Oncofusion

start / graph / absence-q187-no-yeats-inhibitor-has-been-tested-against-sec-l2-or-sec-l3

Analysisstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q187-the-sec-family-and-yeats-selectivity

Four YEATS antagonists exist, four public transcriptome datasets of YEATS inhibition exist, and not one paper or dataset has ever asked what happens to the AFF2- or AFF3-scaffolded complexes — and the analysis needs no wet work

also called no YEATS inhibitor tested on SEC-L2/SEC-L3 · q187 bounded absence

Four different drug-like molecules that block the histone-reading pocket have been published, and their effects on gene activity are freely downloadable. Nobody has checked what they do to the two sister machines that contain the same reader — even though the data to check it are already online.

The same thing, for a scientist

**Bounded absence.** A PubMed search over an 18-string name list covering every published YEATS-pocket antagonist and ENL degrader this project can name — SGC-iMLLT, SR-0813, SR-1114 (PROTAC), TDI-11055, GNE-064 and the inhibitor/inhibitors/inhibition/degrader nominalisations, hyphenated and unhyphenated — intersected with AFF2, AFF3, SEC-L2, SEC-L3, FMR2, LAF4, XIST, imprint* and imprinted returns **0 records for every one of the nine targets**, through a query shape whose positive control returns 14 [E1]. Separately, the entire `SEC-L2` / `SEC-L3` literature is **five records and every one has Luo Z or Lin C on the author list** — the complexes have never been named by an independent group [E2]. **But the absence is `measured-not-analysed`, not `never-measured`, and that is the actionable part.** Four GEO series of pharmacological YEATS inhibition are public: GSE162591/GSE162592 (SR-0813, MV4;11 ChIP-seq and RNA-seq, PMID 34079898) and GSE185091/GSE185093 (TDI-055, MV411 and OCI-AML3 RNA-seq; AFF1, AFF4, Pol II, Pol II S2P, DOT1L, H3K79me2 and PAF1 ChIP-seq in MV4;11 under DMSO versus TDI-055 at 0.5 and 2 h, PMID 36053276) [E3]. **MV4;11 is a KMT2A::AFF1 line and the deposit already contains AFF1 and AFF4 occupancy under a YEATS inhibitor.** What is missing is AFF2 and AFF3 — no antibody, no arm, no intersection with the SEC-L2/SEC-L3 target sets in GSE34097.

Go deeper
The name list, which is what actually bounds this absence

Rules 70-72: a counted absence about a drug class is bounded by the name list, not by the query. The 18 strings tried, each tagged individually as [tiab] (never (A OR B)[tiab], rule 94), run 2026-09-24:

stringrecords alone
"SGC-iMLLT"4
SGCiMLLT4
"SR-0813"2
SR08132
"SR-1114" (ENL PROTAC)1
SR11141
"TDI-11055"3
TDI110552
"GNE-064"1
GNE0641
"TDI-055"0 — dropped by the index
"YEATS inhibitor"0 — dropped
"YEATS inhibitors"5
"YEATS inhibition"0 — dropped
"ENL inhibitor"2
"ENL inhibitors"0 — dropped
"ENL inhibition"0 — dropped
"ENL degrader"3

Union: 18 distinct records. Singular returns 0 and plural returns 5 for the same concept, and hyphenated and unhyphenated forms differ (TDI-11055 3, TDI11055 2) — rule 72 firing twice, exactly as documented.

Where the list came from, because that is what the bound rests on. Thirteen strings were built from the four YEATS-antagonist papers this beat surfaced (PMIDs 30288907, 34079898, 36053276, 36645983). GNE-064 was not among them; it came from reading ana-q159-eleven-abstract-level-absences-retested-against-agent-and-model-names-and-none-was-overturned, which had already assembled a four-name ENL-YEATS agent list in an earlier cycle. Adding it changed no zero, but a name list assembled only from the papers you happened to find is not a bound — the corpus's own prior lists have to be read first.

