Menin CUT&RUN in an IRX1-high KMT2A::AFF1 blast — the missing track in every public deposit
Nobody has ever looked at where menin, the drug target, sits on the DNA in the half of these infant leukaemias that has switched off HOXA. Until someone does, we cannot say whether the drug has anything to grip.
The same thing, for a scientist
GSE252378 — the richest public oncoprotein-occupancy resource for KMT2A-rearranged leukaemia — contains **no menin track in any KMT2A::AFF1 sample**; its only menin CUT&RUN is in the menin-inhibitor-treated KMT2A::ENL pair [E1]. So the central question raised by this beat is unanswerable on existing public data: **in a blast where the oncoprotein has left HOXA and sits at IRX1, is menin there with it?** Kühn's co-IP says menin stays in the complex when IRX1 binds [E2], but that is HEK293T with a tagged bait and says nothing about genomic location in a patient.
Design
Material. Primary or PDX KMT2A::AFF1 blasts, stratified by IRX1 status. Since GSE252378 has no RNA-seq, stratify by the chromatin proxy this beat validated — KMT2A-N occupancy at HOXA9/HOXA10 versus IRX1 — and confirm by IRX1 and HOXA9 RT-qPCR on the same material. Minimum three IRX1-high and three HOXA-high patients; the anti-correlation measured here (rho -0.714 at n=8) would need roughly this to be re-detected.
Tracks, per sample. Menin (MEN1); KMT2A-N1 and KMT2A-N2 (two antibodies, carried separately — they are not replicates); KMT2A-C1/C2 as the wild-type control that defines an oncoprotein target by the deposit's own N/C ratio; H3K4me3; IgG, deep enough that its promoter zero-rate is below 60% — the IgG libraries in GSE252378 are 57-94% zero at promoters, which makes them nearly useless as a per-locus floor 3.
Primary readout. Menin share at the IRX1 promoter and gene body, versus at HOXA9/HOXA10, versus at MEIS1/CDK6/PAX5 as within-sample positives, each normalised within sample.
Controls that must be pre-declared. MEIS1, CDK6, PAX5 (positive, fusion-occupied in all seven patients measured here at 5.4-40.4x); GAPDH (housekeeping); IgG at each reported locus, not globally; and EGR1 must be excluded — it fails its own IgG floor in this assay 3.
Add a spike-in. GSE252378 has none, which is why every number in this beat is a within-sample share and why no absolute statement about oncoprotein levels could be made or checked. A calibrated spike-in would let the next study say whether menin amount differs between subgroups, which is the question a drug developer actually wants answered.
What each outcome would mean
- Menin at IRX1 with the oncoprotein → the menin interface is doing the same job at a different address; menin inhibition should work in the IRX1 subgroup, and the field needs a pharmacodynamic biomarker that is not HOXA9/MEIS1.
- Menin absent from IRX1 while the oncoprotein is there → a menin-independent oncoprotein address exists in primary human material. That is the strongest possible challenge to the menin-interface hypothesis this project could obtain, and it would predict primary resistance to menin inhibitors in this subgroup.
- Menin present but the oncoprotein absent at IRX1 → IRX1 occupancy in my data is wild-type KMT2A, not the fusion, and this beat's central claim needs re-reading. The KMT2A-C tracks argue against it (C is near zero at IRX1) but they are sparse.
- Menin unmeasurable at IRX1 → report as unmeasured, not as absent, and say what the library depth was.
| design | Menin + KMT2A-N1/N2 + KMT2A-C1/C2 + H3K4me3 + deep IgG CUT&RUN on >=3 IRX1-high and >=3 HOXA-high primary or PDX KMT2A::AFF1 blasts, with a calibrated spike-in |
|---|---|
| readout | menin within-sample share at IRX1 promoter and gene body versus HOXA9/HOXA10, against MEIS1/CDK6/PAX5 positives and a locus-level IgG floor |
| controls | MEIS1, CDK6, PAX5 positive; GAPDH housekeeping; per-locus IgG; EGR1 EXCLUDED as a background hotspot; KMT2A-C as the wild-type discriminator; both N antibodies carried separately |
| cost tier | med |
| timeline | 6-9 months, dominated by identifying and consenting IRX1-high primary material |
| critical dependency | IRX1-high primary or PDX material, for which no established model line exists |
- A negative - menin absent from the oncoprotein's address in the adverse subgroup - would argue against menin inhibitors in exactly the patients who most need something, and the field has no second mechanism ready.
- Stratifying by a chromatin proxy risks defining the subgroup by the measurement rather than the biology, which is the error this beat's own concept entry warns about.
- Can IRX1 status be called from chromatin alone, or does the stratification need matched RNA-seq? This beat used a chromatin proxy and validated it only against PROM1.
- Is there banked KMT2A::AFF1 material anywhere with known IRX1 expression status? That, not the assay, is the rate-limiting step.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
GSE252378 contains no menin CUT&RUN in any KMT2A::AFF1 sample; its menin tracks are confined to the menin-inhibitor-treated KMT2A::ENL pair.
GSE252378 - AutoCUT&RUN profiling of MLL-rearranged leukemia samples (hg38 bigWigs and fragment BEDs) · Janssens DH, Ahmad K, Henikoff S · NCBI GEO 2024What this evidence cannot show
Established by reading !Sample_characteristics_ch1 across all 171 samples in the series matrix. It is an absence in one deposit; a menin ChIP in primary t(4;11) material could exist in another deposit not searched exhaustively here.
Evidence that argues against this (1)
- If such a dataset exists elsewhere the experiment is partly already done and should be re-analysed before being commissioned. Janssens DH et al. 2024
- E2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
IRX1 binds the MLL-AF4 complex without changing bound MEN1, LEDGF or DOT1L.
The IRX1/HOXA connection: insights into a novel t(4;11)-specific cancer mechanism · Kuhn A, Loscher D, Marschalek R · Oncotarget 2016What this evidence cannot show
HEK293T, tagged bait, qualitative Western readout. A co-IP establishes complex membership, not genomic location, and the two can dissociate.
Evidence that argues against this (1)
- A Western read as unchanged could miss a two-fold change in bound menin, which at a stoichiometric interface would be biologically large. Kuhn A et al. 2016
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
IgG libraries in GSE252378 have 57-94% of promoters at zero, and the EGR1 promoter fails its own IgG control with KMT2A-N/IgG ratios of 0.50-3.90.
q145 re-analysis of GSE252378: IRX1 and HOXA oncoprotein occupancy across seven KMT2A::AFF1 patients (analyses/q145-irx1-in-hoxa-negative-infants) · Iqbal Lab oncofusion knowledge graph, beat q145 · internal analysis over deposited GSE252378 bigWigs 2026What this evidence cannot show
Measured on this deposit's promoter set; a different promoter definition would shift the zero-rates. The EGR1 ratio is noisy because the IgG libraries are shallow, but the p247 value below 1 is not rescued by that noise.
Evidence that argues against this (1)
- If the IgG libraries are enriched for open chromatin by a mechanism absent from specific-antibody libraries, these floors are too conservative and some withheld claims are real. Janssens DH et al. 2024
the genomic test of a claim currently resting on a HEK293T co-IP
- tests →IRX1 is a second address for the KMT2A::AFF1 oncoprotein, not merely the gene that turns HOXA off
whether menin accompanies the oncoprotein to IRX1
menin genomic occupancy in the HOXA-negative subgroup - measured nowhere public
decides whether a menin inhibitor has a target to engage in this subgroup
the chromatin composition of the adverse state