TOP2A - the proliferation isoform, the one the drugs are actually measured against, and the only one with a germline association in this disease

{
  "genetic_depletion_break_at_kmt2a": "TOP2B",
  "genome_wide_loop_anchor_breaks": "TOP2B",
  "fusion_formation_at_hotspot": "both isoforms",
  "in_vitro_cleavage_of_patient_breakpoint_sequence": "TOP2A",
  "clinical_and_dietary_poisons": "family-level, neither isoform resolved"
}

{
  "study": "PMID 21493871",
  "population": "self-identified Hispanic, Texas",
  "n": "66 ALL cases / 175 controls, replication 137 / 239",
  "top2a_result": "no significant SNP association",
  "positive_loci_in_same_study": [
    "MLL rs525549",
    "MLL rs6589664",
    "EP300 rs5758222",
    "EP300 rs7286979",
    "EP300 rs20551"
  ]
}

{
  "subcellular": "Nucleus. UniProt P11388 (TOP2A_HUMAN, DNA topoisomerase 2-alpha, 1531 aa) was read back only to confirm the identifier.",
  "subnuclear": "A THREE-STATE DYNAMIC EQUILIBRIUM, measured by single-molecule tracking: sequestration in the NUCLEOLUS, substrate searching in TRANSCRIPTION HUBS, and active engagement on chromatin. The equilibrium is responsive to DNA topology, and MYC accelerates TOP2A diffusion - i.e. an oncoprotein this graph already tracks moves TOP2A between these subnuclear states. Independently, ATP depletion rapidly translocates both TOP2A and TOP2B from nucleoplasm to nucleolus; FRAP shows both are highly mobile in both compartments; nucleolar retention of both is abolished within minutes by the RNA polymerase I inhibitor BMH-21, which disperses them back into the nucleoplasm.",
  "how_shown": "single-molecule tracking in human cells with MYC perturbation (PMID 41663397); live-cell imaging and FRAP under ATP depletion with BMH-21 and etoposide challenge (PMID 34728715)",
  "systems": "human non-leukaemic cell lines; no KMT2A-rearranged system",
  "node": "localization-nucleolus-kmt2a-fusion"
}

{
  "query": "(\"topoisomerase II alpha\"[tiab] OR TOP2A[tiab]) AND (nucleolus OR nucleolar OR \"nuclear matrix\" OR localiz*)[tiab]",
  "records": 92,
  "records_in_a_kmt2a_context": 0,
  "date": "2026-09-21",
  "tool": "PubMed E-utilities esearch",
  "bound": "zero in titles and abstracts; supporting figures not searched"
}

{
  "chronos_mean_kmt2a_rearranged": -2.1802,
  "chronos_mean_other_leukaemia": -2.073,
  "difference": -0.1073,
  "pan_essentiality_all_lines": -2.536,
  "selectivity_rank": 983,
  "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": "This block is TOP2A (P11388, 1,531 aa, the 170 kDa form). TOP2B is a separate gene with a separate cell-type distribution and separate drug biology; the etoposide/KMT2A-breakpoint literature is overwhelmingly about TOP2B and must not be transferred here.",
  "expressed_in": {
    "class": 1,
    "summary": "TOP2A is a PROLIFERATION-RESTRICTED protein. In NIH-3T3 cells the 170 kDa form is undetectable until late S phase, peaks in G2-M, falls through mitosis, and is UNDETECTABLE once all cells have reached G0 [E_q69_ct1]. Its cell type is therefore 'whatever is cycling', which in a leukaemia means the blast compartment and in normal marrow the transit-amplifying progenitors rather than the dormant stem cells.",
    "pmids": [
      "1651102"
    ],
    "system_named_in_the_claim": "murine NIH-3T3 fibroblasts, serum-starvation synchronisation, immunoblot - not haematopoietic and not human"
  },
  "required_in": {
    "class": 2,
    "claim": "PAN-ESSENTIAL AND FLOOR-COMPRESSED. Chronos -2.1802 in the 11 KMT2A-rearranged lines against -2.0730 in the 43 other leukaemia lines, pan-essentiality across all lines -2.536. BOTH ARMS ARE PAST -2, so by the rule stated on this entry's own depmap block the rank of 983 of 17,728 is UNINTERPRETABLE rather than meaningful: there is no dynamic range left in which selectivity could appear.",
    "verdict": "TOP2A is required in every proliferating cell that has been tested. That is a statement about the cell STATE the assay imposes, not about KMT2A biology, and the entry must not be read as reporting a KMT2A-selective TOP2A dependency."
  },
  "not_required_in": {
    "claim": "By construction, a cell in G0. TOP2A protein is absent from G0 [E_q69_ct1], so a quiescent leukaemic cell is a cell in which a TOP2A-directed poison has no target. This is the mechanistic form of the persister problem and it belongs in bite_back, where it is now written."
  },
  "nodes": [
    "cell-state-quiescence"
  ],
  "context": "murine fibroblasts for the cell-cycle distribution; DepMap cancer lines for the requirement; no TOP2A cell-cycle measurement in any KMT2A-rearranged cell"
}

