukaemia only appears when TDP2 is working.
The same thing, for a scientist
TDP2 hydrolyses the 5'-phosphotyrosyl bond that tethers TOP2 to the DNA end in a trapped cleavage complex, liberating a 4-nt 5'-cohesive terminus that classical NHEJ can religate without further processing. It is the major, possibly only, 5'-tyrosyl-DNA phosphodiesterase in vertebrate cells, and TDP2-null DT40 cells are selectively hypersensitive to etoposide but not to camptothecin or MMS [E3]. TDP2-dependent NHEJ is both efficient and accurate; Tdp2-deleted mice show lymphoid toxicity, intestinal damage and increased bone-marrow genome instability after TOP2 poisoning [E4]. Directly at the locus of interest, Gomez-Herreros et al. used FISH probes flanking the KMT2A BCR and showed TDP2 protects KMT2A from TOP2-induced breakage, and that TDP2 loss INCREASES etoposide-induced chromosome rearrangements and translocations [E1]. The twist, read from that paper's full text, is a genetic dissociation of junction class: translocation junctions bearing exactly 4 bp of perfect homology were present in wild-type cells and ABSENT in TDP2-null cells, while most junctions in both genotypes had no homology or shorter microhomology [E1]. The authors' interpretation is that TDP2-liberated 4-nt cohesive overhangs occasionally religate to a distal TOP2 break carrying an identical overhang, and they note this junction type has been reported for a therapy-related MLL translocation. TDP2 is therefore not a candidate prevention target - removing it makes breakage and translocation worse - but the 4-bp perfect-homology junction is a specific, mineable signature of a TOP2-and-TDP2-made fusion.
The chemistry, in one paragraph
TOP2 cuts both DNA strands four nucleotides apart and holds each 5' end through a phosphotyrosyl bond to an active-site tyrosine. Normally the reaction reverses. When it does not - because a poison such as etoposide has trapped it, or because the reaction aborted - the cell must remove the protein adduct before any ligase can act. Two routes exist: proteasomal degradation of TOP2 followed by TDP2 hydrolysis of the residual peptide-tyrosyl bond, or nucleolytic excision by MRE11/CtIP which removes sequence with the adduct. The TDP2 route is the error-free one, because the 4-nt 5'-cohesive overhangs it exposes are directly ligatable 14. TDP2 is the major and possibly the only 5'-TDP activity in vertebrate cells, and its loss confers selective etoposide hypersensitivity without hypersensitivity to camptothecin or methyl methanesulfonate, which is the cleanest available demonstration that the activity is TOP2-specific 3.
What was measured AT the KMT2A locus1 deeper
This is the part that belongs to this beat rather than to DNA-repair generally. Gomez-Herreros et al. placed FISH probes flanking the KMT2A locus and scored etoposide-induced breaks as a loss of probe proximity. TDP2 loss increased breakage at KMT2A, and increased chromosome rearrangements and translocations overall 1. They also mapped the partner distribution of etoposide-induced KMT2A translocations by Circos and found no significant difference between wild-type and TDP2-null cells, which they read as TDP2 not influencing where TOP2 cuts - only what happens afterwards.
The cell system is hTERT-RPE-1, a non-transformed retinal pigment epithelial line. That is a limitation this entry should not soften: it is not a haematopoietic cell, and the KMT2A partner spectrum in it is not the clinical recombinome.
The 4-bp perfect-homology junction, and why it matters more than it looks
Sanger sequencing of etoposide-induced KMT2A translocation junctions found that some wild-type junctions carried 4 bp of identical sequence present at the breakpoint in both KMT2A and the partner, and that this class was absent in TDP2-null cells; most junctions in both genotypes had no homology or shorter microhomology 1. The authors' model: TDP2 normally religates the two adjacent cohesive termini it liberated, but occasionally one religates to a distal TOP2-induced break bearing an identical 4-nt overhang. They state explicitly that this junction type has been reported for a therapy-related MLL translocation in leukaemia and has been attributed to TOP2 subunit exchange (domain swapping).
Read as a diagnostic rather than as mechanism, this is a pathway-of-origin marker with a genetic control behind it: a 4-bp perfect-homology junction implies a TOP2-cut, TDP2-processed origin, and its absence in a cohort argues against that origin. No published study has counted this junction class across a de novo infant versus therapy-related KMT2A cohort. That count is the core of ana-junction-microhomology-signature-mining.
