An occupancy readout returned background in every channel of the only drug-exposed patient sample it has been tried in - so a negative from such an assay cannot currently be told apart from an assay failure
If doctors ever want to check whether a menin-blocking drug is working by looking at where menin sits on a patient's DNA, they should know that the one time this was tried, the test came back blank for everything it measured - including the things that should have shown up.
The same thing, for a scientist
In the revumenib-exposed relapse aliquot, menin, the KMT2A N-terminus, the KMT2A C-terminus, ENL and DOT1L are **all** at or below an out-of-sample non-specific reference (0.31x to 0.98x), the top-ranked promoters are mitochondrial pseudogenes, and the three CUT&Tag channels agree with their own replicates at Spearman 0.11-0.25. A pharmacodynamic assay must be able to return a positive in the treated state for its negatives to mean anything. **Here every channel is negative, including the wild-type KMT2A channel, which the drug is not expected to eliminate, and ENL, which the paper's own conclusion says persists.** That pattern - everything negative including the internal positives - is the signature of an assay that has stopped reporting, and it is indistinguishable from complete target clearance using the data available.
The internal positives that should not have gone negative
- KMT2A-C reports wild-type KMT2A, which a menin inhibitor displaces from menin but does not remove from the cell. It reads 0.31x of the non-specific reference.
- ENL is the channel the paper concludes persists. It reads 0.80x.
- DOT1L reads 0.98x, the closest to the reference and the only channel that could be called unchanged.
A treated sample in which the negative control channel and the expected-positive channel are indistinguishable does not support a conclusion in either direction.
What would have to change for an occupancy endpoint to be usable
- An in-sample IgG arm. Without it there is no floor, and a floor is what makes 'background' a measurement rather than an impression.
- A spike-in. Without it a uniform loss and no change are the same number.
- A channel that is not expected to move - a housekeeping-promoter mark such as H3K4me3 - run in the same tubes, to demonstrate the assay still works in the treated state.
- Replicate agreement reported as a release criterion. A pharmacodynamic sample whose replicates agree at 0.25 should not be reported.
The alternative endpoint, which already exists
The phase 1 trial's own pharmacodynamic correlate of remission was reduced oncoprotein-target gene expression, not occupancy. That endpoint is measured on RNA, needs no antibody, needs no background arm, and worked. The companion concept entry gives the mechanistic reason to prefer it: menin displacement is not diagnostic of interface engagement, since a DOT1L inhibitor produces the same menin displacement without touching menin.
| kind | delivery |
|---|---|
| severity | moderate - this is a measurement risk, not a patient-safety risk |
| what went wrong | in the only drug-exposed patient sample with an occupancy readout, all five channels returned background, including the internal positives |
| alternative endpoint | oncoprotein-target gene expression, the phase 1 pharmacodynamic correlate |
affects
[ "drug-revumenib" ]
channel values vs nonspecific reference — the numbers behind the chart
{
"MENIN": 0.42,
"KMT2A_N": 0.33,
"KMT2A_C": 0.31,
"ENL": 0.8,
"DOT1L": 0.98
}replicate agreement in that sample — the numbers behind the chart
{
"MENIN": 0.246,
"ENL": 0.247,
"DOT1L": 0.11
}mitigation
[ "in-sample IgG arm", "defined spike-in", "an unchanging control channel such as H3K4me3 in the same tubes", "replicate agreement as a release criterion", "prefer the RNA target-gene endpoint that already correlated with remission" ]
- An occupancy assay that returns background in the treated state will be read as 'the drug worked completely', which overstates target clearance and argues against combination therapy.
- Conversely, a clinician who learns that the assay failed may discount a genuine complete clearance. The fix is an internal positive channel, not a better interpretation.
- This patient relapsed on revumenib with the fusion transcript still expressed. Whatever the assay said, the disease escaped - which is the outcome any pharmacodynamic endpoint has to be able to predict, and an occupancy endpoint returning background in every channel cannot.
