Oncofusion

start / graph / interface-menin-braf-v600e-the-only-one-with-an-endogenous-menin-lane

Interfacemoderate confidence 3 of 5: One strong study, or several smaller consistent ones.Q128-the-menin-interactome-that-is-not-chromatin

MEN1-BRAF V600E: four methods and an endogenous menin lane - the only one of the nine that is a real observation, and it is still a property of the allele

also called menin-BRAF V600E · MEN1 BRAF neoPPI · EBI-52380398

Of nine cancer genes a database lists as menin partners, this is the only one with real experiments behind it: menin's own protein was pulled down with mutant BRAF in a cancer cell. But the interaction is made by the BRAF V600E mutation, not by menin, and that mutation does not occur in the leukaemia this project studies.

The same thing, for a scientist

**Verdict: DECLINED as a menin partner for this graph, on clause (c) of criterion C2 only.** IntAct curates four MEN1-BRAF records from PMID 35512704, and unlike the other eight partners in this beat they are not one assay: **BRET** in HEK293T (EBI-63963639, Table S2B), **split-luciferase complementation / NanoPCA** in A375 melanoma (EBI-52381059, Table S4), a **GST pull-down** annotated `mutation increasing interaction strength` (EBI-63973327, Data S1 Figure i), and an **anti-tag co-immunoprecipitation** in H1299 lung carcinoma with FLAG-BRAF V600E as bait (EBI-52380398, Figure 4D) [E1]. Figure 4D was read directly from the PMC raster and **MEN1 is one of the blotted endogenous partners**, ctrl versus V600E, IP and WCL lanes [E2]. So one side of this pair is untagged and endogenous, which is true of nothing else in the nine. **It fails anyway**, because every record carries `P15056:p.Val600Glu` and the screen's whole design is wild-type versus mutant: the entity that acquired a partner is BRAF V600E, not menin. BRAF V600E is not a lesion of KMT2A-rearranged leukaemia. **`confidence_overall` on this entry rates the INTERACTION, not the adjudication.** The adjudication is strong; the interaction is what is weak, and a reader scanning the field should see the weak thing.

Go deeper
Why this one is different, stated before the verdict

Everything else in this beat rests on one detection method in one publication. This does not.

recordmethodsystemtagged?source panel
EBI-63963639BRET (proximity)HEK293Tboth sides taggedTable S2(B)
EBI-52381059split-luciferase complementation (NanoPCA)A375 melanomaboth sides taggedTable S4
EBI-63973327GST pull-down, mutation increasing interaction strengthHEK293Tboth sides taggedData S1 Figure i
EBI-52380398anti-tag co-IP, semi-IPH1299 lung carcinomaBRAF tagged, MEN1 endogenousFigure 4D

The fourth row is the one that matters. A semi-IP pulls the tagged bait and blots for endogenous partners, so the menin side is at native abundance and native modification state. That removes the single objection that kills the other eight rows in this beat.

IntAct records the host of that co-IP as H199 lung lymph node carcinoma cell. The paper's legend says H1299. NCI-H1299 is a non-small-cell lung carcinoma derived from a lymph node metastasis, which matches IntAct's descriptor exactly, so this is a typo in the IntAct string and not a second cell line. Reported, not edited.

Why it is declined anyway

Three reasons, in descending order of force.

  1. It is the allele's property, not menin's. All four records carry P15056:p.Val600Glu. The BRET feature is typed mutation causing an interaction and the pull-down feature is typed mutation increasing interaction strength. Figure 4D's control lane is empty vector, not BRAF wild type, so that panel on its own does not show the wild-type protein failing to bind - the BRET and pull-down annotations are what assert that. This graph's question is whether MENIN has a non-chromatin role. An interaction created by a mutation in the other protein cannot answer it.
  2. The lesion is absent from the disease. BRAF V600E is not a recurrent lesion of KMT2A-rearranged infant or paediatric acute leukaemia. Any inference from this row to menin-inhibitor biology in that population would be transporting a result across a lesion the patients do not carry.
  3. BRAF is tagged and overexpressed on the other side in every record, including Figure 4D, where FLAG-BRAF V600E is introduced into H1299 (which is BRAF wild type). So the complex is formed by an ectopically expressed oncoprotein.

