Menin's departure is partial where the fusion's loss is total, so the two are not stoichiometrically coupled
Three hours after the fusion protein is destroyed almost completely, menin has only half left the genes they shared. Half the menin sitting on those genes is being held there by something that is not the fusion.
The same thing, for a scientist
The quantitative core of the beat, stated in the direction that damages the project's central hypothesis as well as the direction that helps it. At fusion-occupied promoters, 3 h after 500 nM dTAG-VHL: the fusion retains **1.0%** of its signal (HA, raw scale, batch 1909x2; 2.8% in batch 190814) while **MENIN retains 50.3%** and DOT1L 40.1%. Scaled against the fusion's own loss, menin has moved about **half** as far as the fusion has, on a channel where a 47-point stratum gap shows the measurement is not blind. **No component of the complex tracks the fusion stoichiometrically.** The helpful reading is that menin does leave fusion-occupied promoters preferentially and substantially, which the menin-KMT2A interface model predicts. The damaging reading is that the coupling is loose enough that menin occupancy is not a readout of fusion occupancy, and that disabling the menin-KMT2A contact cannot be assumed equivalent to removing the fusion - a menin-directed drug leaves the fusion-independent menin pool untouched, and removing the fusion leaves half the menin in place.
The number, with the width ratio beside it as required
Signal instrument (no peak widths apply): HA 0.010 vs MENIN 0.503 at the same 200 genes, 3 h. Peak instrument, for the same channels: HA summit retention 1.9% (treated/control median peak width ratio 2.79, flagged) and 6.4% (1.93, flagged); MEN1 summit retention 83.4% in its top strength decile (0.93, not flagged) and 29.7% over all peaks. The peak numbers are reported here only because the pre-registration requires the width ratio beside every retention figure; the signal numbers are the ones the conclusion rests on, because the peak instrument saturates at strong sites.
Three candidate tethers for the residual menin
- LEDGF/PSIP1, which physically links menin-MLL1 to chromatin and is essential for MLL-fusion leukaemogenesis but dispensable for steady-state haematopoiesis 34.
- Wild-type MLL1, which is present at these promoters and does not redistribute after fusion loss (C-terminal channel, matched stratum gap -0.055) - so it is a stable, not a compensatory, reservoir.
- A slow off-rate of the same fusion-bound pool, in which case the residue would disappear by 24 h. The deposit cannot test this: there is no MENIN ChIP between 3 h and 4 d, and by 4 d the target-gene ratio is 0.437, i.e. barely lower than at 3 h, which argues for a genuine plateau rather than slow kinetics.
Scale and limits
No spike-in exists anywhere in GSE173599, so every number is a within-sample share, and the treated arms are scaled by a 21-gene housekeeping panel whose own raw 3 h H3K27ac ratio averages 0.809 and is forced to 1. A housekeeping normalisation DEFINES the global change to be zero, so only the DIFFERENCE between strata is measurable; a uniform genome-wide loss of any of these proteins would be invisible here. n = 1 per arm for every channel except HA, which has two independent 3 h batches. The cells are HCB1, transformed by KMT2A::MLLT3 (MLL::AF9) - NOT the index fusion of this project, KMT2A::AFF1 - and a prior beat in this corpus found that per-gene ordering transfers between MLLT3 and AFF1 lines while magnitude does not. Because the arms are housekeeping-normalised, a uniform global fall in chromatin-bound menin would be invisible; this entry does not claim that total menin is unchanged, only that the fusion-occupied fraction falls about half as far as the fusion does.
| mechanism class | protein-protein tethering / chromatin residence |
|---|---|
| system | HCB1 human cord-blood cells transformed by KMT2A::MLLT3 with an HA-FKBP12(F36V) degron |
| shown for fusion | KMT2A::MLLT3 (MLL::AF9) in human HCB1 cells; nothing in KMT2A::AFF1 or in B-lineage |
key numbers
{
"fusion_retained_at_its_own_promoters_3h": "1.0% (batch 1909x2), 2.8% (batch 190814)",
"menin_retained_at_fusion_promoters_3h": "50.3%",
"dot1l_retained_at_fusion_promoters_3h": "40.1%",
"menin_retained_at_non_fusion_promoters_3h": "97.4%"
}- A menin inhibitor that displaces the fusion-dependent menin pool leaves the fusion-independent pool in place; if that pool is competent to re-nucleate the complex, it is a resistance reservoir that no dose escalation reaches.