The OR group audits itself and it must be read back. PubMed silently deletes non-matching quoted phrases from a group; the quotedphrasesnotfound list names the five zero-records strings above, so the group ran as 13 of 18 terms. Every deleted term returns 0 on its own, so no recall was lost — but that had to be checked, not assumed, and the querytranslation is the only place it is visible.

The intersections, and the spike control that makes the zeros readable

Query shape: (<13 surviving name strings, each [tiab]>) AND <target>[tiab].

targetrecords
leukemia — positive control through the identical shape14
AFF20
AFF30
"SEC-L2"0
"SEC-L3"0
FMR20
LAF40
XIST0
imprint*0
"imprinted"0

And the bare-operand controls, so the zeros cannot be blamed on either side: AFF2[tiab] = 126, AFF3[tiab] = 123, YEATS[tiab] = 233, "SEC-L2"[tiab] = 2, "SEC-L3"[tiab] = 5.

Every zero came back with a non-empty querytranslation and outputmessages: ["No items found."], which is the genuine-zero signature; none was an instrument failure. Scope: titles and abstracts only. A supplementary figure showing AFF3 protein unchanged under SGC-iMLLT would be invisible to all of this (rule 80), and no full text was searched for any of the nine targets.

Why this is measured-not-analysed, and exactly what to run

The literature absence is real and the data absence is not. Verified 2026-09-24 through the SOFT brief record and attributed by !Series_pubmed_id, never by topic:

seriescontentsource PMID
GSE162591ENL ChIP-seq, MV4;11, ENL/AF9 YEATS chemical inhibition34079898
GSE162592mRNA-seq, MV4;11, same study34079898
GSE185091RNA-seq, MV411 and OCI-AML3, transcriptional changes induced by TDI-05536053276
GSE185093AFF1, AFF4, Pol II, Pol II S2P, DOT1L, H3K79me2, PAF1 ChIP-seq in MV4;11 under DMSO vs TDI-055 at 0.5 and 2 h; Flag-ENL ChIP-seq in MOLM1336053276

The fourth row is the one that matters. MV4;11 carries KMT2A::AFF1, and somebody has already measured scaffold occupancy under a YEATS inhibitor — for AFF1 and AFF4. The missing arm is AFF2 and AFF3, which nobody has ever ChIPped in any cell.

The analysis that closes most of this, with no wet work:

  1. Take the AFF2-responsive and AFF3-responsive gene sets from GSE34097 (ana-q187-sec-family-target-set-overlap-measured reconstructs their sizes; the identities need the deposit).
  2. Ask whether they move in the GSE185091 / GSE162592 YEATS-inhibitor RNA-seq, against the AFF4-responsive set as the internal comparator and a size-matched, expression-matched random set as the null.
  3. If the sibling sets move as much as the AFF4 set, scaffold-blindness has a measurable transcriptional footprint. If they do not, it does not, and mechanism-q187-target-specificity-is-a-scaffold-property-while-the-reader-is-shared should be downgraded to a composition curiosity.

Two things this cannot settle, which is why the absence is only mostly closable by reanalysis. The gene sets come from HEK293T and the drug data from AML lines, so a null result is confounded with cell type. And nothing in any of these deposits touches imprinting, allele-specific expression or neural tissue, which is where risk-q187-yeats-inhibition-touches-an-imprinting-complex-in-an-infant places the liability.

