AFF1-NPM1 proximity: nucleophosmin is the only bait in any published proximity experiment whose neighbourhood contains AFF1, KMT2A and menin together
also called NPM1 BioID AFF1 · nucleophosmin proximity AFF1
Nucleophosmin is a shuttling nuclear protein that is itself one of the commonest things broken in adult leukaemia. When it was tagged and its neighbours listed, the list contained AFF1, KMT2A and menin - the three proteins at the centre of this project - and no other tagged protein managed that.
The same thing, for a scientist
In the K562 50-bait BioID2 map, **NPM1 (P06748) is the only bait whose neighbourhood contains AFF1, KMT2A and MEN1 simultaneously** [E1]. MEN1 is among the least-recovered preys in the whole dataset - **3 baits of 50, the 34.4th percentile** - and its three are BUD13, NPM1 and RPS11; AFF1's four are NPM1, RBM15, SBDS and ZRANB2; the intersection is NPM1 alone [E1][E2]. NPM1 additionally recovers ELL, MLLT1, CCNT1, DOT1L, WDR5, ASH2L, BRD4, NELFE, CDK7, CDC73, RTF1, HCFC1 and CBX8 [E1]. This is **not** an interface in the structural sense - there are no interface residues, no affinity and no structure - and the entry is typed `partner_interface` only because the graph has no proximity-pair type.
Why the three-way co-recovery is worth recording
The menin-interface hypothesis says the therapeutic handle on KMT2A::AFF1 is the menin-KMT2A contact. This project's own structural finding is that menin is nearly the only retained handle, because most famous KMT2A partners bind the discarded half 4.
A proximity map made for a completely unrelated purpose - annotating RNA-binding-protein regulatory modules - independently places menin, KMT2A and AFF1 inside one bait's labelling radius, and only one bait of fifty achieves it 1. That is weak evidence, but it is evidence from an instrument with no stake in the question, which is rare in this graph.
NPM1 is also the right kind of protein for it to be: a nucleolar-nucleoplasmic shuttling chaperone and one of the most frequently mutated genes in adult AML - and NPM1-mutant AML is, with KMT2A-rearranged AML, one of the two genotypes for which menin inhibitors are active. Two menin-sensitive genotypes and a proximity link between their two defining proteins is a coincidence the graph should hold on to, at the confidence it deserves.
Everything wrong with reading it that way
NPM1's neighbourhood is 514 preys. At that size, containing any three nuclear proteins is unsurprising, and NPM1 is one of the most abundant proteins in the nucleolus; abundance drives recovery in both directions 3.
MEN1's three-bait recovery is also fragile. Three of fifty is close to the detection floor and the absence of menin from the other 47 neighbourhoods carries almost no information, because a protein at the threshold appears and disappears between replicates.
And this is wild-type KMT2A, wild-type AFF1 and wild-type menin in a cell with no rearrangement. The fusion is not present anywhere in the experiment 14.
Retained region
Does this map to a region of AFF1 the fusion retains? No, and not because the reading is incomplete. AFF1 was a PREY here, not a bait, so what was labelled is endogenous full-length wild-type AFF1 in a cell with no KMT2A rearrangement. Proximity labelling biotinylates accessible lysines anywhere on the prey, and the mass spectrometry was not run for site-level biotinylation, so the record carries no positional information. Nothing distinguishes a contact with the AFF1 N-terminus, which KMT2A::AFF1 discards, from one with the C-terminal half it keeps.
| partner a | gene-aff1 |
|---|---|
| partner b | gene-npm1 |
| method | BioID2 proximity-dependent biotinylation in K562 (PSI-MI MI:1314), spoke-expanded |
| bait | NPM1 (P06748) |
| prey | AFF1 (P51825) |
| reciprocal | false |
| reciprocity note | No reciprocal experiment is possible in this dataset: AFF1 was never a bait, and no proximity-labelling experiment anywhere in IntAct uses AFF1, AFF4, ELL, MLLT1, MLLT3, MLLT10, KMT2A, MEN1 or DOT1L as bait. |
| druggability | None. There is no measured affinity, no interface and no evidence of direct contact; this is a co-recovery in one bait neighbourhood. |
interface residues a
[]
interface residues b
[]
structures
[]
men1 baits
[ "BUD13", "NPM1", "RPS11" ]
aff1 baits
[ "NPM1", "RBM15", "SBDS", "ZRANB2" ]
- This is a co-recovery in one bait's 514-protein neighbourhood, in a cell line without the fusion. It is filed as a lead, and quoting it as an AFF1-NPM1 interaction would misrepresent it.
- If the menin-KMT2A-AFF1 co-recovery is real and abundance-driven, it predicts nothing about drug response; nucleolar co-residence is not a druggable relation.
