Oncofusion

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Analysisstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q58-set-nup214

Menin has never been tested against SET::NUP214 - a bounded absence in three independent registers: literature, cell-line dependency data, and the founding paper's own blots

also called SET-NUP214 menin absence · is SET::NUP214 menin-dependent

We checked three different places for any experiment asking whether SET::NUP214 leukaemia needs menin, and found none in any of them. That is a gap in the evidence, not a finding that it does not need menin.

The same thing, for a scientist

**Answer to the beat's first headline question: it is untested, and it is untested more thoroughly than the literature count alone shows.** **Register 1 - PubMed.** `(SET-NUP214 OR TAF-I-NUP214) AND (menin OR MEN1 OR revumenib OR ziftomenib OR VTP-50469 OR MI-503 OR "menin inhibitor" OR "menin inhibitors" OR "menin inhibition")` returns **0** [E1]. `LOUCY AND (menin OR MEN1 OR revumenib OR ...)` returns **0** [E1]. `NUP214 AND (menin OR MEN1)` returns **1**, and that one record is a general AML-classification review whose menin content is about KMT2A-rearranged disease [E2]. Operand controls: `menin` alone **2,237**; `SET-NUP214` alone **54**; `SET-NUP214 AND DOT1L` **1** through the identical shape, so the instrument returns ones [E1]. **Register 2 - functional-genomics data.** Neither **LOUCY** nor **MEGAL**, the only two cell lines known to carry SET-NUP214, is present in the DepMap CRISPR gene-effect data served by the Open Targets Platform: **1,258 screens carry a MEN1 gene effect, 8 of them annotated T-Lymphoblastic Leukemia/Lymphoma (TALL-1, SUP-T1, PF-382, JURKAT, DND-41, CCRF-HSB-2-DM, KE-37, PEER), and none of those eight carries SET-NUP214** [E3]. So there is no dependency datum to reason from either, and the absence is structural rather than bibliographic. **Register 3 - the founding paper's own experiments.** The 2008 study ran five different immunoprecipitations in LOUCY and blotted them for SET, CRM1, DOT1L, PP32 and AF10. **Menin appears nowhere in the paper** [E4]. **This confirms the Q55 bounded absence and extends it.** Q55 reported 0 records over four fusion spellings against a control of 2,237. That reproduces exactly. What is new is that the cell-line register is also empty, and that the absence now matters more than it did, because `mechanism-set-nup214-recruits-wild-type-mll1` shows the fusion recruits the protein menin binds.

Go deeper
The name lists, in full, because an absence is only as good as its vocabulary

Fusion names searched: SET-NUP214, SET::NUP214, TAF_I-NUP214, TAF-I-NUP214, SET-CAN, plus the cell line names LOUCY and MEGAL and the bare gene NUP214.

Measured behaviour of each, which is the part a future reader needs:

stringrecordsusable
SET-NUP21454yes
SET::NUP21454yes - PubMed normalises the colons and returns the identical set, so the two spellings are one query, not two
TAF_I-NUP2141yes, but recovers only PMID 20065082
TAF-I-NUP2141same single record
SET-CAN1,375NO - ordinary English, 'set' and 'can'
NUP214220 with AND leukemiayes, expands to a Supplementary Concept
LOUCY33yes
MEGAL4 with AND leukemiayes but tiny

Menin-side names searched: menin, MEN1, revumenib, ziftomenib, VTP-50469, MI-503, MI-2-2, "menin inhibitor", "menin inhibitors", "menin inhibition" - singular, plural and nominalisation per rule 72.

Not searched, and therefore not bounded: conference abstracts not indexed in PubMed (ASH abstracts in particular, where a negative drug screen would plausibly live and die); preprint servers; the supplementary tables of large menin-inhibitor cell-line panels, where LOUCY could appear as an unremarked line without the fusion being named in any indexed field. That last route is the most likely place a datum actually exists.

The trap this analysis had to survive, and one it did not catch first time

Survived: rule 67. Every zero above has a positive control through the identical query shape, and SET-NUP214 AND DOT1L = 1 is that control.

Did not survive first time, and is recorded as a correction to method rather than to a claim: a parallel query, SET-NUP214 AND (H3K79 OR "H3-K79" OR "K79" OR "lysine 79"), returned 0 with the same clean controls - and the conclusion 'nobody has measured a histone mark on SET-NUP214' is false. PMID 18299449 contains an H3K79me2 ChIP across five HOXA promoters. It is invisible because the measurement is in a figure and the abstract never names the mark.

So the honest statement of this analysis's own reliability is: these zeros bound what has been said in a title, abstract or MeSH heading. They do not bound what has been measured. A menin western blot in a supplementary figure of a paper about something else would not appear in any of them. See mechanism-set-nup214-dot1l-recruitment-is-convergent-not-af10-shared for the worked case.