Bounded rejections — what was found, read and not used
  • PMID 22895430, Luo, Lin and Shilatifard, Nat Rev Mol Cell Biol 2012, The super elongation complex (SEC) family in transcriptional control. On topic, and one of only five records naming SEC-L2 or SEC-L3. Not cited as evidence anywhere in this beat because it is a review by the same authors of the same primary paper, and the brief's quality bar prefers the primary. Recorded so a later cycle knows it was seen and why it was passed over.
  • PMID 39327672, ENL mutation and AML: a new model that reveals oncogenic condensate's function in leukemogenesis, Mol Oncol 2025. Surfaced by the "ENL degrader" string. Not used: it concerns ENL hotspot mutations and condensates, a different axis from complex membership, and this graph already holds the condensate-assay caveats.
  • PMID 36645983, benzimidazole ENL inhibitors, Eur J Med Chem 2023. Surfaced by the name list. Not used: a medicinal-chemistry series with no complex-membership or paralogue content; it would only add a fifth name to the name list, which it now has.
  • "SEC-like 2"[tiab], "SEC-like 3"[tiab] and "super elongation complex-like"[tiab] all return 0 with quotedphrasesnotfound. The spelled-out names are not in the index at all; only the hyphenated abbreviations are. A reader repeating this search must use SEC-L2 and SEC-L3.
Facts and figures
statusrun
absence classmeasured-not-analysed
absence class basisFour GEO series of pharmacological YEATS inhibition are public (GSE162591, GSE162592, GSE185091, GSE185093) and the SEC-family target sets are public (GSE34097). The intersection has never been computed. No wet work is required to close most of this absence; the residue that does require wet work is an AFF2 or AFF3 ChIP under a YEATS inhibitor, for which no antibody arm exists in any deposit.
query shape(<13 surviving name strings, each [tiab]>) AND <target>[tiab]
querytranslation example("SGC-iMLLT"[Title/Abstract] OR "SGCiMLLT"[Title/Abstract] OR "SR-0813"[Title/Abstract] OR "SR0813"[Title/Abstract] OR "SR-1114"[Title/Abstract] OR "SR1114"[Title/Abstract] OR "TDI-11055"[Title/Abstract] OR "TDI11055"[Title/Abstract] OR "YEATS inhibitors"[Title/Abstract] OR "ENL inhibitor"[Title/Abstract] OR "ENL degrader"[Title/Abstract]) AND "leukemia"[Title/Abstract]
date2026-09-24
toolPubMed E-utilities esearch via scripts/pubmed_safe.py; NCBI GEO acc.cgi SOFT brief records
name list provenanceBuilt from the four YEATS-antagonist papers surfaced by YEATS[tiab] and ENL[tiab] searches (PMIDs 30288907, 34079898, 36053276, 36645983), then EXTENDED with GNE-064 after reading ana-q159-eleven-abstract-level-absences-retested-against-agent-and-model-names-and-none-was-overturned, which had already assembled a four-name ENL-YEATS agent list this beat did not have. Adding GNE-064 (1 record alone) changed no zero. Rule 88's corollary: check what the corpus already knows before reporting a name list as complete.
bare operand controls
"SEC-L2"[tiab]2.000"SEC-L2"[tiab]: 2"SEC-L3"[tiab]5.000"SEC-L3"[tiab]: 5AFF3[tiab]123.0AFF3[tiab]: 123AFF2[tiab]126.0AFF2[tiab]: 126YEATS[tiab]233.0YEATS[tiab]: 233
name list tried
[
  "SGC-iMLLT",
  "SGCiMLLT",
  "SR-0813",
  "SR0813",
  "SR-1114",
  "SR1114",
  "TDI-11055",
  "TDI11055",
  "GNE-064",
  "GNE064",
  "TDI-055",
  "YEATS inhibitor",
  "YEATS inhibitors",
  "YEATS inhibition",
  "ENL inhibitor",
  "ENL inhibitors",
  "ENL inhibition",
  "ENL degrader"
]
name list terms dropped by the index
[
  "TDI-055",
  "YEATS inhibitor",
  "YEATS inhibition",
  "ENL inhibitors",
  "ENL inhibition"
]
positive control
{
  "target": "leukemia",
  "records": 14,
  "shape": "identical to every zero-returning query in this entry"
}
bare operand controls — the numbers behind the chart
{
  "AFF2[tiab]": 126,
  "AFF3[tiab]": 123,
  "YEATS[tiab]": 233,
  "\"SEC-L2\"[tiab]": 2,
  "\"SEC-L3\"[tiab]": 5
}
geo series available
[
  {
    "accession": "GSE162591",
    "content": "ENL ChIP-seq, MV4;11, ENL/AF9 YEATS chemical inhibition",
    "series_pubmed_id": "34079898"
  },
  {
    "accession": "GSE162592",
    "content": "mRNA-seq, MV4;11, same study",
    "series_pubmed_id": "34079898"
  },
  {
    "accession": "GSE185091",
    "content": "RNA-seq, MV411 and OCI-AML3, transcriptional changes induced by TDI-055",
    "series_pubmed_id": "36053276"
  },
  {
    "accession": "GSE185093",
    "content": "AFF1, AFF4, Pol II, Pol II S2P, DOT1L, H3K79me2, PAF1 ChIP-seq in MV4;11 under DMSO vs TDI-055 at 0.5 or 2 h; Flag-ENL ChIP-seq in MOLM13",