- Does an NPM1 proximity experiment in a KMT2A::AFF1 line still recover menin, and does it recover the FUSION as well as wild-type KMT2A?
- NPM1-mutant AML and KMT2A-rearranged AML are the two menin-inhibitor-responsive genotypes. Is the shared neighbourhood a clue to why, or a coincidence of nuclear abundance?
- Mutant NPM1c is cytoplasmically mislocalised. Does NPM1c's proximity neighbourhood lose menin and KMT2A, and would that be measurable as a pharmacodynamic readout?
- Would a menin bait - which has never been run - recover AFF1 reciprocally? That single experiment would convert this from co-recovery to a two-sided observation.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
In the K562 50-bait BioID2 deposition, NPM1 is the only bait whose 514-prey neighbourhood contains AFF1, KMT2A and MEN1 together; it also recovers ELL, MLLT1, CCNT1, DOT1L, WDR5, ASH2L, BRD4, NELFE, CDK7, CDC73, RTF1, HCFC1 and CBX8.
IntAct PSICQUIC query: pubid:39251607, full 19,403-row deposition (IMEx IM-30059), retrieved 2026-09-19 · IntAct molecular interaction database (EMBL-EBI) 2026What this evidence cannot show
Retrieved from IntAct 2026-09-19. NPM1 is one of the most abundant nucleolar proteins and its 514-prey list is large; three-way co-occurrence in it is weak evidence about any pair. A superlative over fifty baits is a statement about those fifty baits. K562 has no KMT2A rearrangement and no fusion protein is present.
Evidence that argues against this (2)
- In the largest human BioID survey (192 baits, HEK293), a prey's bait profile is dominated by subcellular compartment rather than binding. Co-recovery of nuclear proteins by a nuclear bait is what compartment sharing alone predicts. Go CD et al. 2021
- The founding BioID report describes the reagent as labelling proteins near the bait without binding it; promiscuous labelling of the vicinity is the designed behaviour. Roux KJ et al. 2012
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
MEN1 is recovered by only three of the fifty baits (BUD13, NPM1, RPS11), placing it at the 34.4th percentile of the dataset's baits-per-prey distribution and among its least-recovered preys; AFF1's four baits are NPM1, RBM15, SBDS and ZRANB2, so NPM1 is the sole overlap.
IntAct PSICQUIC query: detmethod:"MI:1314" (proximity-dependent biotin identification) intersected with the UniProt accessions of the super elongation complex, KMT2A, MEN1 and DOT1L, retrieved 2026-09-19 · IntAct molecular interaction database (EMBL-EBI) 2026What this evidence cannot show
Three of fifty is near the detection floor. Absence of menin from the remaining 47 neighbourhoods is not evidence of exclusion - a prey at threshold appears and disappears between replicates, and the deposited list is already filtered for bona fide pairs.
Evidence that argues against this (1)
- A low recovery count is equally well explained by low abundance. Menin is not an abundant nuclear protein, and BioID recovery is abundance-weighted, so its three-bait profile may report copy number rather than a restricted neighbourhood. Roux KJ et al. 2012
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
Proximity biotinylation and affinity purification of chromatin-associated complexes recover few shared partners and enrich for distinct biological processes, and BioID preferentially recovers proteins of lower cellular abundance than the affinity route.
Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. · Lambert JP, et al. · J Proteomics 2015What this evidence cannot show
A methods comparison in HEK293 on histones and Mediator, not on the SEC. It is cited to constrain interpretation, not to support a biological claim.
Evidence that argues against this (1)
- The same paper concludes that both approaches recover biologically meaningful interactions and that BioID complements AP-MS rather than replacing or invalidating it, so it cannot be used to dismiss proximity results wholesale. Lambert JP et al. 2015
- E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
Oncogenic mutant forms of MLL retain an ability to interact with menin but not with other identified complex components, which is why menin is treated in this graph as the principal retained handle on the fusion.
Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. · Yokoyama A, et al. · Mol Cell Biol 2004What this evidence cannot show
2004 affinity purification, the era of evidence this beat was dispatched to supplement. It supports the framing of the menin-interface hypothesis, not the proximity observation.
Evidence that argues against this (1)
- The same result is the sharpest argument that a proximity map of wild-type KMT2A cannot be transferred to the fusion: whatever the wild-type protein's neighbourhood contains, the fusion demonstrably loses most of the wild-type complex. Yokoyama A et al. 2004
AFF1 as prey of the NPM1 BioID2 bait
NPM1 as the bait
- co-occurs with →MEN1 / menin — the adaptor the fusion cannot work without
menin co-recovered in the same neighbourhood; 3 of 50 baits reach MEN1 at all
one of AFF1's four proximity baits