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Mechanismstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q36-menin-interactome

Menin represses NF-kB transactivation — through a mapped central region, a SIRT1 cofactor, and an RPA2 off-switch, in every tissue except the one this project cares about

also called menin NF-kB repression · menin p65 repression · menin-SIRT1-p65

Menin sits on the NF-kB proteins and holds down the genes they switch on, by bringing in an enzyme called SIRT1 that strips an activating mark off NF-kB. All of it was worked out in liver, gut, breast and endocrine cells, and none of it has ever been looked at in leukaemia.

The same thing, for a scientist

**The mechanism.** Menin binds the NF-kB subunits p50, p52 and p65 directly, through their N-termini, using a central region of menin the founding paper maps as **aa 305-381 essential** and IntAct curates as **aa 300-376 necessary**; the functional consequence is dose-dependent, specific repression of p65-mediated transactivation at NF-kB sites and suppression of PMA-stimulated NF-kB activation [E1][E2]. **How the repression works.** Menin recruits **SIRT1**, the deacetylase for p65 K310; a SIRT1 inhibitor or SIRT1 siRNA abolishes menin's inhibitory effect [E3]. So this is not steric occlusion of DNA binding — it is corepressor recruitment, the same architecture menin uses at JunD (`mechanism-menin-jund-transcriptional-repression`) and at TEAD1 and the beta-cell HDAC3 axis. **How it is switched off.** **RPA2** competes: ectopic RPA2 dissolves the menin-p65 complex and relieves repression of NF-kB target genes; RPA2 knockdown does the reverse, and RPA2 is itself induced by NF-kB activators through E2F1, which makes it a feed-forward release [E4]. **Where the evidence comes from.** Transfected reporters in unspecified non-haematopoietic backgrounds (2001), hepatocellular carcinoma tissue and lines (2013), MCF7 and MDA-MB-231 breast lines (2017), and the IEC-17 intestinal crypt line, where reducing menin raises proliferation and cyclin D1 via NF-kB and blocking NF-kB restores both [E5]. **Not one leukaemia experiment exists.** That is the shape of the finding: a well-supported, mechanistically resolved, cofactor-dependent repression, established entirely outside the disease, in a protein whose leukaemic partner NF-kB independently turns out to be required to keep MLL fusions on chromatin.

Go deeper
The same architecture as JunD, and why that is the interesting part

This graph already holds a menin repression mechanism with a corepressor: menin-JunD works by blocking JNK-mediated JunD phosphorylation and, in beta cells, by an HDAC3 axis (mechanism-menin-jund-transcriptional-repression, mechanism-menin-jund-hdac3-pbk-axis-in-beta-cells). NF-kB is the same shape with a different deacetylase: menin binds, recruits SIRT1, SIRT1 deacetylates p65 K310, output falls 3.

The JunD story then produced this graph's sharpest resistance idea: resistance-jund-liberation-menin and mechanism-jund-release-inverts-to-growth-promotion, where a drug that occupies menin's pocket releases a repressed partner and the released partner does something the drug did not intend. NF-kB is the obvious next candidate and it has never been asked.

But there is a structural disanalogy that has to be stated, because it may kill the parallel outright. JunD binds the MBM pocket — the crystallographic site that accepts KMT2A MBM1 and every clinical menin inhibitor (interface-menin-jund-pocket, PDB 3U86 against 3U85). NF-kB does not bind there as far as anyone knows: the mapped requirement is menin 300-381, a linear central region, and no structure exists. If the NF-kB contact does not use the pocket, revumenib would not displace it, and the liberation analogy fails at the first step. That is the cheapest thing to test in this whole beat and it has not been tested.

Tissue divergence, stated as a limit rather than a hedge

This project has a standing rule that a menin partner is not a KMT2A::AFF1 partner. Applied here:

systemresultwhat it licenses
transfected NF-kB reporters, 2001 1menin represses p65 transactivation dose-dependentlymenin can repress NF-kB
HCC tissue and lines 3repression requires SIRT1; menin is down-regulated in HCCa mechanism, in liver cancer
MCF7, MDA-MB-231 4RPA2 relieves the repressiona release valve, in breast cancer
IEC-17 intestinal crypt line 5menin knockdown raises proliferation and cyclin D1 via NF-kB; NF-kB blockade restores boththe repression is growth-restraining in one epithelium
any leukaemia cellnothing 6nothing

The IEC-17 result 5 is the closest thing to a functional prediction for leukaemia and it is the one most likely to mislead: it says that losing menin releases NF-kB and that the released NF-kB drives proliferation. That is exactly the direction that would matter for a menin inhibitor. It is also a rat intestinal crypt line with no relationship to a blast, and cyclin D1 is not the readout that matters in KMT2A-rearranged disease.