    "series_pubmed_id": "36053276"
  }
]
measurements
[
  {
    "quantity": "records_linking_a_named_yeats_antagonist_to_a_sibling_sec_complex",
    "subject": "11-term YEATS-antagonist OR group [tiab] INTERSECT each of AFF2, AFF3, SEC-L2, SEC-L3, FMR2, LAF4, XIST, imprint*, imprinted",
    "value": 0,
    "units": "records",
    "n": 9,
    "universe": "PubMed titles and abstracts, all years, run 2026-09-24; 13-term name list including GNE-064; identical query shape returns 14 for 'leukemia'; bare operands AFF2 126, AFF3 123, YEATS 233",
    "null": null,
    "note": "0 for all nine targets. Genuine zeros: every response carried a non-empty querytranslation and outputmessages 'No items found.'"
  },
  {
    "quantity": "sec_l2_and_sec_l3_records_with_an_independent_last_author",
    "subject": "union of \"SEC-L2\"[tiab] and \"SEC-L3\"[tiab], author-checked",
    "value": 0,
    "units": "records of 5",
    "n": 5,
    "universe": "PubMed titles and abstracts, 2026-09-24; the five are PMIDs 22547686, 22895430, 26728555, 28180295, 30535390",
    "null": null,
    "note": "Luo Z or Lin C is an author on all five. Bounds adoption of the NAMES, not study of the objects — the nomenclature is the originating laboratory's own coinage."
  }
]
How this could bite us back
  • This entry's headline zero is easy to over-read as 'nobody has looked at YEATS inhibition at all'. The opposite is true: the class is well developed, has an on-target resistance mutation, works in PDX models and has an in vivo therapeutic window in the index fusion. What is absent is one specific comparison, and stating the absence loudly should not be allowed to imply the field is empty.
  • Closing this absence by reanalysis can only produce an interpretable POSITIVE. The sibling target sets are HEK293T and the drug data are AML, so a null intersection is confounded with cell type and must not be published as 'YEATS inhibition spares SEC-L2 and SEC-L3'. Pre-register that asymmetry before running it.
  • This graph already contains both halves of a contradiction about resistance to this class. `mechanism-rate-limiting-steps-and-compensation` records the TDI-11055 CRISPR-Cas9 resistance screen and praises it as good practice; `drug-sgc-imllt` says in data.resistance that no resistance selection has been reported for any YEATS antagonist. A reader who opens the drug entry gets the wrong answer. Reported here, not edited, with the settling citation: PMID 36053276, DOI 10.1158/2159-8290.CD-21-1307, abstract read 2026-09-24.
Still open
  1. Do the AFF2- and AFF3-responsive gene sets move under SR-0813 or TDI-055? GSE34097 supplies the sets, GSE162592 and GSE185091 supply the response, and the comparison has never been made. This is the single cheapest experiment in this beat and it needs no cells.
  2. Does AFF1 or AFF4 chromatin occupancy change under TDI-055 in MV4;11? GSE185093 already contains that measurement and this beat did not download it. If scaffold occupancy is unaffected while Pol II falls, the reader is an anchoring device and not a scaffold-retention device, which is the cleanest possible confirmation of the two-surface model.
  3. Is there an AFF2 or AFF3 antibody that works for ChIP in a human leukaemia line? Every experiment that would close the rest of this absence needs one, and the defining purification used Flag-tagged over-expressed bait rather than endogenous ChIP for both scaffolds.
  4. Has any YEATS antagonist been profiled for allele-specific expression or imprinting effects in any tissue? The three imprinting-related zeros above bound almost nothing, because no AML pharmacology paper would report it. The bound that would mean something is a query in an epigenetics archive, and it has not been run.
Every source behind this entry (4)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    A PubMed query joining an 18-string name list of published YEATS-pocket antagonists and ENL degraders (SGC-iMLLT, SGCiMLLT, SR-0813, SR0813, SR-1114, SR1114, TDI-11055, TDI11055, GNE-064, GNE064, TDI-055, YEATS inhibitor/inhibitors/inhibition, ENL inhibitor/inhibitors/inhibition, ENL degrader; each tagged [tiab] individually) to each of AFF2, AFF3, SEC-L2, SEC-L3, FMR2, LAF4, XIST, imprint* and imprinted returns zero records for all nine, run 2026-09-24, while the identical query shape with 'leukemia' returns 14 and the bare operands return AFF2 126, AFF3 123, YEATS 233.