Why TDP2 is not a prevention target, stated before anyone proposes it
The intuition 'block the repair that finishes the fusion' fails here in the same way it fails for Poltheta (see mechanism-nhej-vs-alt-ej-at-fusion-junctions). TDP2 loss increases rather than decreases TOP2-induced translocation 1, sensitises mice to TOP2-induced lymphoid and intestinal toxicity and raises bone-marrow genome instability 4. Biallelic human TDP2 loss-of-function causes SCAR23, a recessive paediatric-onset spinocerebellar ataxia with drug-resistant epilepsy and intellectual disability 5, so the phenotype of chronic TDP2 inhibition in a developing child is partly knowable and it is bad. TDP2 inhibitors exist and are being developed for the opposite purpose - to potentiate etoposide in tumours - not as prophylaxis. This entry records the direction of the arrow so that a future cycle does not have to rediscover it.
| mechanism class | protein-adduct removal and end-joining at topoisomerase-II-linked DSBs |
|---|---|
| enzyme | TDP2 (TTRAP, EC 3.1.4.-), 5'-tyrosyl-DNA phosphodiesterase |
| substrate | 5'-phosphotyrosyl bond linking TOP2 to a 4-nt 5'-cohesive DNA overhang |
| direction of effect for prevention | WRONG WAY - TDP2 inhibition increases TOP2-induced translocation. Not a prevention target. |
| human loss of function phenotype | SCAR23 (MIM 616949 not asserted here): paediatric-onset recessive spinocerebellar ataxia, drug-resistant epilepsy, intellectual disability |
| diagnostic use | 4 bp perfect-homology junction as a TOP2-cut/TDP2-processed origin marker; never counted across de novo versus therapy-related KMT2A cohorts |
kmt2a specific measurements
{
"system": "hTERT-RPE-1, etoposide, FISH probes flanking the KMT2A locus",
"tdp2_loss_effect_on_kmt2a_breakage": "increased",
"tdp2_loss_effect_on_translocation_frequency": "increased",
"tdp2_loss_effect_on_partner_distribution": "no significant difference by Circos analysis",
"junction_class_dissociation": "4 bp perfect-homology junctions present in wild-type, absent in TDP2-null; majority of junctions in both genotypes blunt or shorter microhomology",
"source": "E1"
}- TDP2 inhibition, the obvious way to 'block the repair that completes the fusion', increases rather than decreases TOP2-induced translocation. It is a hazard, not a prophylaxis.
- TDP2 inhibitors under development are intended to potentiate etoposide in tumours; any such agent used in a child receiving an epipodophyllotoxin would, on this evidence, be expected to raise secondary-leukaemia risk.
- Germline TDP2 loss in humans causes progressive cerebellar degeneration and drug-resistant epilepsy, so chronic systemic inhibition has a known and severe developmental phenotype to argue against.
- The 4-bp junction signature is a marker, not a target: identifying a fusion as TOP2-made after the fact changes nothing about the leukaemia already present.
- How many of the sequenced KMT2A genomic junctions in the published recombinome carry exactly 4 bp of perfect homology, and does that fraction differ between therapy-related and de novo infant cases? Nobody has counted, and the count would be a direct aetiological readout.
- Does TDP2 loss change breakage at KMT2A in a haematopoietic cell, or only in RPE-1? The only locus-level measurement is in a retinal epithelial line.
- Do individuals with biallelic TDP2 loss (SCAR23) have any excess of haematological malignancy? With five reported patients the question is unanswerable now, but a registry note would be cheap.
- Is the TOP2-domain-swap model that the 4-bp junction is attributed to ever directly demonstrated, or only inferred from junction structure?
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
TDP2 protects the KMT2A locus from TOP2-induced breakage and suppresses etoposide-induced chromosome rearrangements and translocations, but a rare subclass of KMT2A translocation junctions carrying exactly 4 bp of perfect homology is present in wild-type and absent in TDP2-null cells.
TDP2 suppresses chromosomal translocations induced by DNA topoisomerase II during gene transcription · Gomez-Herreros F, Zagnoli-Vieira G, Ntai I, et al. · Nature communications 2017What this evidence cannot show
Full text read via Europe PMC fullTextXML (PMC5550487, 32,989 characters of body text). Cells are hTERT-RPE-1 and MCF7, not haematopoietic; breakage at KMT2A is scored by FISH probe separation, not by sequencing; the 4-bp junction class is a small number of Sanger-sequenced junctions and the authors themselves write that 'further work is required to confirm this observation'. Etoposide doses are pharmacological.
Evidence that argues against this (1)
- The paper's own framing places it against the mainstream finding that classical NHEJ MAKES human translocations rather than preventing them. The authors state the contrast explicitly: 'This is in contrast to DSBs induced by recombinant nucleases, which in human cells implicate NHEJ in the formation of chromosome translocations.' Their proposed resolution is that TOP2-induced ends are chemically different - 4-nt cohesive overhangs that religate without processing - so a repair pathway can be protective for one break chemistry and translocation-generating for another. Any general statement of the form 'NHEJ makes fusions' or 'NHEJ prevents fusions' is therefore under-specified unless the break chemistry is named. Ghezraoui H et al. 2014
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Conversion of a trapped TOP2 cleavage complex into an irreversible TOP2-linked double-strand break requires proteasomal degradation and TDP2 phosphodiesterase activity, and is about two-fold faster at transcribed loci.
Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity · Canela A, Maman Y, Huang SN, et al. · Molecular cell 2019What this evidence cannot show
Read from the abstract. Note the apparent tension with E1: here TDP2 is required to MAKE the irreversible break, there TDP2 SUPPRESSES the translocation. Both can be true because they measure different endpoints (an END-seq-visible free end versus a scored translocation), but the two statements should never be quoted side by side without this sentence.