Facts and figures
scriptnone - run interactively via NCBI E-utilities, Open Targets GraphQL, Cellosaurus and Europe PMC on 2026-09-20
statusrun
verdictUNTESTED, bounded in three registers
not a conclusionThis is an absence of testing, not a negative result. Nothing here says SET::NUP214 is menin-independent.
pubmed counts
(SET-NUP214 OR TAF-I-NUP2…0.000(SET-NUP214 OR TAF-I-NUP214) AND menin-vocabulary: 0LOUCY AND menin-vocabulary0.000LOUCY AND menin-vocabulary: 0SET-NUP214 AND menin0.000SET-NUP214 AND menin: 0NUP214 AND (menin OR MEN1)1.000NUP214 AND (menin OR MEN1): 1SET-NUP214 AND DOT1L (pos…1.000SET-NUP214 AND DOT1L (positive control, identical shape): 1LOUCY (operand control)33.0LOUCY (operand control): 33SET-NUP214 (operand contr…54.0SET-NUP214 (operand control): 54menin (operand control)2,237menin (operand control): 2237
pubmed counts — the numbers behind the chart
{
  "(SET-NUP214 OR TAF-I-NUP214) AND menin-vocabulary": 0,
  "LOUCY AND menin-vocabulary": 0,
  "SET-NUP214 AND menin": 0,
  "NUP214 AND (menin OR MEN1)": 1,
  "menin (operand control)": 2237,
  "SET-NUP214 (operand control)": 54,
  "LOUCY (operand control)": 33,
  "SET-NUP214 AND DOT1L (positive control, identical shape)": 1
}
depmap
{
  "screens_with_men1_gene_effect": 1258,
  "t_lymphoblastic_lines": 8,
  "loucy_present": false,
  "megal_present": false,
  "loucy_depmap_id": "ACH-000104",
  "loucy_id_source": "Cellosaurus CVCL_1380 DR DepMap cross-reference, fetched 2026-09-20"
}
registers searched
[
  "PubMed titles/abstracts/MeSH",
  "DepMap CRISPR gene effect via Open Targets",
  "the founding paper's full text"
]
registers not searched
[
  "conference abstracts (ASH in particular)",
  "preprint servers",
  "supplementary tables of menin-inhibitor cell-line panels, where LOUCY could appear unremarked",
  "GEO depositions attached to menin-inhibitor papers"
]
hypotheses
[
  "hyp-set-nup214-hoxa-runs-through-recruited-wild-type-mll1"
]
experiments
[
  "exp-menin-in-the-set-nup214-complex-and-menin-inhibitor-in-loucy"
]
How this could bite us back
  • A bounded absence is frequently quoted forward as a negative result. This entry should be cited as 'untested' and never as 'menin-independent', and the difference decides whether a SET::NUP214 patient would be offered a menin inhibitor off-label.
  • If someone runs the experiment and it is negative, that negative will also be n=1 or n=2 in cell lines, which is not enough to exclude menin dependence in patients either.
Still open
  1. Does LOUCY appear, unremarked, in the cell-line panel of any published menin-inhibitor study? That is the single most likely place an answer already exists, and it is reachable only by reading supplementary tables, not by any query.
  2. Would adding LOUCY and MEGAL to a dependency screen be worth it? Two lines is thin, but it is the entire available model space for this fusion, and the graph currently reasons about SET::NUP214 with no functional-genomics datum at all.
  3. Should the graph's other 'no menin-binding motif, therefore menin-independent' inferences be re-audited for the wild-type-recruitment failure mode found here?
Every source behind this entry (4)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    PubMed esearch on 2026-09-20 returns 0 records for `(SET-NUP214 OR TAF-I-NUP214) AND (menin OR MEN1 OR revumenib OR ziftomenib OR VTP-50469 OR MI-503 OR "menin inhibitor" OR "menin inhibitors" OR "menin inhibition")`, 0 for the same menin clause against `LOUCY`, and 0 for `SET-NUP214 AND menin`; the operand controls are 2,237 for `menin` alone, 54 for `SET-NUP214` alone, 33 for `LOUCY` alone, and 1 for `SET-NUP214 AND DOT1L` through the identical query shape.

    What this evidence cannot show

    Bounded absence. Query translations were read back on every zero; PubMed expands `menin` to 'men1 protein human'[Supplementary Concept] OR 'menin'[All Fields] OR 'menin s'[All Fields], so the clause is not a bare string match. Bound: titles, abstracts and MeSH only - not full text, not figures, not supplementary material, not conference abstracts, not preprints. Also note the standing registry trap that MENIN is an author surname, which inflates rather than deflates a count and is therefore not a risk to a zero.

    Evidence that argues against this (1)
    • A zero of exactly this shape, with exactly these controls, was FALSE as a conclusion in this same beat. `SET-NUP214 AND (H3K79 OR "H3-K79" OR "K79" OR "lysine 79")` returns 0 with a clean positive control, and yet PMID 18299449 contains an H3K79 dimethylation ChIP across five HOXA promoters - invisible because the measurement is in a figure and the abstract never names the mark. The menin zeros above are bounded by abstracts, not by papers, and a menin blot in a supplementary figure would not appear in any of them. Van Vlierberghe P et al. 2008
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.review

    `NUP214 AND (menin OR MEN1)` returns exactly 1 PubMed record, PMID 35682627, a review of molecular classification and therapy resistance in adverse-genetics AML; its NUP214 content is DEK-NUP214 as a HOX-upregulating lesion and its menin content is not about any NUP214 fusion, so the single hit is an incidental co-mention and not a counter-example.

