The second handle on the retained fragment is CK2-dependent, not 14-3-3-dependent
also called CK2 second handle · phospho-gated LEDGF handle hypothesis
This project has assumed menin is essentially the only grip on the part of KMT2A that leukaemia fusions keep. We think there is a second grip - the one LEDGF holds - and that it can be loosened by blocking the enzyme CK2 rather than by blocking menin.
The same thing, for a scientist
The cycle-28 structural finding that **menin is very nearly the only retained handle** was the premise this beat was sent to test through 14-3-3. The 14-3-3 route closed: **S821 is not phosphorylated in a 130-site phosphoproteomic re-analysis, no canonical motif acceptor in KMT2A is, and no paper has ever reported 14-3-3 binding KMT2A directly.** But the premise fails anyway, by a different route. **KMT2A residues S136 and S142, both retained, are CK2 phosphosites whose occupancy raises LEDGF/p75 IBD affinity, and whose loss to alanine impairs MLL1-fusion transformation while phosphomimetic substitution rescues it.** The hypothesis: **the LEDGF IBM is a second, phosphorylation-gated, menin-pocket-independent handle on the retained fragment, and CK2 is its upstream drug target.** It is a weaker handle than menin and it is real.
The claim, stated so it can be attacked
- The fragment retained by every KMT2A fusion carries a LEDGF/p75-binding motif at 111-160.
- That motif's affinity for the LEDGF IBD is raised 2- to 10-fold by phosphorylation.
- On KMT2A the phospho-acceptors are S136 and S142, curated as CK2 sites.
- S136A/S142A significantly reduces fusion transformation capacity; S136D/S142D almost fully rescues it.
- Therefore the fusion's chromatin engagement depends on a kinase-written mark that menin inhibitors do not touch, and a CK2 inhibitor should reduce fusion-LEDGF association.
Steps 1-4 are published. Step 5 is the hypothesis, and it has never been tested: no CK2 inhibitor experiment on the KMT2A IBM appears in the literature this beat searched.
Why this is not just the menin interface again
Menin and LEDGF form a composite clamp on adjacent stretches of one KMT2A chain, so the arms are not independent in cells. That is a genuine objection and it is why this is a hypothesis rather than a finding.
But the arms are pharmacologically independent in a way that matters: revumenib occupies the menin pocket and does nothing to the IBD, and MEN1 resistance mutations at the menin pocket have no reason to protect the IBM. If the clamp has two arms and only one has a drug, the second arm is where resistance lives and where the next drug goes. The graph already records resistance-men1-interface-mutations; this hypothesis predicts those mutants remain sensitive to IBM disruption.
That prediction is the cleanest test and it is also the most clinically consequential thing in this beat.
What would kill it
- A CK2 inhibitor that does not reduce fusion-LEDGF association at fusion target loci in a t(4;11) line, at a dose and time where wild-type MLL1 stabilisation has not yet occurred.
- A demonstration that the S136A/S142A transformation defect is LEDGF-independent - e.g. that it persists in PSIP1-null cells.
- A measured Kd showing the phospho and non-phospho IBM both bind the IBD far outside any druggable window.
- Evidence that the composite clamp cannot be disassembled one arm at a time in cells.
And the honest asymmetry: confirming it does not overturn the menin-interface programme. Menin remains the stronger arm, the measured one (53 nM and 72 nM) and the one with approved drugs. This hypothesis says the retained fragment has two handles, not that it has a better one.