Evidence that argues against this (1)
- In the same experimental year, the locus-level study found that TDP2 loss INCREASED etoposide-induced chromosome rearrangements and translocations, including breakage at KMT2A. So 'TDP2 is required for the break' and 'TDP2 protects against the translocation' are simultaneously on record, and an entry that uses TDP2 dependence to argue for a preventive intervention is reading only one of them. Gomez-Herreros F et al. 2017
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
TDP2/TTRAP is the major, if not the only, 5'-tyrosyl-DNA phosphodiesterase activity in vertebrate cells, and TDP2-deleted DT40 cells are highly sensitive to etoposide but not hypersensitive to camptothecin or methyl methanesulfonate.
TDP2/TTRAP is the major 5'-tyrosyl DNA phosphodiesterase activity in vertebrate cells and is critical for cellular resistance to topoisomerase II-induced DNA damage · Zeng Z, Cortes-Ledesma F, El Khamisy SF, Caldecott KW · The Journal of biological chemistry 2011What this evidence cannot show
Chicken DT40 cells. 'Major if not the only' is the authors' own hedge and should be kept; a minor redundant activity would change the interpretation of every TDP2-null phenotype downstream.
Evidence that argues against this (1)
- TDP2's specificity claim is bounded by the fact that a nucleolytic route exists in parallel: the same laboratory's mouse work shows that in the ABSENCE of TDP2, TOP2-induced breaks are still repaired, only less accurately, which means a second adduct-removal pathway is operating and its output - not TDP2's - is what a TDP2-null junction spectrum reports. Gomez-Herreros F et al. 2013
- E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
TDP2 functions in NHEJ and liberates ligation-competent DSB termini; its absence impairs both the capacity and the accuracy of TOP2-induced DSB repair, and Tdp2-deleted mice show lymphoid toxicity, severe intestinal damage and increased bone-marrow genome instability after TOP2 poisoning.
TDP2-dependent non-homologous end-joining protects against topoisomerase II-induced DNA breaks and genome instability in cells and in vivo · Gomez-Herreros F, Romero-Granados R, Zeng Z, et al. · PLoS genetics 2013What this evidence cannot show
Mouse and MEF systems under exogenous TOP2 poison. The bone-marrow genome-instability readout is micronucleus-scale, not translocation-junction-scale, so it does not by itself say KMT2A fusion frequency rises.
Evidence that argues against this (1)
- The protective phenotype is measured entirely under exogenous TOP2 poisoning. Nothing in this work establishes that TDP2 is load-bearing for spontaneous, drug-free breakage of the kind proposed for de novo infant KMT2A-rearranged disease, where the leading cleavage models are TOP2-independent: apoptosis-induced cleavage of the KMT2A BCR is unaffected by the catalytic TOP2 inhibitor merbarone. Betti CJ et al. 2005
- E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Biallelic loss-of-function mutations in TDP2 cause SCAR23, a recessive paediatric-onset spinocerebellar ataxia with drug-resistant epilepsy, intellectual disability and progressive cerebellar atrophy.
Consolidating the Role of TDP2 Mutations in Recessive Spinocerebellar Ataxia Associated with Pediatric Onset Drug Resistant Epilepsy and Intellectual Disability (SCAR23) · Ciaccio C, Castello R, Esposito S, et al. · Cerebellum (London, England) 2019What this evidence cannot show
Five patients total at the time of writing, from three families. A germline null phenotype across development is not a model of partial pharmacological inhibition in an adult - the standing database-scope caution in the Queen brief applies here as it does to pLI. It is cited to say the gene is not dispensable in humans, not to predict a drug's toxicity profile.
Evidence that argues against this (1)
- The germline-versus-pharmacology gap cuts the other way too: TDP2-null DT40 cells are viable and grow, and TDP2 loss produces NO hypersensitivity to camptothecin or methyl methanesulfonate, so the enzyme is not broadly required for genome maintenance. A SCAR23 phenotype therefore constrains chronic developmental loss and says little about transient inhibition. Zeng Z et al. 2011
adduct removal step downstream of TOP2 trapping at the KMT2A locus
for TOP2 break chemistry, NHEJ via TDP2 SUPPRESSES translocation, the opposite direction to nuclease-induced breaks
- depends on →Chromatin loop anchors are DNA-break hotspots - and the two papers that established it disagree about why
TDP2 activity is required for conversion of trapped TOP2cc into an irreversible loop-anchor DSB
TDP2 loss increases etoposide-induced breakage at the KMT2A locus measured by flanking FISH probes
counts the 4-bp perfect-homology class whose TDP2 dependence that entry records
TDP2 inhibition, the obvious repair-blocking move, increases KMT2A breakage and translocation
TDP2 removes the 5'-phosphotyrosyl adduct this drug creates
closes a forward reference: the mechanism entry named TDP2 and no gene entry existed
end protection versus resection decides whether a TDP2-liberated 4-nt overhang religates or is processed
TDP2 loss raises MLL breakage AND MLL-AF4 fusions together in isogenic TK6; a rejoining mechanism predicts both, so it does not dissociate them