Facts and figures
repressorgene-men1
nfkb regionN-terminus of the NF-kB proteins sufficient
corepressorSIRT1, deacetylating p65 at K310
antagonistRPA2, which dissolves the menin-p65 complex and is itself induced by NF-kB activation via E2F1
uses mbm pocketunknown, and this is the decisive unknown - JunD and KMT2A both use the pocket that clinical menin inhibitors occupy, and no evidence places NF-kB there
targets
[
  "gene-rela",
  "gene-nfkb1",
  "gene-nfkb2"
]
menin region
{
  "paper": "aa 305-381 essential (PMID 11526476)",
  "intact_curation": "aa 300-376 necessary binding region",
  "note": "one deletion series, two presentations; not independent mappings"
}
systems studied
[
  "transfected NF-kB reporter assays (2001)",
  "hepatocellular carcinoma tissue and lines (2013)",
  "MCF7 and MDA-MB-231 breast lines (2017)",
  "IEC-17 intestinal crypt-like line (2008)"
]
systems not studied
[
  "any leukaemia cell line",
  "any haematopoietic primary cell",
  "any KMT2A-rearranged system",
  "any system under a menin inhibitor"
]
How this could bite us back
  • If a menin inhibitor relieves this repression, the drug raises NF-kB output in a disease where canonical NF-kB sustains the leukaemia stem cell programme - a resistance mechanism built into the mechanism of action.
  • The corepressor is SIRT1, and SIRT1 activity depends on NAD+, which is perturbed by chemotherapy, fasting and infection. A repression with a metabolic cofactor is a repression that varies between patients and between days.
  • RPA2 gives the tumour a cheap, non-genetic way to switch this repression off without touching menin at all.
Still open
  1. Does the menin-NF-kB contact use the MBM pocket? If not, no menin inhibitor can relieve this repression and the whole liberation question is moot.
  2. Is SIRT1 the executing corepressor in a haematopoietic cell, or is that hepatocyte-specific?
  3. Is RPA2 expressed at levels in KMT2A-rearranged blasts that would already keep the menin-p65 complex dissolved, making the repression irrelevant before any drug is given?
  4. Does menin occupy NF-kB target promoters in a KMT2A-rearranged cell, or only NF-kB-independent MLL targets? A menin ChIP intersected with the published RELA ChIP would answer this from existing data types.
Every source behind this entry (6)
  1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

    The NF-kB proteins p50, p52 and p65 interact specifically and directly with menin in vitro and in vivo; the region of NF-kB proteins sufficient for binding is the N-terminus; amino acids 305-381 of menin are essential for this binding; menin represses p65-mediated transcriptional activation on NF-kB sites in a dose-dependent and specific manner; and PMA-stimulated NF-kB activation is suppressed by menin.

    The tumor suppressor protein menin interacts with NF-kappaB proteins and inhibits NF-kappaB-mediated transactivation. · Heppner C, Bilimoria KY, Agarwal SK, Kester M, Whitty LJ, Guru SC, Chandrasekharappa SC, Collins FS, Spiegel AM, Marx SJ, Burns AL · Oncogene 2001
    PMID 11526476DOI
    What this evidence cannot show

    `established` for the reported system only. Transfected reporter assays, 2001, before menin's structure was solved; the cell backgrounds are not stated in the abstract and are not haematopoietic anywhere in the paper's framing. Full text unreadable: no PMCID from Europe PMC or from efetch, and the DOI resolves to a 303-character redirect stub (the Nature-portfolio failure mode of route 5). Detail beyond the abstract comes from IntAct's curation.

    Evidence that argues against this (1)
    • Menin's effect on NF-kB is not unconditional or one-directional in later work: it requires SIRT1, it is reversed by RPA2, and in an intestinal line the relationship is inferred from correlation between menin level, NF-kB activity and cyclin D1 rather than from a direct binding perturbation. Theillaumas A et al. 2008
  2. E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    IntAct curates the MEN1-RELA interaction from PMID 11526476 with a necessary binding region on MEN1 of residues 300-376, MEN1-NFKB1 with both an anti-bait co-immunoprecipitation and a pull-down, and MEN1-NFKB2 with a pull-down only; no other publication in IntAct supports any of the three pairs.

    What this evidence cannot show

    The 300-376 and 305-381 figures are the same underlying deletion series read off different presentations of one paper; they are not two independent mappings and must not be averaged or treated as replication.