| statement | The fragment retained by all KMT2A fusions carries a second, menin-pocket-independent handle - the LEDGF/p75 IBD-binding motif at residues 111-160 - whose affinity is gated by CK2 phosphorylation of S136 and S142, making CK2 a drug target for loosening the fusion's chromatin grip by a route that MEN1 resistance mutations do not protect. |
|---|---|
| origin | literature-gap |
| prior probability | 0.45 |
predictions
[ "a CK2 inhibitor reduces fusion-LEDGF co-occupancy at fusion target loci before wild-type MLL1 stabilisation becomes measurable", "S136A/S142A fusion transformation defect is abolished in PSIP1-null cells", "MEN1 resistance-mutant lines remain sensitive to IBM disruption", "phospho-S136/S142 IBM binds the LEDGF IBD measurably more tightly than the unphosphorylated peptide" ]
experiments
[ "exp-ck2-inhibitor-two-route-separation", "exp-14-3-3-bridge-pulldown-t411" ]
analyses
[ "ana-kmt2a-phosphosite-atlas-retained-vs-lost", "ana-kmt2a-s821-phosphosite-verdict" ]
falsifiers
[ "CK2 inhibition does not reduce fusion-LEDGF association at any dose or time before wild-type MLL1 accumulates", "the S136A/S142A transformation defect persists in PSIP1-null cells", "measured Kd places both phospho and non-phospho IBM outside any druggable window", "the composite clamp cannot be disassembled one arm at a time in cells" ]
menin mbm1 kd conditions
{
"_why": "Added by king sweep 2026-09-21 (Q82 corrections-owed #3). This entry quotes the menin-MBM1 53 nM figure. That number is NOT comparable to the KMT2A CXXC-DNA affinities without stating its buffer, and the omission is how a 1,300-fold 'discrepancy' was manufactured.",
"value": "53 nM",
"motif": "KMT2A MBM1, residues 4-15, FITC-labelled peptide at 15 nM",
"method": "fluorescence polarisation",
"buffer": "50 mM Tris, pH 7.5, 50 mM NaCl, 1 mM DTT",
"nacl_mM": 50,
"companion_itc": "72 nM by ITC, 50 mM phosphate pH 7.5, 50 mM NaCl, 1 mM beta-mercaptoethanol, 27 C",
"source_pmid": "20961854",
"source_quote": "\"in the FP buffer (50 mM Tris, pH 7.5, 50 mM NaCl, 1 mM DTT) used for binding experiments (Kd measurements)\" -- Grembecka 2010 JBC, Methods, fetched and read from PMC3003368 on 2026-09-21",
"do_not_compare_naively": {
"against": "KMT2A CXXC-DNA Kd 44 uM (PMID 20010842, Cierpicki 2010)",
"because": "that measurement was made at 300 mM NaCl -- verbatim from its Methods, \"50 mM phosphate buffer (pH 7.1), 300 mM NaCl, 2 mM DTT at 25 C\" (PMC2908503, read 2026-09-21) -- SIX-FOLD more salt, on a salt-sensitive protein-DNA contact, against a hydrophobic peptide pocket that is not.",
"best_matched_pair": "44 uM at 300 mM NaCl vs the 5.7 uM tagless CXXC measurement at 150 mM NaCl gives 108-fold against menin, not ~1,000-fold",
"see": "ana-the-menin-affinity-comparison-was-made-at-one-sixth-the-salt"
},
"added": "2026-09-21"
}cxxc dna kd conditions
{
"_why": "Added by king sweep 2026-09-21 (cycle 46). This entry quotes the KMT2A CXXC-DNA 44 uM. That number is a property of five choices, not of the molecule, and quoting it bare is how this graph manufactured a 1,300-fold 'discrepancy' with the menin contact.",
"value": "44 uM",
"construct": "isolated CXXC domain, KMT2A 1147-1203, untagged, 15N-labelled",
"ligand": "DNA pal oligonucleotide, one CpG element",
"method": "NMR titration",
"buffer": "50 mM phosphate, pH 7.1, 300 mM NaCl, 2 mM DTT, 25 C",
"nacl_mM": 300,
"source_pmid": "20010842",
"source_quote": "\"Determination of the dissociation constants by NMR for the CXXC domain (MLL 1147-1203) and mutants was performed by titration of 15N-labeled protein with concentrated solutions of DNA pal oligonucleotide. Experiments were carried out in 50 mM phosphate buffer (pH 7.1), 300 mM NaCl, 2 mM DTT at 25 C.\" -- Cierpicki 2010 NSMB, Methods, fetched and read from PMC2908503 on 2026-09-21. The result sentence reads \"The wild type protein yielded a Kd of 44 uM\".",
"this_is_the_high_salt_end": "300 mM NaCl is roughly twice physiological ionic strength and SIX TIMES the 50 mM the menin-MBM1 53 nM was measured in. The same domain measured tagless at 150 mM NaCl gives 5.7 uM -- 7.7-fold tighter from salt alone.",
"do_not_compare_naively": {
"against": "menin-MBM1 53 nM (PMID 20961854), measured at 50 mM NaCl by FP",
"best_matched_pair": "108-fold, not ~1,000-fold",
"see": "ana-the-menin-affinity-comparison-was-made-at-one-sixth-the-salt"
},
"added": "2026-09-21"
}- Confirming this does not weaken the menin programme; menin remains the measured, stronger, druggable arm. A second handle is an addition, and a project that read it as a replacement would be making a mistake this entry does not support.
- CK2 is constitutive and pleiotropic. A retained-fragment handle whose only drug is a pan-CK2 inhibitor is a handle with no selectivity.
- Both CK2 routes displace the fusion from chromatin. If a trial works, it will not be possible to say which route did it, and the medicinal chemistry that follows could be optimised against the wrong substrate.
- The IBD is shared with HIV integrase, POGZ and JPO2. Freeing it has consequences nobody has characterised in a blast.
- Does the IBM arm survive in MEN1-mutant, menin-inhibitor-resistant cells? That single experiment decides whether this is a resistance-stage therapy.
- Can the two CK2 routes be separated pharmacologically, or is every CX-4945 experiment in this disease permanently confounded?
