Oncofusion

start / graph / absence-q140-the-sem-menin-inhibitor-arm-of-gse159608-carries-only-h3k4me3-and-no-spike-in

Analysisestablished confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.Q140-sem-menin-arm

Bounded absence: in GSE159608's SEM line, VTP-50469 was profiled for H3K4me3 only - no menin, no H3K27ac, no H3K79me2, no RNAP2 and no IgG under the drug - and no library in the series carries a spike-in normalisation, so an absolute change in any mark is unmeasurable here

The dataset that contains the menin inhibitor experiment in infant-leukaemia cells only measured one chemical mark under the drug, and measured nothing that would let anyone tell whether the mark went down everywhere or just moved around. Both limits are worth writing down, because they bound what anybody can conclude from this dataset - including us.

The same thing, for a scientist

Enumerated directly from the 41 SEM sample records of GSE159608. **Under 30 uM VTP-50469, 72 h: H3K4me3 only** (GSM5139713, GSM5139714). Under 30 uM EPZ-5676: H3K4me3 (GSM5139711/12) and H3K27ac (GSM5139707/08). Under DMSO: H3K4me3, H3K27ac, IgG, RNAP2-Ser5P. **Menin (GSM5139719/20), H4K16ac (GSM5139715/16), DOT1L, ENL, KMT2A N- and C-terminal, H3K27me3, H3K36me3, H3K4me1 and H3K9me3 exist in SEM with NO drug arm at all.** Separately, the deposit's stated processing is *'the fraction of counts at each base pair scaled by the size of the reference sequence'* - a compositional, depth-normalised track with no exogenous spike-in, in any of the 419 samples.

Go deeper
The two absences do different work

The missing marks mean the menin-inhibitor experiment in the index fusion's own line has no internal control mark, so the peak-share confound cannot be resolved (see the peak-share entry). A single H3K27ac or IgG library under VTP-50469 would have done it, at no extra cells.

The missing spike-in means no measurement in this deposit can distinguish 'the mark fell everywhere' from 'the mark moved'. This is not a defect of the deposit - genome-scaled normalisation was the field standard - but it is an absolute bound on what can be concluded, and it applies to the depositors' own published claims as much as to ours. 12

The sharpest missing experiment, named

Menin CUT&Tag under VTP-50469 in SEM does not exist in this deposit. The line has excellent menin libraries (GSM5139719/20, 7.6M and 9.0M fragments, and they are each other's nearest neighbour at r=0.749) and a menin-inhibitor arm, and the two were never crossed. The single most direct readout of a menin inhibitor - does menin leave chromatin in the infant-derived index-fusion line - is one library away and absent. 1

How the absence was bounded

By enumeration of every SEM record in the series, not by a search. All 41 titles, antibodies and treatment fields were read and cross-checked against the signal (see the antibody self-sorting entry), so this is a complete census of one deposit rather than a query that could return a false zero. The absence claim is scoped to GSE159608 and says nothing about other deposits. 1

Facts and figures
scopeGSE159608, SEM line, 41 libraries
spike innone in any of the 419 samples
methodcomplete enumeration of the deposit, not a query
absence classnever-measured
absence class basisEnumerated from all 41 SEM sample records: under VTP-50469 only H3K4me3 was assayed, so the other channels were never measured in that arm.
vtp arm
{
  "H3K4me3": [
    "GSM5139713",
    "GSM5139714"
  ]
}
epz arm
{
  "H3K4me3": [
    "GSM5139711",
    "GSM5139712"
  ],
  "H3K27ac": [
    "GSM5139707",
    "GSM5139708"
  ]
}
dmso arm
{
  "H3K4me3": [
    "GSM5139709",
    "GSM5139710"
  ],
  "H3K27ac": [
    "GSM5139705",
    "GSM5139706"
  ],
  "IgG": [
    "GSM5139717",
    "GSM5139718"
  ],
  "RNAP2S5p": [
    "GSM5139722",
    "GSM5139723"
  ]
}
no drug arm at all
[
  "Menin",
  "H4K16ac",
  "KMT2A N-term",
  "KMT2A C-term",
  "DOT1L",
  "ENL",
  "ELL",
  "H3K27me3",
  "H3K36me3",
  "H3K4me1",
  "H3K9me3"
]
How this could bite us back
  • This absence is the reason the menin-interface hypothesis is under-tested where it matters most. Every occupancy dataset that could falsify it in an infant-derived line is either missing the drug arm or missing the control mark.
Still open
  1. Has any group deposited menin CUT&RUN or ChIP under a menin inhibitor in SEM specifically? This project has repeatedly found the menin-inhibitor chromatin literature to be adult-line-derived, and this is the sharpest instance yet.
  2. Would the depositors' raw data allow a retrospective spike-in estimate from carry-over E. coli DNA left by the pA-Tn5? One SEM library is named AutoCUTnRUN_HsEc, which suggests a human/E. coli hybrid reference was used for at least some samples - if so, a spike-in ratio may be recoverable from the alignments even though it was not deposited.
Every source behind this entry (3)
  1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset

    Of 41 SEM libraries in GSE159608, exactly two carry a VTP-50469 treatment field and both are H3K4me3; menin, H4K16ac, KMT2A N/C, DOT1L, ENL, H3K27me3, H3K36me3, H3K4me1 and H3K9me3 in SEM have no drug arm.

    GSE159608: Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia (419 samples, hg19 fragment BEDs) · Janssens DH, Meers MP, Wu SJ, Babaeva E, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S · NCBI Gene Expression Omnibus 2021
    What this evidence cannot show

    Enumerated from the GEO sample records, cached and live, on 2026-09-23. The census covers the SEM line only; other lines and the patient samples in this 419-sample series were not enumerated for this entry.

    Evidence that argues against this (1)
    • An enumeration bounds only this deposit. GSE159608 is one of several Henikoff-lab KMT2A series and a menin-inhibitor arm for another mark could exist in a sibling accession; this entry does not exclude that and a sibling-series sweep would be the way to test it. Janssens DH et al. 2021
  2. E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset

    The deposited tracks are normalized counts scaled by reference sequence size, with no exogenous spike-in reported in the data-processing fields of any sample.

    GSE159608: Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia (419 samples, hg19 fragment BEDs) · Janssens DH, Meers MP, Wu SJ, Babaeva E, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S · NCBI Gene Expression Omnibus 2021
    What this evidence cannot show

    Read from the !Sample_data_processing fields. Absence of a spike-in in the processing description is strong but not absolute evidence that none was used; no spike-in genome appears in the fragment BEDs either, which we checked by counting off-reference contigs while binning.

    Evidence that argues against this (1)
    • One SEM library is named AutoCUTnRUN_HsEc, which implies a human/E. coli hybrid reference for at least part of the series. If E. coli reads were retained upstream, a spike-in ratio may be recoverable from the raw data even though no spike-in normalisation was deposited - which would partly overturn this absence. Janssens DH et al. 2021
  3. E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

    The publication behind this deposit reports the menin-inhibitor sensitivity of gene-body H3K4me3 enrichment, which is the claim these two libraries support.

    Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia · Janssens DH, Meers MP, Wu SJ, Babaeva E, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S · Nature Genetics 53:1586-1596 2021
    PMID 34663924DOI
    What this evidence cannot show

    Read from the abstract; the figure-level detail of which libraries support which panel was not retrieved, so this entry does not assert that the paper used only these two libraries for that claim.

    Evidence that argues against this (2)
    • The publication's claim is about aberrant H3K4me3 enrichment in GENE BODIES in aggregate. This entry's partition is at menin-bound PROMOTERS, which is a different genomic compartment and a different quantity, so the publication supports that the libraries are informative about menin inhibition without supporting the specific contrast measured here.
    • Citing the deposit's own publication to justify the deposit's arms is close to circular: the authors chose which libraries to make because of the claim they intended to support, so the absence of a menin or second-mark arm under VTP is not an oversight this entry has discovered but a scope decision, and framing it as a gap presumes their question was this one.
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