What would overturn this verdict: a co-IP of endogenous menin with endogenous BRAF V600E in a V600E-mutant line, with a V600E-negative isogenic control - which is the shape of Figure 4E(i) in the same paper, done for other partners in flag-knockin RKO cells but not, as far as the legend says, for menin.

Where this could still matter, and it is not leukaemia

Cycle 72 asked this and it is worth keeping open with the stronger evidence now attached. BRAF V600E is the defining lesion of hairy cell leukaemia and is recurrent in Langerhans cell histiocytosis, melanoma and a minority of lung adenocarcinoma. In none of those has anyone asked whether menin is in the V600E complex at endogenous levels, or whether a menin inhibitor changes anything downstream of V600E. That is a cheap question with an approved drug on each side of it, and this entry exists partly so that the question has somewhere to hang.

Facts and figures
partner agene-men1
partner bBRAF
partner b uniprotP15056
partner b length AA766
partner a uniprotO00255
partner a length AA610
verdictDECLINED
adjudicated byQ128, cycle 91, 2026-09-23
druggabilityNot assessable. No region, residue or domain is mapped on either protein in any record, so it is not known whether the menin-inhibitor MBM pocket is involved, and no structure exists.
alleleP15056:p.Val600Glu
n methods4
endogenous sideMEN1, in the Figure 4D semi-IP
intact miscore0.6
absence classmeasured-not-reported
absence class noteThe wild-type BRAF versus V600E BRET comparison against MEN1 was measured by the qHT-dS platform and is in Mo et al. Table S2(A)/S2(B) inside PMC9597701; nobody in this project has read the number. Separately, no experiment anywhere has tested endogenous menin against endogenous BRAF V600E, which is never-measured and needs wet work.
interface residues a
[]
structures
[]
ligands
[
  "drug-revumenib",
  "drug-ziftomenib"
]
records
[
  "EBI-63963639 (bret, HEK293T)",
  "EBI-52381059 (split luciferase complementation, A375)",
  "EBI-63973327 (pull down, HEK293T)",
  "EBI-52380398 (anti tag coip, H1299)"
]
intact feature types
[
  "mutation causing an interaction",
  "mutation increasing interaction strength",
  "mutation"
]
c2
{
  "a_second_method": true,
  "b_endogenous_side": true,
  "c_wild_type": false,
  "admitted": false,
  "failing_clause": "c"
}
How this could bite us back
  • If this complex is real in V600E disease, a menin inhibitor occupying the MBM pocket would not necessarily disrupt it, because no record maps the contact to that pocket. A combination built on 'revumenib blocks the BRAF V600E-menin axis' would be assuming an interface nobody has mapped.
  • The reverse bite-back is the more likely one. A BRAF inhibitor given to a patient also on a menin inhibitor would be acting on a protein that, on this evidence, sits in a complex with the menin inhibitor's target - and nobody has looked for an interaction between the two drugs' effects, because nobody has written this partner down.
  • Importing this row into KMT2A-rearranged leukaemia would be the classic error this project keeps catching: a mechanism demonstrated in a lesion the index population does not carry, used to justify an intervention in that population.
Still open
  1. Does endogenous menin co-precipitate with endogenous BRAF V600E in a V600E-mutant line, against a V600E-negative isogenic control? Mo et al. did exactly this design in flag-knockin RKO cells for KEAP1, VHL and BCL2L1; menin is not named in that legend.
  2. Is MEN1 drawn in the Figure 4A BRAF V600E spoke diagram, and in which edge colour? Red is Go-PPI (gain), cyan is comPPI (shared with wild type). The 1050x666 raster was legible for panel 4D and not decisively for 4A, and the answer changes whether the authors themselves called menin a gain.
  3. Does a menin inhibitor do anything in a BRAF V600E disease - hairy cell leukaemia, Langerhans cell histiocytosis - where the complex, if real, would exist? No menin-inhibitor study in any of those diseases was found.
  4. Where on menin does BRAF V600E bind? No region, residue or domain is mapped on any of the four records, so the question of whether the menin inhibitor pocket is involved cannot even be posed yet.
Every source behind this entry (3)
  1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    IntAct record(s) EBI-63963639 (bret, HEK293T); EBI-52381059 (split luciferase complementation, A375); EBI-63973327 (pull down, HEK293T); EBI-52380398 (anti tag coip, H1299) curate a MEN1-BRAF interaction from PMID 35512704. Detection method bioluminescence resonance energy transfer (BRET), interaction type 'proximity', host Homo sapiens HEK293T embryonic kidney cell, both partners epitope-tagged (NanoLuc donor on BRAF, Venus acceptor on MEN1). The BRAF side carries feature(s) P15056:p.Val600Glu, typed by IntAct as 'mutation causing an interaction, mutation increasing interaction strength, mutation'. The row is annotated to Table S2(B) of the paper. intact-miscore 0.60.