- Is there a molecule that blocks the IBD without freeing it for HIV integrase, POGZ and JPO2?
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Phosphorylation of the LEDGF/p75 IBD-binding motif switches partner affinity 2- to 10-fold; on MLL1 the phosphorylatable serines S136 and S142 are required for full transformation capacity of MLL1 fusions in colony assays, with phosphomimetic substitution rescuing oncogenic activity, and UniProt curates both residues as CK2 sites.
Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation. · Sharma S, et al. · Proc Natl Acad Sci U S A 2018What this evidence cannot show
Read via the PMC HTML page on 2026-09-19 after fullTextXML and efetch db=pmc both failed. The paper's directly reported CK2 treatment experiment is on POGZ; the MLL1 evidence is site mutagenesis plus a transformation assay in murine cells. No CK2 inhibitor was applied to MLL1 in that study, which is why step 5 is a hypothesis.
Evidence that argues against this (1)
- A 2- to 10-fold affinity switch on an interaction whose absolute affinity has never been measured for KMT2A could sit anywhere relative to a druggable window; the menin arm of the same clamp is measured at 53 and 72 nM, and the LEDGF arm has no number at all in the structural literature. Cermáková K et al. 2014
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
CK2 inhibition in KMT2A-rearranged cells produces a chromatin phenotype on the fusion: CX-4945 reduced genome-wide MLL-AFF1, AFF4 and ELL2 occupancy in SEM cells and delayed leukaemic progression in an MLL-AF9 mouse model, although the published mechanism for that effect runs through stabilisation of wild-type MLL1 rather than through the IBM.
Regulation of MLL/COMPASS stability through its proteolytic cleavage by taspase1 as a possible approach for clinical therapy of leukemia. · Zhao Z, et al. · Genes Dev 2019What this evidence cannot show
Full text read via Europe PMC (PMC6317322). This evidence cuts both ways for the hypothesis: it shows a CK2 inhibitor does displace the fusion from chromatin, and it attributes that displacement to a different CK2 substrate on the lost fragment. The two routes were not separated in that study and are confounded in every published CX-4945 experiment in this disease.
Evidence that argues against this (1)
- The paper explicitly reports that CX-4945 increased full-length MLL1 without altering MLL-AF4 protein levels and attributes chimera displacement to competition from stabilised wild-type MLL1. If that is the whole effect, the IBM route contributes nothing and this hypothesis is redundant with an already-published mechanism. Zhao Z et al. 2019
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
The 14-3-3 route to a second retained handle is closed: S821, the only canonical 14-3-3 motif acceptor in the retained fragment, is absent from a 130-site phosphoproteomic re-analysis of KMT2A, as are the acceptors of both other canonical motif matches, and an alias-expanded literature search returns no report of 14-3-3 binding KMT2A directly.
Proteins API proteomics-PTM, Q03164, and PubMed alias-expanded 14-3-3 queries run 2026-09-19 · EMBL-EBI 2026What this evidence cannot show
Pooled public phosphoproteomics misses conditional sites, and PhosphoSitePlus could not be queried (HTTP 403). The literature absence is of PubMed-indexed records. Both bounds are stated in the entries they come from.
Evidence that argues against this (1)
- KMT2A is recovered as a 14-3-3 client by six paralogues in one interactome and by YWHAG in a second study, and that remains the best-reproduced proximity relation in the graph's KMT2A record. A closed motif route is not a closed interaction. Segal D et al. 2023
the contact the hypothesis is about
- depends on →CSNK2A1 (casein kinase 2 alpha) - the one kinase that turns up three separate times in KMT2A biology
CK2 as the upstream drug target
contradicts the menin-only reading of the retained fragment, without displacing menin as the stronger arm
- related to →MEN1 drug-interface mutations — the first proof that a chromatin drug can drive Darwinian escape in patients
predicts MEN1-mutant resistant cells remain sensitive to IBM disruption
- depends on →S821 is not phosphorylated in any dataset we could query: the 14-3-3 motif candidate is dead as stated
the closed 14-3-3 route that this hypothesis replaces
- ← testsSeparating CK2's two routes into KMT2A leukaemia, which every published experiment has confounded
isogenic wild-type-null arm separates the IBM route from the taspase1 route
a second regulated PTM in retained sequence, unstudied where the CK2 one is demonstrated in the fusion
first physical recovery of any CK2 subunit from an MLL-fusion affinity purification - the regulatory one
First evidence in this graph that bears on which catalytic subunit the CK2 hypothesis means: Csnk2a2 is PREDOMINANTLY EXPRESSED IN TESTIS with a gametogenic null phenotype (PMID 12950107), and CSNK2A2 is expressed-but-not-required in KMT2A-rearranged lines - so CK2 activity in a leukaemic cell is far more likely to be alpha's. Supports the attribution rather than undermining it (Q93 2026-09-21)