- Has any menin-inhibitor trial collected on-treatment chromatin occupancy, as opposed to expression? None was found in this beat.
- Would an H3K4me3 channel in the same treated tubes have demonstrated the assay still worked? None exists for this pair, though H3K4me3 exists elsewhere in the deposit.
- What blast fraction would be needed for an occupancy assay to resolve fusion sites in a post-therapy marrow? Nobody has stated a threshold.
- E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
Every measured channel in the revumenib-exposed sample, including the wild-type-reporting C-terminal channel and the channel the paper says persists, is at or below an out-of-sample non-specific reference.
analyses/menin-under-revumenib-in-an-infant-patient-pair - pre-registered re-analysis of GSE252378 samples 148752 and 152985 · Q143-menin-under-drug-in-infants (Oncofusion Knowledge Graph) · this repository 2026What this evidence cannot show
n = 1 aliquot; the reference is an IgG from a different patient with a different fusion, CUT&RUN only, so it is not a background control for the CUT&Tag channels at all. This is the strongest available statement and it is not a strong one.
Evidence that argues against this (1)
- A relapse sample after therapy may contain a large fraction of non-leukaemic cells, in which case every fusion-driven channel is diluted and the assay is reporting sample composition rather than assay failure. Blast fraction is not recorded. Janssens DH et al. 2024
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
The phase 1 trial's pharmacodynamic correlate of clinical response was reduced oncoprotein-target gene expression, an RNA endpoint rather than an occupancy endpoint.
The menin inhibitor revumenib in KMT2A-rearranged or NPM1-mutant leukaemia · Issa GC, Aldoss I, DiPersio J, Cuglievan B, Stone R, Arellano M, Thirman MJ, Patel MR, Dickens DS, Shenoy S, Shukla N, Kantarjian H, Armstrong SA, Perner F, Perry JA, Rosen G, Bagley RG, Meyers ML, Ordentlich P, Gu Y, Kumar V, Smith S, McGeehan GM, Stein EM · Nature 615:920-924 2023What this evidence cannot show
An observed correlation in a dose-escalation trial, not a validated surrogate; it establishes that an RNA endpoint was usable, not that it is sufficient.
Evidence that argues against this (1)
- MEN1 pocket mutations confer clinical resistance while leaving the drug in the body, so an RNA endpoint will read 'no response' without distinguishing inadequate exposure from target-site mutation - which an occupancy or a genotyping assay could. Perner F et al. 2023
- E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
A DOT1L inhibitor removes menin from fusion-occupied promoters about as effectively as destroying the fusion does, so menin displacement is not specific to menin-pocket engagement.
A Menin-MLL Inhibitor Induces Specific Chromatin Changes and Eradicates Disease in Models of MLL-Rearranged Leukemia · Krivtsov AV, Evans K, Gadrey JY, Eschle BK, Hatton C, Uckelmann HJ, Ross KN, Perner F, Olsen SN, Pritchard T, McDermott L, Jones CD, Jing D, Braytee A, Chacon D, Earley E, McKeever BM, Claremon D, Gifford AJ, Lee HJ, Teicher BA, Pimanda JE, Beck D, Perry JA, Smith MA, McGeehan GM, Lock RB, Armstrong SA · Cancer Cell 36:660-673.e11 2019What this evidence cannot show
Measured in a KMT2A::MLLT3 degron system by a previous cycle of this project, not in a patient and not in the index fusion.
Evidence that argues against this (1)
- That measurement was made in a KMT2A::MLLT3 degron cell line, so its transfer to a clinical decision about a patient assay is an analogy across fusion, species-of-system and scale, and the magnitude should not be carried across even though the direction probably does. Olsen SN et al. 2022
the drug whose pharmacodynamic readout is at issue
the measurement this risk is drawn from
menin displacement is not diagnostic of interface engagement
an unrecorded exposure compounds an uninterpretable readout
the mechanism entry this risk follows from
menin occupancy as an endpoint