TOP2B - the isoform most etoposide-induced KMT2A breaks depend on, resolved genetically and not resolvable pharmacologically

{
  "break_at_kmt2a_under_etoposide": "TOP2B-dependent, by genetic depletion (E2)",
  "loop_anchor_fragility": "attributed to TOP2B (E3)",
  "productive_fusion_formation": "requires BOTH isoforms (E4)",
  "pharmacological_separation": "NONE. ChEMBL files etoposide against a PROTEIN FAMILY target containing both accessions (E5).",
  "verdict": "The literature resolves the isoform genetically and does not resolve it pharmacologically. Any therapeutic sentence naming TOP2B is naming, not measurement."
}

{
  "subcellular": "Nucleus. UniProt Q02880 (TOP2B_HUMAN, DNA topoisomerase 2-beta, 1626 aa) was read back only to confirm the identifier.",
  "subnuclear": "Nucleoplasm and NUCLEOLUS, with the nucleolar pool inducible and reversible: ATP depletion rapidly translocates TOP2B from nucleoplasm to nucleolus, FRAP shows it is highly mobile in both, and the RNA polymerase I inhibitor BMH-21 immediately disperses it back. A second, GENOMIC-ARCHITECTURAL address is separately established: TOP2B's proximal interactome contains cohesin subunits and nucleolar rDNA proteins, and TOP2B binds at topological domain borders with cohesin and CTCF. THE SUBNUCLEAR FACT THAT MATTERS MOST HERE IS A PROXIMITY MEASUREMENT: 2-3% of transcribing MLL/KMT2A alleles are in close nuclear proximity to one of the recurrent translocation partner loci, AF9 or AF4, consistent with their sharing TRANSCRIPTION FACTORIES - and most etoposide-induced chromosome breaks in the MLL locus, plus the overall genotoxicity of etoposide, are TOP2B-dependent.",
  "how_shown": "live-cell imaging and FRAP under ATP depletion with BMH-21 (PMID 34728715); BioID proximity proteomics, ChIP and Hi-C (PMID 27582050); 3D FISH gene-proximity measurement with TOP2B-dependent etoposide-induced break mapping at the MLL locus (PMID 22615413)",
  "systems": "human non-leukaemic cells for the nucleolar and Hi-C work; human cells carrying the MLL locus for the proximity and break work - the gene-proximity result is the one piece of subnuclear evidence in this tranche that is about the KMT2A locus itself",
  "node": "localization-transcription-factories-pol2-clusters"
}

{
  "query": "(TOP2B[tiab] OR \"topoisomerase II beta\"[tiab] OR \"topoisomerase IIbeta\"[tiab]) AND (MLL[tiab] OR KMT2A[tiab])",
  "records": 6,
  "records_with_top2b_protein_localization_in_a_kmt2a_r_cell": 0,
  "operand_controls": {
    "(TOP2B OR \"topoisomerase II beta\")[tiab] AND (nucleolus OR nucleolar OR \"nuclear matrix\" OR localiz*)[tiab]": 40
  },
  "date": "2026-09-21",
  "tool": "PubMed E-utilities esearch",
  "bound": "zero in titles and abstracts; supporting figures not searched"
}

{
  "chronos_mean_kmt2a_rearranged": -0.1394,
  "chronos_mean_other_leukaemia": -0.0718,
  "difference": -0.0675,
  "pan_essentiality_all_lines": -0.0001,
  "selectivity_rank": 2349,
  "rank_denominator": 17728,
  "provenance": "Joined 2026-09-21 from analyses/depmap-kmt2a-selective-scan-full (generated 2026-09-19T10:12:06Z), the project's own genome-wide scan over 11 KMT2A-rearranged and 43 other leukaemia DepMap lines. NOT re-fetched and NOT independent of that scan: every caveat it carries applies here, including that the KMT2A-rearranged arm is a small number of lines drawn from nine individuals, that the rank denominator is 17,728 genes, and that a difference is not a dependency. Added because only 26 of 308 gene entries carried this number, which made any KMT2A-selectivity question answerable for 8% of the corpus.",
  "how_to_read": "A negative difference means MORE required in KMT2A-rearranged lines than in other leukaemia lines. A rank near 17,728 is ANTI-selective. Neither is evidence of a fusion-driven dependency on its own: check pan_essentiality_all_lines before calling anything selective, and note that a paralogue-redundant gene can score near zero for reasons that have nothing to do with this disease - see ana-the-paralogue-redundancy-excuse-is-not-tested-and-my-proxy-decided-the-answer."
}

