At gene resolution the menin inhibitor is the stronger single agent, and only the combination approaches the degron
Comparing the two drugs head to head on how much fusion protein they knock off its target genes: the menin inhibitor beats the DOT1L inhibitor, and only using both together comes close to simply destroying the fusion outright.
The same thing, for a scientist
Re-derivation of the paper's headline drug comparison at per-gene resolution, which adds an ordering the corpus did not have. Median HA TSS signal at the authors' 200 target genes after 4 days (batch 200908, the only batch carrying the combination arm): **EPZ-5676 0.439 > VTP-50469 0.270 > combination 0.0857 > dTAG-VHL 0.050**. At the 417 non-target genes in the same sheet: 0.481, 0.438, 0.206, 0.181. The independent 1912x2 batch, which lacks a combination arm, reproduces the single-agent ordering (EPZ 0.362, VTP 0.254, dTAG 0.015). So **the menin inhibitor is the stronger single agent on this endpoint in both batches**, the combination recovers roughly 90% of the degron's effect, and the preferential-versus-global character differs: the degron and the combination act preferentially at target genes, while EPZ-5676 alone is nearly as strong at non-target genes as at target genes.
What this adds to the existing corpus entry
This corpus already records, from the peak calls, that neither single agent comes close to degrading the fusion and only the combination does. That conclusion stands. What is new here is (a) the single-agent ordering - menin inhibitor ahead of DOT1L inhibitor, in two independent batches - and (b) the stratum profile: EPZ-5676's effect is close to uniform across strata (0.439 vs 0.481) while VTP-50469's is preferential (0.270 vs 0.438) and the combination's is strongly preferential (0.086 vs 0.206).
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. Single doses, single durations, one cell line; a potency comparison at one concentration each is not a comparison of the drug classes.
| script | analyses/menin-retention-by-ha-occupancy/analyze_controls.py |
|---|---|
| status | run |
| result summary | HA at 200 target genes, 4 d, batch 200908: EPZ 0.439, VTP 0.270, combo 0.0857, dTAG 0.050. Non-target: 0.481, 0.438, 0.206, 0.181. Batch 1912x2 reproduces the single-agent ordering. |
| peak width ratio note | Signal instrument; the HA peak arms for these samples all exceed the 1.3 width trigger and are not used. |
inputs
[ "GSE173599_TSS_signal_Figure5.xlsx", "GSE173599_TSS_signal_Figure4.xlsx" ]
- The combination is the arm that works and is also the arm that removes the most signal from NON-target genes (0.206 vs 0.181 for the degron), so combination toxicity is predicted to be on-mechanism and not avoidable by scheduling.
- If the menin inhibitor is the stronger single agent, resistance pressure falls first on MEN1, and MEN1 interface mutations are already documented in patients.
- Does the combination's advantage survive dose-matching, or is it an artefact of comparing a 100 nM menin inhibitor with a 250 nM to 1 uM DOT1L inhibitor?
- Is the near-uniform effect of EPZ-5676 across strata a sign that DOT1L inhibition acts on general elongation rather than on fusion targets specifically?
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
Median HA TSS signal at target genes after 4 days is 0.439 for EPZ-5676, 0.270 for VTP-50469, 0.086 for the combination and 0.050 for dTAG-VHL.
GSE173599_TSS_signal_Figure5.xlsx - per-gene HA and H3K27ac TSS signal after 4 days of EPZ-5676, VTP-50469, the combination or dTAG-VHL (batch 200908) · Olsen SN et al. · NCBI GEO supplementary file 2022What this evidence cannot show
One concentration each (EPZ 1 uM in this batch's H3K27ac arms, 250 nM in the HA arms of the other batch; VTP 100 nM), one duration, n=1 per arm. A single-concentration comparison does not rank the drug classes.
Evidence that argues against this (1)
- Dose and exposure are not matched between the two agents, so the ordering could reverse at different concentrations; the paper does not present a dose-response for this endpoint. Olsen SN et al. 2022
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
The independent 1912x2 batch reproduces the single-agent ordering (EPZ 0.362, VTP 0.254 at target genes).
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
No combination arm in that batch; different EPZ concentration.
Evidence that argues against this (1)
- The two batches used different EPZ-5676 concentrations (250 nM and 1 uM in different arms), so reproducing an ordering across them is weaker evidence than a matched replicate would be. Olsen SN et al. 2022
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
The authors conclude that combined DOT1L/MENIN inhibition resembles MLL::AF9 degradation whereas single-agent treatment has more modest effects.
MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape · Olsen SN, Godfrey L, Healy JP, Choi YA, Kai Y, Hatton C, Perner F, Haarer EL, Nabet B, Yuan GC, Armstrong SA · Molecular Cell 82(6):1140-1155.e11 2022What this evidence cannot show
Their conclusion; this analysis reproduces it and adds the single-agent ordering and the stratum profile.
Evidence that argues against this (1)
- Resembling a degron on fusion occupancy is not the same as resembling it on cell fate; the paper's own phenotypic data show the degron induces apoptosis as well as differentiation, which single agents largely do not. Olsen SN et al. 2022
reproduces that conclusion at gene resolution and adds the single-agent ordering (menin inhibitor ahead of DOT1L inhibitor, both batches)
- related to →Pinometostat (EPZ-5676) — the DOT1L inhibitor, and the most instructive failure in this field
EPZ-5676 4 d: HA 0.439 at target genes, 0.481 at non-target - nearly uniform across strata
class read-across only: the menin-inhibitor arm here is the tool compound VTP-50469, not a clinical agent