    What this evidence cannot show

    Read live from the IntAct REST endpoint on 2026-09-23; field names quoted are the REST JSON's own. A miscore of 0.60 is low on IntAct's 0-1 scale and is what a single-method, single-publication row scores by construction, so it is a restatement of the evidence thinness rather than an independent grade of it. The underlying supplementary table was not parsed; the allele and feature type are IntAct's curation of it.

    Evidence that argues against this (1)
    • IntAct's featureType vocabulary is the curator's reading of the paper, not the paper's own words. 'mutation causing an interaction' (MI:2227) and 'mutation with no effect' (MI:2226) both presuppose that a wild-type comparison was made and interpreted. If IntAct has typed a row wrongly, every verdict built on the type is wrong in the same direction, and the only way to check is the paper's own supplementary table. Mo X et al. 2022
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    PMID 35512704 is a quantitative high-throughput differential BRET screen (qHT-dS) of 17,792 wild-type/mutant interaction pairs in live HEK293T cells, built specifically to find interactions a cancer mutation creates and the parental protein does not make. In its 198,614-character PMC full text (PMC9597701), 'menin' and 'MEN1' occur exactly twice and both are the same key-resources row for a ThermoFisher anti-menin antibody (PA5-79663, RRID:AB_2746778). Menin is discussed in no sentence of the narrative, results or discussion.

    Systematic discovery of mutation-directed neo-protein-protein interactions in cancer. · Mo X, Niu Q, Ivanov AA, Tsang YH, Tang C, Shu C, Li Q, Qian K, Wahafu A, Doyle SP, Cicka D, Yang X, Fan D, Reyna MA, Cooper LAD, Moreno CS, Zhou W, Owonikoko TK, Lonial S, Khuri FR, Du Y, Ramalingam SS, Mills GB, Fu H · Cell 2022
    PMID 35512704DOI
    What this evidence cannot show

    Full text retrieved by efetch db=pmc and searched after tag-stripping and entity unescaping, so a mention inside a figure image is invisible to it - and one is: MEN1 is a blotted row in Figure 4D. The supplementary tables that hold every menin number in this paper were not parsed. So 'menin is absent from the paper' would be false; the defensible claim is that menin is absent from the paper's prose.

    Evidence that argues against this (1)
    • A proximity or affinity signal measured between two tagged, co-overexpressed proteins in a heterologous cell line is a real measurement and is not a demonstration that the complex forms at endogenous stoichiometry in any tissue. The Mo et al. platform is explicitly a co-expression BRET screen in live HEK293T cells, and its own validation arm exists because the primary screen output is a candidate list, not a partner list. Mo X et al. 2022
  3. E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    UniProtKB P15056 (BRAF) is 766 aa. Subcellular location: Nucleus (ECO:0000250, by similarity), Cytoplasm (ECO:0000269), Cell membrane (ECO:0000269). Tissue specificity: Brain and testis MEN1 (O00255, 610 aa) carries a single subcellular location, Nucleus, with experimental evidence (ECO:0000269), and tissue specificity 'Ubiquitous'.

    What this evidence cannot show

    UniProt subcellular-location comments are curated pointers, and rule 91 in this project's brief established that an ECO:0000269 code means a curator read AN experiment, not necessarily THE experiment or the best one. The cited papers behind these location lines were not opened here. Uncoded lines are recorded as uncoded and not discarded.

    Evidence that argues against this (1)
    • A compartment mismatch is a prior, not a refutation. Proteins move: menin's own UniProt record annotates only Nucleus, yet the founding localisation paper (PMID 9465067) maps at least two NLSs and UniProt does not cite it, which this project recorded as rule 91. An argument from UniProt compartments is therefore an argument from an incomplete record on both sides of the pair. UniProt Consortium 2026
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