    What this evidence cannot show

    TITLES AND ABSTRACTS ONLY. A measurement of AFF2 or AFF3 in a supplementary figure of any of the 18 name-list records would be invisible to this and no full text was searched. The OR group ran as 13 of 18 terms — PubMed's `quotedphrasesnotfound` names the five dropped ("TDI-055", "YEATS inhibitor", "YEATS inhibition", "ENL inhibitors", "ENL inhibition"), each of which returns 0 on its own, so no recall was lost, but the group is smaller than the list. GNE-064 was added only after reading an existing corpus entry that already carried it, which means a compound published under a code neither this beat nor that entry knows about would still be missed; the list was never built from a chemistry database.

    Evidence that argues against this (1)
    • The zeros for XIST, imprint* and imprinted are the least informative in the table and should not be quoted as though they were the same kind of finding as the AFF2/AFF3 zeros. No medicinal-chemistry or AML-pharmacology paper would be expected to mention imprinting whatever the biology, so those three zeros are close to guaranteed by publication convention and bound almost nothing. The AFF2 and AFF3 zeros are the informative ones, because a paralogue-selectivity panel is exactly the sort of thing a probe paper does report — and SGC-iMLLT's own paper does report selectivity, over YEATS2, YEATS4 and bromodomains, and not over complex membership. Moustakim M et al. 2018
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    The complete PubMed literature naming SEC-L2 or SEC-L3 in a title or abstract is five records — PMIDs 22547686, 22895430, 26728555, 28180295 and 30535390 — and Luo Z or Lin C is an author on every one of them, so no group independent of the originating laboratory has ever named either complex.

    What this evidence cannot show

    This bounds who has used the NAMES, not who has studied the objects. A paper reporting an AFF2 or AFF3 complex without adopting the SEC-L2/SEC-L3 nomenclature is invisible here — and the nomenclature is this laboratory's own coinage, so non-adoption is the expected behaviour of an independent group rather than evidence of neglect. The spelled-out forms 'SEC-like 2' and 'SEC-like 3' are not in the index at all (0 records, quotedphrasesnotfound), so the abbreviations are the only reachable strings. Titles and abstracts only.

    Evidence that argues against this (1)
    • Lu and colleagues did characterise the SEC family independently, by tandem affinity purification, and argued explicitly for combinatorial composition — but their antibody panel is AFF1, AFF4, ELL1, ELL2, ENL, AF9, CycT1 and CDK9, with no AFF2 and no AFF3, so they neither adopted nor tested the nomenclature. Their paper is the closest thing to independent work on this family and it is silent on precisely the two members this beat is about, which means the single-laboratory dependence is real but is a coverage gap rather than a credibility problem. Lu H et al. 2015
  3. E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset

    Four GEO series of pharmacological YEATS inhibition are public and were verified by SOFT brief record on 2026-09-24: GSE162591 (ENL ChIP-seq, MV4;11) and GSE162592 (mRNA-seq, MV4;11), both recording !Series_pubmed_id 34079898; and GSE185091 (RNA-seq, MV411 and OCI-AML3, transcriptional changes induced by TDI-055) and GSE185093 (AFF1, AFF4, Pol II, Pol II S2P, DOT1L, H3K79me2 and PAF1 ChIP-seq in MV4;11 under DMSO versus TDI-055 at 0.5 or 2 h, plus Flag-ENL ChIP-seq in MOLM13), both recording !Series_pubmed_id 36053276.