{
  "evidence_class_key": "concept-expressed-required-maintains-three-evidence-classes",
  "maintains_state": {
    "class": 3,
    "states": [],
    "claim": "NO. TOP2A has not been shown to MAINTAIN any cell state. The relationship runs the other way: the cell state determines whether TOP2A is present. This is an explicit negative and it is a 'not applicable' rather than an 'unpublished' - the evidence class simply does not fit this gene.",
    "distinguishing_not_applicable_from_unpublished": "not applicable. TOP2A is a cell-cycle-restricted effector enzyme, not a state-setting factor, and no experiment in the literature searched proposes it as one."
  },
  "expressed_in_state": {
    "class": 1,
    "states": [
      "cell-state-quiescence"
    ],
    "relation": "ABSENT FROM, not present in",
    "claim": "TOP2A protein is undetectable in G0 and appears only from late S phase, peaking in G2-M [E_q69_ct1].",
    "pmids": [
      "1651102"
    ]
  },
  "bounded_query": {
    "date": "2026-09-21",
    "tool": "NCBI esearch db=pubmed",
    "query": "TOP2A[tiab] AND (proliferat* OR \"S phase\" OR \"cell cycle\")[tiab] AND (leukemia OR leukaemia)[tiab]",
    "count": 12,
    "on_topic_after_title_check": 0,
    "note": "none of the 12 is a cell-state measurement of TOP2A in a KMT2A-rearranged cell. A second query, TOP2A[tiab] AND (\"proliferation marker\" OR Ki-67 OR \"Ki67\" OR blasts)[tiab], returns 96 records, essentially all solid-tumour immunohistochemistry using TOP2A as a proliferation index - which is itself the finding: the field treats TOP2A as a READOUT of cell state rather than a determinant of it.",
    "positive_control": "both operand clauses return large counts separately and the joined query returns 12 rather than 0, so the shape demonstrably returns a one (brief rule 67).",
    "bound": "titles and abstracts only; supporting figures not searched (brief rule 80)"
  },
  "confidence": "moderate",
  "caveats": "The cell-cycle distribution is a 1991 murine fibroblast immunoblot naming the proteins only by molecular weight; the TOP2A identification is standard but is an identification. No TOP2A cell-cycle or quiescence measurement exists in any KMT2A-rearranged cell. The DepMap number for TOP2A is floor-compressed in both arms and carries no selectivity information at all.",
  "counter_evidence": {
    "note": "Treating TOP2A as simply 'the proliferation isoform' understates it: the 170 kDa enzyme is not merely correlated with cycling but is extractable from nuclei at LOWER salt than the 180 kDa form, i.e. the two enzymes differ in chromatin association as well as in abundance, so a cell-cycle account alone does not explain the division of labour. The authors say so themselves - 'the different patterns of expression of the two forms suggest that they perform different functions'.",
    "citation": {
      "title": "Proliferation- and cell cycle-dependent differences in expression of the 170 kilodalton and 180 kilodalton forms of topoisomerase II in NIH-3T3 cells.",
      "authors": "Woessner RD, Mattern MR, Mirabelli CK, Johnson RK, Drake FH",
      "year": 1991,
      "venue": "Cell Growth Differ",
      "pmid": "1651102",
      "type": "paper"
    }
  }
}

