Oncofusion

start / graph / mechanism-q144-a-hundred-fold-between-patient-range-in-oncoprotein-occupancy-constrains-the-menin-interface-to-be-a-permission-not-a-dial

Mechanismmoderate confidence 3 of 5: One strong study, or several smaller consistent ones.Q144-unbounded-magnitude

The menin interface is identical in all 27 of these patients and the amount of chromatin their oncoproteins occupy differs by up to two orders of magnitude - so the interface can be a permission for binding but cannot be what sets how much binding happens

Every one of these fusion proteins has the same menin-binding handle. The amount of DNA they actually sit on differs a hundredfold between children, so the handle cannot be what decides the amount - something else in each child's cells is.

The same thing, for a scientist

**The constraint, stated as a bound.** The menin-binding motifs MBM1 and MBM2 lie in the retained KMT2A N-terminus and are present, intact and identical in **every** KMT2A fusion in this cohort - AFF1, ENL, AFDN, AF10, AF9 and EPS15 alike, since all six break downstream of the menin-binding region. Across those same 27 samples the number of promoters passing the published oncoprotein criterion runs **%d to %d**, with a %sx spread between the 10th and 90th percentiles and a %sx ratio between the largest and smallest non-zero count, and the spread **widens** after depth matching [E1]. **Therefore an invariant interface is compatible with a hundred-fold range in occupancy.** The interface cannot be the quantitative determinant. This is the amount-side twin of the corpus's existing address-side constraint, which was derived from one patient's two disease states: an unchanged interface is compatible with an almost completely changed target set [E2]. **Together the two say the interface sets neither WHERE the fusion goes nor HOW MUCH of it goes there.** **What the interface can still be, and this is not a weakening of the drug rationale.** A necessary permission. Menin inhibition removes a required contact and the fusion leaves chromatin - which this beat's own positive control shows at the extreme, with the post-menin-inhibitor aliquot the only one of 27 calling zero promoters [E3]. A gate that must be open for anything to happen is fully compatible with something else deciding how much happens once it is open. **What would refute this constraint.** A demonstration that the between-patient occupancy range is driven by *menin abundance* rather than by the fusion. Menin concentration varies between cells, and a fusion whose recruitment is menin-limited would show exactly this spread with an invariant interface - the interface would then be the mechanism and menin the dial. **This deposit cannot test that**, because it contains menin CUT&Tag in only one patient's two aliquots [E1]. A menin channel in the other 26 would settle it, and it is the single most valuable missing measurement identified by this beat. **And the alternative that must be excluded first.** Tumour purity. A marrow with few blasts dilutes the fusion signal with normal cells whose N/C ratio is near one, which lowers the call count with no change in the leukaemic cells. **The deposit records no blast percentage**, so the ranking of patients by occupancy is not yet separable from a ranking by purity, and this mechanism entry inherits that uncertainty.

Go deeper
Why the six-partner cohort makes the argument stronger than a single-fusion one

If the spread were measured within one fusion partner, a reader could attribute it to breakpoint position or partner dosage. It spans six partners and four institutions, and the amplitude does not sort by partner (see the companion entry). Whatever sets the amount is therefore shared across partners - which points at the host cell, not at the fusion.

How this could bite us back
  • If the amount of oncoprotein on chromatin is set by the host cell rather than by the fusion, then a menin inhibitor's pharmacodynamic effect size is a patient property, and a trial that reads response as a fixed fall in target-gene expression will misclassify the low-occupancy end of the distribution.
  • A gate-not-dial interface means menin inhibition should be near-binary in effect at the interface itself, so partial responses are more likely to come from incomplete drug exposure or from oncoprotein-independent maintenance of the program than from partial interface blockade.
Still open
  1. Is menin abundance the dial? A menin CUT&Tag channel in more than one patient of this cohort would answer it directly and none exists.
  2. Does blast percentage explain the occupancy ranking? The deposit records none; the submitting institutions will hold it.
Every source behind this entry (3)
  1. E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset

    Across 27 KMT2A-rearranged patient samples carrying six different fusion partners, all of which retain the menin-binding N-terminus, the number of promoters passing the published oncoprotein criterion ranges from 0 to 2282, a 20.01x spread between the 10th and 90th percentiles, widening to 61.10x after depth matching; and the deposit contains a menin channel in only one patient.

    GSE252378 - KMT2A oncoproteins induce epigenetic resistance to targeted therapies (171 GSMs, AutoCUT&RUN / AutoCUT&Tag, hg38 fragment BEDs and bigWigs) · Janssens DH, Henikoff S (Fred Hutchinson Cancer Center / Van Andel Institute) · NCBI Gene Expression Omnibus 2024
    What this evidence cannot show

    Promoters rather than the authors' peak intervals; within-sample shares with no spike-in, so this is a statement about the N-biased fraction of a library rather than about molecules per cell. The claim that all six partners retain MBM1/MBM2 rests on the standard KMT2A breakpoint cluster region lying downstream of the menin-binding domain and was not re-genotyped per patient here.

    Evidence that argues against this (1)
    • Tumour purity is a complete alternative explanation for a between-patient occupancy range and the deposit records no blast percentage. Until purity is controlled, the ranking of patients by oncoprotein occupancy is not established as a ranking of leukaemic-cell biology, and this constraint on the interface weakens accordingly. Janssens DH et al. 2024
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset

    Within one patient, between the B-ALL and its lineage-switched AML, the N/C-defined fusion-target promoter set changes almost completely while the menin-binding motifs are unchanged.

    GSE252378 - KMT2A oncoproteins induce epigenetic resistance to targeted therapies (171 GSMs, AutoCUT&RUN / AutoCUT&Tag, hg38 fragment BEDs and bigWigs) · Janssens DH, Henikoff S (Fred Hutchinson Cancer Center / Van Andel Institute) · NCBI Gene Expression Omnibus 2024
    What this evidence cannot show

    That measurement is this corpus's own prior computation on the same deposit, re-read from the q142 entry rather than recomputed here, and its set-overlap statistic was reported without a chance floor.

    Evidence that argues against this (1)
    • The overlap statistic that argument rests on has a chance floor that was never computed, and this beat measures a floor of about 0.07 on its own universe. The direction of that argument survives because it compares two numbers computed the same way, but its force depends on a comparison the entry did not make. Janssens DH et al. 2024
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In the one patient profiled before and during menin-inhibitor treatment, the treated aliquot is the only sample of 27 calling zero oncoprotein-target promoters, and the paper reports its oncoprotein and menin as reduced to undetectable levels.

    MLL oncoprotein levels influence leukemia lineage identities · Janssens DH, Duran M, Otto DJ, Wu W, Xu Y, Kirkey D, Mullighan CG, Yi JS, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S · Nature Communications 15:9341 2024
    What this evidence cannot show

    One patient, no vehicle arm, and the two aliquots differ in lineage as well as in drug exposure, so the drug effect and the lineage switch are totally confounded.

    Evidence that argues against this (1)
    • Because the treated aliquot is also the lineage-switched one, its zero could be a property of the AML state rather than of the drug. The other lineage-switched pair in the deposit (p279 to p318) was not menin-inhibitor treated and its AML aliquot calls 1,894 promoters, which argues against a pure lineage explanation but does not exclude one, since the two patients carry different fusion partners. Janssens DH et al. 2024
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