    What this evidence cannot show

    Abstract-level title-check of the single hit, which is the standard this brief requires before recording a count as a result. The classification as incidental rests on the abstract; the full text was not read, so a buried menin-plus-NUP214 statement inside the review cannot be excluded - but a review would not be primary evidence in any case.

    Evidence that argues against this (1)
    • PUBLISHED CONFLICTING RESULT. The query token, not the biology, is what returns one record. The premise this absence is used to support - that a KMT2A-free nucleoporin fusion is outside the menin axis - has been tested directly in the other nucleoporin-fusion family and came out the opposite way: in murine NUP98-HOXA9 and NUP98-JARID1A lines the menin-MLL1 inhibitor VTP50469 is active at an IC50 the authors report as similar to KMT2A-rearranged and NPM1c cells, MLL1 and the NUP98 fusion protein are both evicted from chromatin, and VTP50469 prolongs survival in NUP98-NSD1 and NUP98-JARID1A patient-derived xenografts. So a NUP214-scoped menin query returning 1 bounds the string NUP214 and bounds nothing about whether a nucleoporin fusion can be menin-dependent. Heikamp EB et al. 2022
  3. E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database

    Neither LOUCY (DepMap ACH-000104) nor MEGAL appears in the DepMap CRISPR gene-effect dataset served by the Open Targets Platform GraphQL API: a MEN1 query returns 1,258 screens with a gene effect, of which 8 are annotated 'T-Lymphoblastic Leukemia/Lymphoma' - TALL-1 (-0.809), SUP-T1 (-0.688), PF-382 (-0.543), JURKAT (-0.470), DND-41 (-0.264), CCRF-HSB-2-DM (-0.046), KE-37 (+0.080) and PEER (+0.445) - and none of the eight carries SET-NUP214.

    What this evidence cannot show

    Fetched 2026-09-20. The DepMap release version is NOT stated in the API response, so the release is unverified - the same limitation this project's existing DepMap analyses record. The absence of LOUCY was checked two ways: by its DepMap id ACH-000104 (resolved from Cellosaurus CVCL_1380) and by cell-line name across all 1,258 screens. The eight T-lymphoblastic MEN1 values are reported here only to show the comparator set exists and is small; they are RAW gene effects over a mixed panel and are NOT a lineage-split selectivity claim, which this fetch is not powered to make.

    Evidence that argues against this (1)
    • METHODOLOGICAL DEFEATER, and it applies to the instrument rather than to the fetch. A pooled CRISPR gene-effect value on MEN1 is a poor readout for menin dependence in this disease, and this beat's own sibling item measures why: MEN1's mean Chronos gene effect across 1,208 lines is -0.36 and it is NOT flagged essential - in a graph whose central hypothesis is a menin dependency that revumenib converts into a 22.8% CR+CRh rate (95% CI 12.7 to 35.8) in centrally confirmed KMT2A-rearranged relapsed/refractory acute leukaemia in the AUGMENT-101 phase 2. A register that fails to register the dependency in the arm where it is clinically demonstrated cannot bound it in the arm where it is untested, so the absence of LOUCY and MEGAL from DepMap is a weaker fact than it reads as. Issa GC et al. 2025
  4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    The founding SET-NUP214 study ran anti-NUP214, anti-PP32, anti-SET, anti-CRM1 and anti-hDOT1L immunoprecipitates in LOUCY and blotted for SET, CRM1, DOT1L and AF10; the strings 'menin' and 'MEN1' do not occur anywhere in its full text.

    What this evidence cannot show

    A string search of the flattened full text obtained via the PMC HTML route (PMC2343598, 68,564 characters after tag-strip-then-unescape per rule 61). It bounds this paper only. In 2008 the menin-KMT2A interaction was known but no menin inhibitor existed, so the absence is unsurprising and carries little weight as evidence that the authors considered and rejected the idea.

    Evidence that argues against this (1)
    • THE SOURCE'S OWN SCOPE IS THE OBJECTION, and a later paper says why it matters. The 2008 blot list is evidence about what the authors looked for under their own model, in which CRM1 and DOT1L supplied the mechanism and menin had nowhere to enter. The route by which menin could enter was proposed thirteen years later and is INDIRECT: SET-NUP214 interacts with MLL via the SET acidic region of the fusion, and the two cooperatively enhance HOXA10 promoter activity, with neither region alone sufficient. Menin binds wild-type MLL1, not the fusion - so no anti-menin blot on a SET-NUP214 immunoprecipitate would have been designed in 2008 even by authors who had considered the idea, and the absence of that blot is close to uninformative about the hypothesis it is cited against. Cigdem S et al. 2021
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