    Evidence that argues against this (1)
    • A curated interaction inherits every limitation of the single experiment behind it. Anti-bait co-immunoprecipitation and affinity-capture mass spectrometry cannot distinguish a direct contact from a shared-complex association, tagged-bait overexpression can create contacts that do not occur at endogenous stoichiometry, and a partner curated from one publication has by definition never been independently replicated. The enumeration is accurate about the database; the database is not a statement about the blast. Heppner C et al. 2001
  3. E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

    Menin represses p65 acetylation through recruitment of SIRT1, the enzyme that deacetylates p65 at lysine 310; a SIRT1 inhibitor or SIRT1-specific siRNA abolishes the inhibitory role of menin. Menin expression is frequently down-regulated in hepatocellular carcinoma tissues and cells.

    PMID 23224434DOI
    What this evidence cannot show

    Hepatocellular carcinoma tissues and cell lines only. Mol Biol Rep is a low-visibility venue and this result has not been independently replicated in thirteen years. The SIRT1 dependence has never been tested in a haematopoietic cell, and SIRT1 inhibitors are pleiotropic.

    Evidence that argues against this (1)
    • If the repression is executed by SIRT1 recruitment rather than by occlusion, an MBM-pocket ligand need not relieve it at all - which would make the whole liberation analogy with JunD inapplicable to NF-kB. Murai MJ et al. 2011
  4. E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

    Menin interacts with RPA2; ectopic RPA2 expression inhibits formation of the menin-p65 complex and represses menin's inhibitory effect on NF-kB-regulated genes, while RPA2 knockdown promotes menin-p65 complex formation and represses NF-kB-mediated gene expression. RPA2 is induced via an E2F1-dependent mechanism in cells treated with the NF-kB activators TNF-alpha or LPS.

    PMID 28007956DOI
    What this evidence cannot show

    MCF7 and MDA-MB-231 breast cancer lines, with over-expression and knockdown rather than endogenous perturbation; no haematopoietic system. The E2F1 induction arm rests on pharmacological NF-kB activation with TNF-alpha and LPS.

    Evidence that argues against this (1)
    • A breast-cancer result is being used to describe a repression mechanism this graph applies to leukaemia, and RPA2's replication role gives a competing explanation for the same observation. The direction also matters: relieving menin's inhibition of NF-kB in a cell where menin anchors the fusion is not obviously the same event as in a cell where it does not. Heppner C et al. 2001
  5. E5established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

    In the IEC-17 intestinal crypt-like cell line, reducing menin expression increases the transcriptional activity of the cyclin D1 promoter; blockade of the NF-kB pathway restores proliferation, cell cycle, cyclin D1 transcription and cyclin D1 protein to the levels seen with menin present.

    Relation between menin expression and NF-kappaB activity in an intestinal cell line. · Theillaumas A, Blanc M, Couderc C, Poncet G, Manship B, Chayvialle JA, Roche C, Cordier-Bussat M · Mol Cell Endocrinol 2008
    PMID 18590796DOI
    What this evidence cannot show

    One epithelial crypt-like cell line. The authors describe their own result as supporting a 'correlation between cyclin D1 expression, NF-kB activity and menin expression', not a demonstrated causal chain through the menin-p65 contact. The read-out is cyclin D1, which is not a meaningful axis in KMT2A-rearranged disease.

    Evidence that argues against this (1)
    • This is the only published system in which losing menin measurably releases NF-kB and the released NF-kB drives proliferation - the exact prediction a menin inhibitor would make. Its weight is limited entirely by the fact that it is an intestinal crypt line. Theillaumas A et al. 2008
  6. E6strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    No published work examines menin and NF-kB in leukaemia. (menin OR MEN1) AND (NF-kappaB OR NFkB) AND (leukemia OR leukaemia) returns 3 PubMed records and all three are removed by title-checking; the broader query without the leukaemia term returns 21 records, every one of them endocrine, hepatic, intestinal, breast, prostate or neural.

    What this evidence cannot show

    Title/abstract search. It cannot see supplementary data, and it structurally misses any leukaemia paper that studies NF-kB without naming menin - which is the case for the most relevant paper in existence, PMID 24054986.

    Evidence that argues against this (1)
    • The absence is of the JOIN, not of either half: NF-kB in MLL leukaemia is well studied, and menin-NF-kB is well studied. Reporting this as 'menin and NF-kB are unstudied' would be wrong; it is the intersection that is empty. Kuo HP et al. 2013
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