Oncofusion

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Analysisstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q29-mllt3-yeats-loss

Every human t(9;11) cell line, with every accession fetched and read back: eleven lines, ten patients, and two of them are B-ALL

also called MLL-AF9 cell lines · KMT2A-MLLT3 cell line panel

Eleven human cell lines carry this translocation, but two of them come from the same man, so there are ten patients. Nine are monocytic leukaemias and two are infant B-cell leukaemias that almost nobody uses.

The same thing, for a scientist

Cellosaurus was swept on 2026-09-20 for `KMT2A-MLLT3`, `MLL-AF9` and `MLL-MLLT3`, restricted to human parent lines (no `HI` hierarchy line) whose record carries the structured fusion comment `KMT2A + HGNC; HGNC:7136; MLLT3`, and every accession was then re-fetched individually with the primary name read back - because a prior cycle of this project recorded NOMO-1 from memory as CVCL_1274, which resolves to an endometrial adenocarcinoma [E1]. **Eleven human parent lines carry the fusion as a patient lesion: THP-1 (CVCL_0006), MOLM-13 (CVCL_2119), MOLM-14 (CVCL_7916), NOMO-1 (CVCL_1609), Mono-Mac-6 (CVCL_1426), IMS-M1 (CVCL_A623), UG3 (CVCL_5382), YBT-5 (CVCL_YJ20), YCU-AML2 (CVCL_E7AL), KOPB-26 (CVCL_7972) and YACL95 (CVCL_D4A3)** [E1]. MOLM-13 and MOLM-14 are one individual (Cellosaurus OI cross-reference, and both from the same founding report) [E1][E2], so the panel is **ten patients**. Ages span **under 1 year to 64 years**; nine records are monocytic or myeloid and **two - KOPB-26 (female, 1 year 1 month) and YACL95 (sex unspecified, under 1 year) - are childhood B-ALL** [E1]. Only one line in the panel carries a published residue-level fusion structure: **YCU-AML2, KMT2A intron 8 fused to MLLT3 intron 4** [E3]. One correction is owed outside this beat's folder and is recorded below.

Go deeper
The panel, with everything that was read back

All rows fetched from https://api.cellosaurus.org/cell-line/<accession>?format=txt on 2026-09-20 1.

lineaccessionsexagedisease (NCIt)sitenotable co-lesions
THP-1CVCL_0006M1Ychildhood acute monocytic leukemiaperipheral bloodNRAS p.Gly12Asp het; TP53 p.Arg174fs*3 het
MOLM-13CVCL_2119M20Yadult acute monocytic leukemia; MDSperipheral bloodFLT3-ITD het; OI CVCL_7916
MOLM-14CVCL_7916M20Yadult AMLperipheral bloodFLT3-ITD; OI CVCL_2119
NOMO-1CVCL_1609F31Yadult acute monocytic leukemiabone marrowKRAS p.Gly13Asp het; TP53 fs; EP300 splice
Mono-Mac-6CVCL_1426M64Yadult acute monocytic leukemiaperipheral bloodTP53 p.Arg273His; RUNX1-ATP8A2; OI CVCL_1425
IMS-M1CVCL_A623M33Yadult AMLbone marrow-
UG3CVCL_5382F26Yadult acute monocytic leukemiaperipheral blood-
YBT-5CVCL_YJ20M63Yadult AMLbone marrowestablished as DOT1L-inhibitor-sensitive
YCU-AML2CVCL_E7ALM5Ychildhood acute monocytic leukemiaperipheral bloodKRAS p.Gly12Ala hom; CDKN2A/B homozygous deletion; MECOM overexpression
KOPB-26CVCL_7972F1Y1Mchildhood B-ALL, t(v;11q23.3)peripheral bloodNSD2 p.Glu1099Lys het; TP53 P278L and R283fs
YACL95CVCL_D4A3unspecified<1Ychildhood B-ALL, t(v;11q23.3)--

Ten patients, not eleven, because MOLM-13 and MOLM-14 were established from the same individual 12.

The two B-ALL lines nobody uses, and why that is the panel's biggest hole

248 of 612 genotyped KMT2A::MLLT3 patients have ALL and 157 of those are infants. The panel contains two B-ALL lines, both from patients around or under one year, and neither appears anywhere in this graph's mechanistic literature.

  • KOPB-26 (CVCL_7972) is the better characterised of the two: female, 1 year 1 month, peripheral blood, childhood B-ALL with t(v;11q23.3) MLL rearranged, carrying NSD2 p.Glu1099Lys and two TP53 variants 1. It appears in the 1992 survey of 14 leukaemia and lymphoma lines with 11q23 translocations 5 and in the 1994 RT-PCR survey of chimeric mRNAs in 11q23 leukaemias 6.
  • YACL95 (CVCL_D4A3) has a thinner record: sex unspecified, under 1 year, childhood B-ALL, fusion attributed to a 2017 report 1.