{
  "claim": "No histone or DNA modification has been measured under TOP2A perturbation, and the approved symbol cannot reach the one paper that pairs a topoisomerase with H3K4.",
  "date_measured": "2026-09-21",
  "tool": "NCBI esearch db=pubmed (eutils), querytranslation read back from every response",
  "queries": [
    {
      "query": "TOP2A[tiab] AND H3K4[tiab]",
      "querytranslation": "\"TOP2A\"[Title/Abstract] AND \"H3K4\"[Title/Abstract]",
      "count": 0,
      "errorlist_note": "warninglist outputmessages ['No items found.']; quotedphrasesnotfound empty, so both terms are indexed"
    },
    {
      "query": "TOP2B[tiab] AND H3K4[tiab]",
      "querytranslation": "\"TOP2B\"[Title/Abstract] AND \"H3K4\"[Title/Abstract]",
      "count": 0,
      "role": "the paralogue, same zero, run because rule 66-69 traps in this family are recorded in this entry's own identifier_trap field"
    },
    {
      "query": "topoisomerase[tiab] AND H3K4me3[tiab]",
      "querytranslation": "\"topoisomerase\"[Title/Abstract] AND \"H3K4me3\"[Title/Abstract]",
      "count": 7,
      "role": "THE OPERAND CONTROL, AND IT BREAKS THE ZERO. Titles read in full: PMID 36766705 (Taspase1/TOP2/H3K4, cited here - ON TOPIC), 38287116 (USP7/KDM5B/ZBTB16/TOP2A axis in nasopharyngeal carcinoma - TOP2A is a downstream transcript, not a chromatin actor), 26842758 (SMARCA4 recruits TOPOISOMERASE 1, and FACT is required for TOP1 binding to H3K4me3 - TOP1, the wrong enzyme family), 27225843 (replication-coupled histone marks in yeast, topoisomerase depletion intensifies H3K9ac ahead of the fork), 22053002 (PARP1/adipogenesis, topoisomerase II inhibitor used as a tool), 33256213 (fear-memory reconsolidation, DSBs and H3K4me3), 29530928 (Arabidopsis meiotic DSBs, SPO11 topoisomerase-like). 1 of 7 on topic for TOP2 plus a histone mark; 1 more (26842758) is a genuine topoisomerase-reads-a-mark result but for TOP1."
    },
    {
      "query": "Taspase1[tiab] AND topoisomerase[tiab]",
      "querytranslation": "\"Taspase1\"[Title/Abstract] AND \"topoisomerase\"[Title/Abstract]",
      "count": 1,
      "role": "confirms the pairing is a single paper, PMID 36766705 - so the link between this graph's taspase1 arm and its topoisomerase arm rests on one 2023 report and is not corroborated"
    },
    {
      "query": "TOP2A[tiab] AND MLL[tiab] AND H3K4[tiab]",
      "querytranslation": "\"TOP2A\"[Title/Abstract] AND \"MLL\"[Title/Abstract] AND \"H3K4\"[Title/Abstract]",
      "count": 0,
      "role": "the three-term form, also zero; the paper exists and none of these shapes finds it"
    },
    {
      "query": "TOP2A[tiab] AND histone[tiab]",
      "querytranslation": "\"TOP2A\"[Title/Abstract] AND \"histone\"[Title/Abstract]",
      "count": 38,
      "role": "breadth control - the symbol reaches 'histone' in quantity, so the zeros above are specific to the MARK tokens rather than a dead symbol. Titles not read; not counted as support."
    }
  ],
  "symbols_searched": [
    "TOP2A",
    "TOP2B",
    "topoisomerase",
    "Taspase1",
    "H3K4",
    "H3K4me3",
    "histone",
    "MLL"
  ],
  "symbols_not_searched": [
    "TOP2",
    "topoisomerase IIalpha",
    "topo II",
    "DNA topoisomerase 2-alpha",
    "etoposide",
    "H3K79",
    "H3K27ac"
  ],
  "absence_class": "naming-artefact-plus-never-measured",
  "absence_class_basis": "Two things at once. The H3K4 zeros under both symbols are a NAMING artefact - the class noun returns the paper - which makes them unsafe as absences (rules 71, 80). The residual absence, that no mark has been measured under TOP2A perturbation, is bounded by titles and abstracts only and by a name list that omits 'topo II' and the etoposide route, so it is a floor.",
  "reopening_condition": "Any ChIP/CUT&RUN for any histone mark under TOP2A knockdown, TOP2 poisoning or etoposide exposure reopens this; so does any report of a chromatin-state dependence for TOP2 cleavage at the KMT2A breakpoint cluster region. Re-run must use the class noun 'topoisomerase' and the spelled-out isoform names, not the HGNC symbols."
}