- Conversely, a therapy that removes the fusion leaves half the menin at those promoters, so fusion-directed degraders would not be expected to phenocopy menin inhibition on a chromatin readout - and a trial using menin occupancy to compare them would misrank them.
- MEN1 interface mutations already arise clinically and prevent eviction of menin AND MLL1 from chromatin, so the loose coupling documented here has a demonstrated route to clinical resistance.
- Which tether holds the residual half - LEDGF/PSIP1, wild-type MLL1, or neither? A PSIP1 ChIP in the same degron line would separate the first from the rest and does not exist.
- Does the residual fraction differ between KMT2A::MLLT3 and KMT2A::AFF1? The AFF1 N-terminus carries the same menin-binding motifs but a different elongation module.
- Is the fusion-independent menin pool transcriptionally active at those promoters, or a passive reservoir?
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
At fusion-occupied promoters 3 h after degradation, the fusion retains 1.0-2.8% of its signal while menin retains 50.3% and DOT1L 40.1%.
GSE173599_TSS_gene_body_signal_Figure3.xlsx - per-gene housekeeping-normalised TSS and gene-body ChIP signal, DMSO vs dTAG-VHL 3 h and 24 h, 16 channels · Olsen SN et al. · NCBI GEO supplementary file 2022What this evidence cannot show
HA is on a raw scale and the others are housekeeping-normalised, so the comparison is of fractional change within each channel, not of absolute amounts. n=1 per arm except HA. KMT2A::MLLT3, not KMT2A::AFF1.
Evidence that argues against this (1)
- Menin is required for MLL-fusion leukaemogenesis through a high-affinity N-terminal binding motif, so a model in which menin is only loosely coupled to the fusion has to explain why disrupting that motif is sufficient to abolish transformation. Yokoyama A et al. 2005
- E2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
By 4 days the menin ratio at target genes is 0.437, barely below the 3 h value of 0.503, which argues for a plateau rather than slow kinetics.
GSE173599_TSS_signal_Figure4.xlsx - per-gene HA, DOT1L and MENIN TSS signal after 4 days of EPZ-5676, VTP-50469 or dTAG-VHL (batch 1912x2) · Olsen SN et al. · NCBI GEO supplementary file 2022What this evidence cannot show
Different batch, different normalisation floor and a 4-day differentiation confound; the two timepoints are not strictly comparable in level.
Evidence that argues against this (1)
- The 3 h and 4 d values come from different batches with different floors and a 4-day differentiation confound, so a plateau is not the only reading; slow kinetics with a batch offset would look the same. Olsen SN et al. 2022
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Menin links MLL proteins to chromatin through LEDGF/PSIP1, supplying a fusion-independent tether.
Menin critically links MLL proteins with LEDGF on cancer-associated target genes · Yokoyama A, Cleary ML · Cancer Cell 14(1):36-46 2008What this evidence cannot show
Biochemistry and transformation assays; not a post-degradation occupancy measurement.
Evidence that argues against this (1)
- Menin is required for MLL-fusion leukaemogenesis through its direct high-affinity contact with the fusion N-terminus, so a model in which half of promoter-bound menin is fusion-independent must explain why blocking that one contact is sufficient to abolish transformation. Yokoyama A et al. 2005
- E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
LEDGF/p75 is dispensable for steady-state haematopoiesis but essential for MLL-rearranged leukaemogenesis, and its loss decreases MLL occupancy at MLL target genes.
LEDGF/p75 is dispensable for hematopoiesis but essential for MLL-rearranged leukemogenesis · El Ashkar S, Schwaller J, Pieters T, Goossens S, Demeulemeester J, Christ F, et al., De Rijck J · Blood 131(1):95-107 2018What this evidence cannot show
Conditional mouse knockout; mouse rather than human, and MLL occupancy rather than menin occupancy is the measured readout.
Evidence that argues against this (1)
- If LEDGF loss reduces MLL occupancy, LEDGF may tether the complex rather than menin specifically, in which case removing the fusion should also remove the LEDGF-dependent pool - which is not what is observed. El Ashkar S et al. 2018
menin moves about half as far as the fusion does at the fusion's own promoters; the coupling is not stoichiometric
- related to →KMT2A::MLLT3 (MLL-AF9), t(9;11)(p21.3;q23.3)
fusion retains 1.0-2.8% at its own promoters while menin retains 50.3%
the mechanism statement rests on the partitioned measurement
supplies the magnitude: the fusion-independent menin pool at fusion promoters is about half the total