    What this evidence cannot show

    Verified by `acc.cgi?acc=<GSE>&targ=self&form=text&view=brief` for each of the four series, reading !Series_title, !Series_status and !Series_pubmed_id; attribution is by the deposit's own PMID field and not by topic match. `expected_absent_terms` records the load-bearing negative: AFF2 and AFF3 appear in none of the four overall-design strings. This beat did NOT download any of the four, enumerate their samples, or check whether processed differential-expression tables are among the supplementary files — so 'the reanalysis is cheap' is an inference, not a verified fact. GEO keyword search is also unreliable here: `SGC-iMLLT` in db=gds translated to bare `SGC[All Fields]` and returned 4,516, which is noise; only the accession-level SOFT reads in this item are trustworthy.

    Evidence that argues against this (1)
    • These are AML datasets — MV4;11, MOLM13, OCI-AML3 — and the SEC-family target sets they would be intersected with come from HEK293T. A null result in that intersection is fully confounded with cell type, so the proposed reanalysis can produce a positive finding but cannot produce a clean negative. That asymmetry has to be pre-registered before anyone runs it, or a comfortable zero will be read as an answer. Luo Z et al. 2012
  4. E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

    Pharmacological YEATS-pocket occupancy is a validated, on-target intervention with in vivo activity: SR-0813 is a potent selective ENL/AF9 YEATS inhibitor (IC50 25 nM) and ENL YEATS inhibition alone is sufficient to selectively suppress ENL target genes including HOXA9/10, MYB and MYC; TDI-11055 displaces ENL from chromatin by blocking the YEATS-acylated-histone interaction, a CRISPR-Cas9 mutagenesis screen recovered an ENL mutation conferring resistance to it (validating on-target activity), and it blocks disease progression in cell-line and patient-derived xenograft models of MLL-rearranged and NPM1-mutated AML.

    Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia. · Liu Y, Li Q, Alikarami F, Barrett DR, Mahdavi L, Li H, Tang S, Khan TA, Michino M, Hill C, Song L, Yang L, Li Y, Pokharel SP, Stamford AW, Liverton N, Renzetti LM, Taylor S, Watt GF, Ladduwahetty T, Kargman S, Meinke PT, Foley MA, Shi J, Li H, Carroll M, Chen CW, Gardini A, Maillard I, Huggins DJ, Bernt KM, Wan L · Cancer Discovery 2022
    What this evidence cannot show

    This item combines two papers' abstracts: the SR-0813 / SR-1114 claims are from PMID 34079898 (Garnar-Wortzel et al., ACS Cent Sci 2021, DOI 10.1021/acscentsci.0c01550) and the TDI-11055 claims from the cited PMID 36053276. Both are AML — MLL-rearranged and NPM1-mutated — and neither is infant B-lineage KMT2A::AFF1. Neither abstract mentions AFF2, AFF3, SEC-L2 or SEC-L3, which is the point of the `expected_absent_terms` above. Abstracts only; neither full text was read by this beat.

    Evidence that argues against this (1)
    • The resistance mutation recovered against TDI-11055 is the strongest available argument that pocket occupancy is on-target - and it is equally an argument that resistance to this class is one point mutation away. Note a live internal contradiction rather than a gap: `mechanism-rate-limiting-steps-and-compensation` already records this screen and calls it 'pre-announcing the escape route', while `drug-sgc-imllt` states in data.resistance that 'no resistance selection has been reported for any YEATS antagonist'. Both are in this graph, they cannot both be right, and the second is the one that is wrong. Reported, not edited - the entry belongs to beat q159. Garnar-Wortzel L et al. 2021
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