Oncofusion

start / graph / interface-menin-spop-declined-single-bret-no-allele-effect

Interfaceweak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.Q128-the-menin-interactome-that-is-not-chromatin

MEN1-SPOP is four alleles of ONE BRET assay, all 'mutation with no effect' - declined, with a nuclear-speckle confound

also called menin-SPOP · SPOP mutation with no effect · EBI-63732205

A database lists SPOP, a ubiquitin-ligase adaptor, as a menin partner. The basis is one automated screen over four SPOP mutants, none of which changed the signal, and both proteins concentrate in the same crowded nuclear bodies where a proximity assay is hard to interpret.

The same thing, for a scientist

**Verdict: DECLINED.** IntAct curates four MEN1-SPOP records from PMID 35512704 - EBI-63732205, EBI-63735878, EBI-63743193, EBI-63944378 - four alleles of **one** BRET assay: `p.Tyr87Cys`, `p.Phe102Cys`, `p.Phe133Leu`, `p.Phe133Val`, HEK293T, type 'proximity', **Table S2(B)**, intact-miscore **0.27**, all typed **`mutation with no effect`** [E1]. Menin appears nowhere in the paper's prose [E2]. **SPOP adds a confound the other rows do not have:** UniProt annotates SPOP to Nucleus **speckle** with experimental evidence [E3], and a BRET signal between two proteins that both concentrate in a sub-nuclear body reports co-compartmentalisation at least as readily as it reports a complex. F133L is the allele the paper carried into its own Figure 4H validation panel against BRD4, NCOA3/SRC3 and c-JUN; menin is not among them. **Criterion C2: fails (a), (b) and (c).** **`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
Four records, one measurement
IntAct ACallelefeatureTypemethodtablemiscore
EBI-63732205p.Phe102Cysmutation with no effectbretST2B0.27
EBI-63735878p.Phe133Leumutation with no effectbretST2B0.27
EBI-63743193p.Tyr87Cysmutation with no effectbretST2B0.27
EBI-63944378p.Phe133Valmutation with no effectbretST2B0.27

All four are MATH-domain substrate-binding substitutions - Y87, F102, F133 - the prostate-cancer hotspot residues that abolish SPOP's grip on its degrons. None of them changed the menin signal. For a substrate receptor whose substrate-binding cleft has been disabled four different ways, an unchanged association is a direct argument that whatever is being measured is not substrate recognition.

The nuclear-speckle confound, which is specific to this pair

BRET reports that a NanoLuc donor and a Venus acceptor are within roughly 10 nm. In a cell where both partners are over-expressed and both concentrate into the same sub-nuclear compartment, that distance is satisfied by crowding, without any direct or even indirect complex.

UniProt O43791 annotates SPOP to Nucleus speckle with ECO:0000269 3. SPOP is in fact a well-known former of nuclear membraneless bodies and its self-assembly is part of how it works. Menin is nuclear and abundant. So the single measurement behind this row is the measurement least able to distinguish a complex from co-localisation, applied to the pair where co-localisation is most likely.

This project already holds the general version of this warning - its condensate entries record that the two commonest assays cannot tell the two models apart. This is the same problem arriving through a database row rather than through a condensate paper.

The E3-adaptor pattern

SPOP is the substrate-recognition adaptor of a CUL3-RBX1 E3 ubiquitin ligase. FBXW7 is the substrate-recognition subunit of an SCF. ZC3HC1/NIPA is an F-box protein of a further SCF. Three of this beat's nine partners are E3 substrate receptors. Under a null where the nine were drawn at random from the ~2,000-gene OncoPPi v2 library, three substrate receptors would be unremarkable; the point is not the count but that the class has a known assay pathology. Overexpressed substrate receptors bind promiscuously, and they are enriched in AP-MS and proximity datasets for that reason. See hyp-q128-three-of-menins-nine-declined-partners-are-e3-ligase-substrate-receptors, which states the pattern as a hypothesis with both a biological and an artefactual arm, and which names the null this section deliberately does not compute.

Facts and figures
partner agene-men1
partner bSPOP
partner b uniprotO43791
partner b length AA374
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.
allelefour MATH-domain substrate-binding substitutions; see records
n methods1
n records but one assay4
intact miscore0.27
source panelTable S2(B), primary screen CARINA output
specific confoundboth proteins are nuclear and SPOP is annotated to nuclear speckles (ECO:0000269); BRET cannot separate a complex from co-compartmentalisation
absence classmeasured-not-reported
absence class noteWild-type SPOP BRET against MEN1 is in Mo et al. Table S2(A) inside PMC9597701, unread by this project.
interface residues a
[]
structures
[]
ligands
[
  "drug-revumenib",
  "drug-ziftomenib"
]
records
[
  "EBI-63732205 (p.Phe102Cys)",
  "EBI-63735878 (p.Phe133Leu)",
  "EBI-63743193 (p.Tyr87Cys)",
  "EBI-63944378 (p.Phe133Val)"
]
intact feature types
[
  "mutation with no effect"
]
c2
{
  "a_second_method": false,
  "b_endogenous_side": false,
  "c_wild_type": false,
  "admitted": false,
  "failing_clause": "a, b and c"
}
How this could bite us back
  • SPOP degrades BRD4, and BRD4 is a genuine part of the KMT2A-fusion elongation machinery this project cares about. A reader could construct a menin-SPOP-BRD4 story from this row; it would rest on four BRET wells and on SPOP mutants that all failed to change anything.
  • If menin does concentrate in nuclear bodies with SPOP, a menin inhibitor could alter that partitioning without altering any chromatin readout, and nothing in any trial or preclinical study would detect it.
Still open
  1. What is the wild-type SPOP BRET value against MEN1 in Table S2(A)?
  2. Does menin enter SPOP nuclear bodies? A single co-immunofluorescence would separate co-compartmentalisation from complex formation far more cheaply than any interaction assay, and no such image exists for this pair.
  3. Is menin a CUL3-SPOP substrate? Four substrate-cleft mutants leaving the signal unchanged argues against it, which makes this a near-free negative that could be stated properly if the wild-type value were read.
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-63732205 (p.Phe102Cys); EBI-63735878 (p.Phe133Leu); EBI-63743193 (p.Tyr87Cys); EBI-63944378 (p.Phe133Val) curate a MEN1-SPOP 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 SPOP, Venus acceptor on MEN1). The SPOP side carries feature(s) four MATH-domain substrate-binding substitutions; see records, typed by IntAct as 'mutation with no effect'. The row is annotated to Table S2(B), primary screen CARINA output of the paper. intact-miscore 0.27.

    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 0.27 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 O43791 (SPOP) is 374 aa. Subcellular location: Nucleus (ECO:0000269), Nucleus speckle (ECO:0000269), Cytoplasm (ECO:0000269). Tissue specificity: Widely expressed 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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