{
  "evidence_class_key": "concept-expressed-required-maintains-three-evidence-classes",
  "paralogue_warning": "TOP2A and TOP2B are separate genes with DISTINCT cell-type distributions and distinct drug biology. Do not let one stand for the other. This block is TOP2B (Q02880, 1,626 aa, the 180 kDa form).",
  "expressed_in": {
    "class": 1,
    "summary": "TOP2B is present in NON-PROLIFERATING and terminally differentiated cells as well as cycling ones. In NIH-3T3 cells the 180 kDa form is constant once cells enter the cycle and is STILL PRESENT after every cell has reached G0, where the 170 kDa form (TOP2A) is undetectable [E_q69_ct1]. This is the defining cell-type difference between the two paralogues.",
    "pmids": [
      "1651102"
    ],
    "system_named_in_the_claim": "murine NIH-3T3 fibroblasts, 1991, serum-starvation synchronisation and immunoblot - not haematopoietic and not human"
  },
  "required_in": {
    "class": 2,
    "claim": "In MICE, Top2b is required in POSTMITOTIC NEURONS: neurogenesis is normal in IIbeta-mutant mice but motor axons fail to contact skeletal muscle, sensory axons fail to enter the spinal cord, and the pups die of breathing impairment shortly after birth [E_q69_ct2]. Top2b is likewise required for survival of postmitotic cells in the developing retina [E_q69_ct3].",
    "pmids": [
      "10615047",
      "24463367"
    ],
    "the_shape_of_the_requirement": "the requirement is for cells that have ALREADY LEFT the cycle. Neurogenesis - the proliferative phase - is explicitly normal. That is a cell-type answer of a kind a dependency screen structurally cannot give, because every DepMap line is by construction proliferating."
  },
  "not_required_in": {
    "claim": "NO KMT2A-rearranged-selective requirement of any size. Chronos -0.1394 in the KMT2A-rearranged arm against -0.0718 in other leukaemias, difference -0.0675, rank 2,349 of 17,728, pan-essentiality -0.0001. The gene is essentially dispensable for proliferation in EVERY line.",
    "why_that_is_expected_rather_than_disappointing": "TOP2B's published requirement is in postmitotic cells. A proliferation screen selects exactly the cell state in which TOP2B is least needed, so the near-zero pan-essentiality is a property of the assay's cell state and is not evidence that TOP2B does not matter."
  },
  "nodes": [
    "cell-type-neuron"
  ],
  "context": "murine development for the requirement; murine fibroblasts for the expression pattern; no measurement in any KMT2A-rearranged cell"
}

{
  "evidence_class_key": "concept-expressed-required-maintains-three-evidence-classes",
  "maintains_state": {
    "class": 3,
    "states": [
      "cell-state-quiescence"
    ],
    "claim": "TOP2B is the topoisomerase II that PERSISTS in the quiescent state: after serum starvation drives every NIH-3T3 cell into G0 the 180 kDa enzyme is still present while the 170 kDa enzyme is undetectable, and the 180 kDa form also requires a higher salt concentration to extract from isolated nuclei, indicating tighter chromatin association [E_q69_ct1].",
    "pmids": [
      "1651102"
    ],
    "system_named_in_the_claim": "murine NIH-3T3 fibroblasts"
  },
  "why_this_matters_for_the_etoposide_thread": "the graph's TOP2B interest is the etoposide-associated KMT2A breakpoint. If TOP2B is the isoform present in a QUIESCENT or slowly cycling cell, then a TOP2B-mediated break can be generated in a cell that is not in S phase - which is the only way a transplacental or in utero break in a fetal progenitor is compatible with the low cycling fraction of that compartment. This is offered as a lead, not a result: no experiment in this entry tests it.",
  "bounded_query": {
    "date": "2026-09-21",
    "tool": "NCBI esearch db=pubmed",
    "query": "TOP2B[tiab] AND (quiescent OR postmitotic OR \"post-mitotic\" OR nondividing OR \"non-proliferating\" OR differentiated)[tiab]",
    "count": 33,
    "note": "a healthy count, none of it in a KMT2A-rearranged cell. A second query, \"topoisomerase II beta\"[tiab] AND (\"nonproliferating\" OR \"non-proliferating\" OR quiescent OR \"growth-arrested\")[tiab], returns 3.",
    "bound": "titles and abstracts only; supporting figures not searched (brief rule 80)"
  },
  "confidence": "moderate",
  "caveats": "The G0 result is from 1991, in murine fibroblasts, by immunoblot, and predates the alpha/beta nomenclature - the paper names the proteins only by molecular weight (170 kDa and 180 kDa). Assigning 180 kDa to TOP2B is a standard and uncontested identification but it is an identification, not something the paper asserts in those words, and it is recorded here as such. No cell-cycle or quiescence measurement of TOP2B exists in any KMT2A-rearranged cell.",
  "counter_evidence": {
    "note": "The same measurement that makes TOP2B 'the quiescent-cell enzyme' also shows it is present at CONSTANT level once cells enter the cycle - i.e. TOP2B is not restricted to quiescence, it is merely not excluded from it. And Top2b-mutant mice have entirely normal neurogenesis, which is the proliferative phase, so the gene is dispensable where cells divide. A reading in which TOP2B is 'the non-dividing cell's topoisomerase' overstates a difference in cell-cycle DEPENDENCE as a difference in cell-cycle DISTRIBUTION.",
    "citation": {
      "title": "DNA topoisomerase IIbeta and neural development.",
      "authors": "Yang X, Li W, Prescott ED, Burden SJ, Wang JC",
      "year": 2000,
      "venue": "Science",
      "pmid": "10615047",
      "doi": "10.1126/science.287.5450.131",
      "type": "paper"
    }
  }
}