This is the single most actionable observation in the entry. A t(9;11) infant B-ALL model already exists in two independent lines and this project's beat on the YEATS asymmetry could be run in the index lineage rather than in monocytic cells.

A correction owed outside this folder

ana-kmt2a-r-line-panel-monocytic-audit (in data/graph/nodes/cells/) retains Mono-Mac-1 (CVCL_1425) as 'the only line that is monocytic, non-KMT2A-rearranged, and free of a HOXA-axis fusion or a menin-dependent genotype' - the sole clean comparator in its control arm.

What the accessions say 1:

  • Mono-Mac-1 (CVCL_1425) carries no gene-fusion comment at all in Cellosaurus.
  • Mono-Mac-6 (CVCL_1426) carries KMT2A + MLLT3; KMT2A-MLLT3, MLL-MLLT3, MLL-AF9, sourced to the 1995 report that detected an MLL-AF9 fusion transcript in Mono Mac 6 4.
  • The two records are cross-linked by OI in both directions, i.e. same individual, and Mono-Mac-1's own TP53 annotation in the Mono-Mac-6 record is flagged 'from autologous cell line Mono-Mac-1'.

So Mono-Mac-1's status as a KMT2A-rearranged-negative comparator rests on an absence of annotation, not on a measurement, in a line derived from a patient whose other line is annotated KMT2A::MLLT3. This is not proof that Mono-Mac-1 carries the fusion - subclonal or evolutionary differences between two lines from one patient are possible and the 1995 paper examined Mono Mac 6 only - but it does mean the audit's control arm currently has zero comparators that have been shown to be fusion-negative, rather than one. The fix is cheap: the fusion has a known genomic junction and Mono-Mac-1 is in DepMap (ACH-001129), so an RNA-seq fusion call would settle it.

Recommended action: change the wording in ana-kmt2a-r-line-panel-monocytic-audit from 'the only clean comparator' to 'the only comparator not positively disqualified, and its fusion status is unannotated rather than negative in a line autologous with the KMT2A::MLLT3-positive Mono-Mac-6 (Cellosaurus CVCL_1425 / CVCL_1426; PMID 7833491)'. I have not edited that file.

Bounded rejection: what the sweep returned and this entry set aside

The Cellosaurus search for KMT2A-MLLT3 and MLL-AF9 returns several hundred records, the great majority of which are engineered derivatives of THP-1 and MOLM-13 - Abcam single-gene knockout panels, HyCyte knockouts, EDITGENE Cas9 and CopGFP derivatives, THP-1h/THP-1l subclones, an ara-C-resistant MOLM-13. All were excluded by requiring the absence of an HI (hierarchy) line, because a knockout derivative is not an independent patient sample and counting them inflates the panel roughly fiftyfold.

Also returned and excluded: MLL/AF9 Cas9 (CVCL_C8ZF), a mouse line (NCBI_TaxID=10090), whose fusion is a transgene.

A first, fielded query restricted to ca:"Cancer cell line" with pagination returned only two of the eleven lines and was discarded as unreliable; the working method was to page the unfielded query and filter on the structured fusion comment text. A reader re-running this should use the second method.

And one line this method could not see at all. SDEY-AML1, a human AML line with KMT2A::MLLT3 and a co-occurring IKZF1::EVX1 fusion, was reported in 2026 and has no Cellosaurus accession (numFound: 0 on 2026-09-20). It is a twelfth line by the literature's count and an eleventh by the database's. Recorded in ana-mllt3-yeats-loss-enumeration-searched-read-and-rejected.

