Oncofusion

start / graph / mechanism-q125-what-fills-the-fusions-vacated-sites-is-polycomb-and-what-leaves-with-it-is-h3k4me3

Mechanismmoderate confidence 3 of 5: One strong study, or several smaller consistent ones.Q125-the-h2ak119ub-arm-of-the-pcgf1-knockout

The chromatin exchange at a menin-inhibited fusion site, measured in one experiment: H2AK119ub and H3K27me3 in, H3K4me3 out, in proportion to how much fusion left - and PCGF1 loss attenuates the in-fill without abolishing it

also called the eviction exchange · polycomb in, H3K4me3 out · the graded handoff at a menin-inhibited site

When the drug removes the fusion protein from a stretch of DNA, that stretch does not just go quiet by default - it is actively taken over by the cell's silencing machinery, and the 'active' chemical tag is removed at the same time. How much of each happens depends on how much fusion was removed.

The same thing, for a scientist

**A single deposited experiment measures all four channels in the same cells at the same time**, which is why this is stated as one mechanism rather than four observations. Murine MLL-AF9, 500 nM VTP-50469 48 h against DMSO 72 h, at the fusion's own top-0.1% occupancy set stratified into four quartiles by how much FLAG signal the drug removed [E1]: | at the MOST-evicted quartile | control genotype | PCGF1-KO | |---|---:|---:| | fusion (FLAG), median VTP/DMSO share ratio | **0.0569** (Q117) | not deposited | | RING1B occupancy | **1.3808** (Q117) | not deposited | | **H2AK119ub** | **1.4450** / **1.0151** (two conventions) | 1.1325 / 0.8842 | | **H3K27me3** | **2.0007** | 1.0134 | | **H3K4me3** | **0.9491** | 0.7852 | **The ordering is the mechanism.** Q117 established that RING1B occupancy rises where the fusion falls and is flat elsewhere; this beat establishes that **the mark RING1B deposits rises there too, more cleanly than RING1B itself did (Spearman +1.000 against +0.400)**, that PRC2's mark follows it, and that H3K4me3 is removed in the same places. **All four channels are graded by the same variable - the depth of fusion eviction - and none of them is graded in a baseline-matched null** [E1] [E2]. **PCGF1 is a rate-limiting but not necessary component of the in-fill.** Losing it reduces the H2AK119ub gain by 0.31 and 0.13 in two conventions and the H3K27me3 gain by 0.99, and the knockout's residual gain is still eviction-graded. That is the expected shape when the ligase RING1A/B is shared with canonical PRC1 and PCGF1 is one of six paralogs [E1].

Go deeper
What is NOT established, in the order a reader will assume it
  • Not transcription. 'Silenced' here means two repressive marks up and one active mark down. No RNA measurement from these cells has been located, so whether these bins stop being transcribed is unmeasured in this experiment.
  • Not causality or order. Everything is one timepoint. H3K4me3 loss could precede, follow or be independent of polycomb gain, and the H3K27me3 gain could be PRC2 responding to H2AK119ub via JARID2/AEBP2 or an independent event.
  • Not abundance. Every number is a within-sample share and is blind to uniform change, so 'gain' means 'a larger share of this mark sits at these bins', not 'there is more of this mark'.
  • Not the index fusion. This is murine MLL-AF9 (KMT2A::MLLT3), a myeloid model. This graph exists for infant B-lineage KMT2A::AFF1, and no equivalent measurement in a human KMT2A::AFF1 line has been identified in any series.
  • Not an endogenous fusion. S_FLAG is defined by a FLAG ChIP of a retrovirally over-expressed tagged MLLAF9 construct.
Facts and figures
systemmurine MLL-AF9 (KMT2A::MLLT3), cell line MLLAF9, myeloid, blood, Mus musculus taxid 10090
shown for fusionmurine MLL-AF9 (KMT2A::MLLT3) with a retrovirally over-expressed FLAG-tagged construct; NOTHING in KMT2A::AFF1 or in any B-lineage model, and no human line at all
epigenetic readoutH2AK119ub, H3K27me3 and H3K4me3 share ratios at 2 kb resolution, stratified by fusion-eviction depth
absence classmeasured-not-analysed
absence class noteEvery channel in this mechanism was deposited in GSE260742 and public from 2025-11-23; the fusion and RING1B halves were analysed by Q117 in cycle 68 and the three histone marks by this beat. What is NEVER-MEASURED for this mechanism is the transcriptional consequence in these cells, the time ordering of the four events, and any equivalent in a human KMT2A::AFF1 line.
absence class assigned2026-09-23 (Q125)
steps
[
  "VTP-50469 disrupts the menin-KMT2A interface and the tagged fusion's share at its own top bins falls, most steeply in the quartile Q117 defines as Q1 (median FLAG VTP/DMSO share ratio 0.0569)",
  "RING1B occupancy rises 1.3808-fold at those same bins and is flat or falling elsewhere (Q117); KDM2B is already there in DMSO and does not move",
  "H2AK119ub, RING1A/B's product, rises there - 1.4450 and 1.0151 in two conventions, Spearman +1.000 against eviction depth (this beat)",
  "H3K27me3 rises there, 2.0007, Spearman +1.000 - consistent with PRC2 recruitment downstream of H2AK119ub via JARID2/AEBP2, though nothing here tests that route",
  "H3K4me3 falls there, 0.9491, Spearman -1.000 - the active mark leaves the same bins the repressive marks occupy",
  "Losing PCGF1 attenuates the H2AK119ub and H3K27me3 gains without abolishing either; the knockout's residual gain is still eviction-graded"
]
How this could bite us back
  • Every step after eviction is a step a resistant cell can lose while still looking drug-engaged on a fusion-occupancy assay: PCGF1, BCOR, BCORL1, KDM2B, RING1B and the PRC2 arm are all candidate resistance nodes, and BCOR and BCORL1 loss are recurrent in myeloid leukaemia.
  • If the therapeutic effect needs polycomb deposition, then the depth of eviction matters less than the capacity to fill in, and a more potent menin inhibitor may not be a better one in a polycomb-deficient cell.
  • H3K4me3 loss at the vacated sites is also a loss at sites where wild-type KMT2A works, so the same exchange is a plausible route to on-target toxicity in normal haematopoiesis.
Still open
  1. Does the exchange happen in human KMT2A::AFF1? Nothing in this mechanism has been shown outside murine MLL-AF9, and the corpus's recurring finding is that its evidence is partner-imported.
  2. What is the time order? A single timepoint cannot separate 'polycomb fills the gap' from 'H3K4me3 is removed and polycomb follows'. GSE260742 deposits an H2AK119ub and H3K27me3 timecourse (GSM8123441-446, 8 h and 24 h only) which this beat deliberately did not touch.
  3. Is the residual in-fill in the PCGF1 knockout canonical PRC1? A PCGF2 or PCGF4 ChIP would say and none is deposited.
Every source behind this entry (2)
  1. E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset

    In one deposited experiment (GSE260742, murine MLL-AF9), at the most-evicted quartile of the fusion's own top-0.1% set under 500 nM VTP-50469 48 h, H2AK119ub rises to 1.4450 and 1.0151 in two replicate conventions and H3K27me3 to 2.0007 while H3K4me3 falls to 0.9491, all monotone in eviction depth; in the isogenic PCGF1-knockout the same quantities are 1.1325 / 0.8842, 1.0134 and 0.7852.

    What this evidence cannot show

    NO SPIKE-IN NORMALISATION IS POSSIBLE. Q117 verified zero hits for the entire spike-in vocabulary across all 419,824 characters of GSE260742's 158 sample records and no scale factor is deposited, so every cross-condition number here is a WITHIN-SAMPLE SHARE, which cancels the unknown per-sample scale factor exactly and IS BLIND TO A UNIFORM CHANGE BY CONSTRUCTION. Nothing here measures any mark's abundance; everything measures its distribution. EXPOSURE ASYMMETRY: DMSO 72 h and SGC0946 5 uM 72 h are matched, VTP-50469 500 nM is 48 h, so every VTP ratio is a LOWER BOUND on the 72-hour effect - identical in both genotypes, so the genotype DIFFERENCE is unaffected. REAGENTS: H2AK119ub is Ubiquityl-Histone H2A (Lys119) (D27C4) XP Rabbit mAb, NEB 8240S, and it CANNOT distinguish PRC1.1 from canonical PRC1 - RING1A/B is the ligase in both and PCGF1 is one of six PCGF paralogs - nor deposition from loss of a deubiquitinase. The H3K27me3 and H3K4me3 reagents are NOT RESOLVED and are recorded unresolved rather than guessed; `antibod` occurs zero times in the 158 GEO records. S_FLAG is defined by DYKDDDDK Tag (D6W5B) Rabbit mAb, NEB 14793S, on a RETROVIRALLY OVER-EXPRESSED tagged MLLAF9 construct, so it is the over-expressed molecule's sites and not an endogenous fusion's. THE KNOCKOUT is one CRISPR guide, one clone C1, no second clone, no rescue and NO deposited PCGF1 protein or transcript measurement. SYSTEM: murine MLL-AF9 (KMT2A::MLLT3) myeloid blood cells, NOT the infant B-lineage KMT2A::AFF1 disease this graph is about. One timepoint, so no order and no causality. n = 1 per condition per convention; H3K27me3 and H3K4me3 have one convention and no spread. The quartile stratification is Q117's own DEVIATION 3 and the genotype difference at a quartile is a POST HOC application of this beat's thresholds.

    Evidence that argues against this (1)
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset

    Q117 established in the same series and the same murine culture that RING1B occupancy rises 1.3808-fold at the most-evicted quartile against 0.8708, 0.8070 and 0.8792 elsewhere, and that BCOR rises 1.4433 against 1.2701-1.3304, while KDM2B is already present and does not move (1.087 against 0.9859-1.0067) - so the PRC1.1 machinery is pre-positioned and its catalytic subunit is recruited where the fusion leaves.

    What this evidence cannot show

    Read from a committed results.json in this repository rather than re-measured. Q117's own quartile analysis is recorded there as its DEVIATION 3, i.e. post hoc in that beat. RING1B, BCOR and KDM2B are occupancy ChIPs of proteins, not measurements of any mark; the Spearman of Q117's RING1B series against eviction depth is 0.400, materially weaker than the +1.000 this beat measures for the mark.

    Evidence that argues against this (1)
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