Facts and figures
statusrun
run date2026-09-20
result summaryEleven human patient-derived KMT2A::MLLT3 lines exist, from ten patients (MOLM-13/MOLM-14 autologous). Ages <1Y to 64Y. Nine myeloid/monocytic, two childhood B-ALL (KOPB-26, YACL95). Only YCU-AML2 has a published intron-level fusion structure. Mono-Mac-1's status as a fusion-negative comparator rests on absent annotation in a line autologous with the fusion-positive Mono-Mac-6.
n lines11
n patients10
n b all lines2
n myeloid lines9
age range<1Y to 64Y
method noteA fielded Cellosaurus query restricted to ca:'Cancer cell line' returned only 2 of the 11 lines and was discarded; the working method was to page the unfielded query and filter on the structured fusion comment.
inputs
[
  "https://api.cellosaurus.org/search/cell-line?q=KMT2A-MLLT3 (and MLL-AF9, MLL-MLLT3), paged, filtered on the structured fusion comment and on absence of an HI line",
  "individual https://api.cellosaurus.org/cell-line/<accession>?format=txt fetches for all twelve accessions discussed"
]
lines
[
  {
    "name": "THP-1",
    "accession": "CVCL_0006",
    "sex": "Male",
    "age": "1Y",
    "disease": "childhood acute monocytic leukemia",
    "lineage": "monocytic",
    "site": "peripheral blood",
    "co_lesions": [
      "NRAS p.Gly12Asp het",
      "TP53 p.Arg174fs*3 het"
    ],
    "depmap": "ACH-000146"
  },
  {
    "name": "MOLM-13",
    "accession": "CVCL_2119",
    "sex": "Male",
    "age": "20Y",
    "disease": "adult acute monocytic leukemia; MDS",
    "lineage": "monocytic",
    "site": "peripheral blood",
    "co_lesions": [
      "FLT3-ITD het"
    ],
    "depmap": "ACH-000362",
    "same_individual_as": "CVCL_7916"
  },
  {
    "name": "MOLM-14",
    "accession": "CVCL_7916",
    "sex": "Male",
    "age": "20Y",
    "disease": "adult AML",
    "lineage": "myeloid",
    "site": "peripheral blood",
    "co_lesions": [
      "FLT3-ITD"
    ],
    "same_individual_as": "CVCL_2119"
  },
  {
    "name": "NOMO-1",
    "accession": "CVCL_1609",
    "sex": "Female",
    "age": "31Y",
    "disease": "adult acute monocytic leukemia",
    "lineage": "monocytic",
    "site": "bone marrow",
    "co_lesions": [
      "KRAS p.Gly13Asp het",
      "TP53 p.Cys242Alafs*5 het",
      "EP300 c.730-10T>C het"
    ],
    "depmap": "ACH-000168"
  },
  {
    "name": "Mono-Mac-6",
    "accession": "CVCL_1426",
    "sex": "Male",
    "age": "64Y",
    "disease": "adult acute monocytic leukemia",
    "lineage": "monocytic",
    "site": "peripheral blood",
    "co_lesions": [
      "TP53 p.Arg273His",
      "RUNX1-ATP8A2 fusion"
    ],
    "same_individual_as": "CVCL_1425"
  },
  {
    "name": "IMS-M1",
    "accession": "CVCL_A623",
    "sex": "Male",
    "age": "33Y",
    "disease": "adult AML",
    "lineage": "myeloid",
    "site": "bone marrow"
  },
  {
    "name": "UG3",
    "accession": "CVCL_5382",
    "sex": "Female",
    "age": "26Y",
    "disease": "adult acute monocytic leukemia",
    "lineage": "monocytic",
    "site": "peripheral blood"
  },
  {
    "name": "YBT-5",
    "accession": "CVCL_YJ20",
    "sex": "Male",
    "age": "63Y",
    "disease": "adult AML",
    "lineage": "myeloid",
    "site": "bone marrow",
    "note": "established and characterised as DOT1L-inhibitor-sensitive"
  },
  {
    "name": "YCU-AML2",
    "accession": "CVCL_E7AL",
    "sex": "Male",
    "age": "5Y",
    "disease": "childhood acute monocytic leukemia",
    "lineage": "monocytic",
    "site": "peripheral blood",
    "co_lesions": [
      "KRAS p.Gly12Ala hom",
      "CDKN2A homozygous deletion",
      "CDKN2B homozygous deletion",
      "MECOM overexpression"
    ],
    "fusion_structure": "KMT2A intron 8 fused to MLLT3 intron 4"
  },
  {
    "name": "KOPB-26",
    "accession": "CVCL_7972",
    "sex": "Female",
    "age": "1Y1M",
    "disease": "childhood B-ALL with t(v;11q23.3)",
    "lineage": "B-lymphoid",
    "site": "peripheral blood",
    "co_lesions": [
      "NSD2 p.Glu1099Lys het",
      "TP53 p.Pro278Leu",
      "TP53 p.Arg283fs"
    ]
  },
  {
    "name": "YACL95",
    "accession": "CVCL_D4A3",
    "sex": "unspecified",
    "age": "<1Y",
    "disease": "childhood B-ALL with t(v;11q23.3)",
    "lineage": "B-lymphoid"
  }
]
lines with residue or intron level fusion structure
[
  "YCU-AML2"
]
excluded
[
  "engineered knockout and reporter derivatives of THP-1 and MOLM-13 (several hundred records, excluded by requiring no HI hierarchy line)",
  "MLL/AF9 Cas9 (CVCL_C8ZF), a mouse line whose fusion is a transgene"
]
correction owed
{
  "entry": "ana-kmt2a-r-line-panel-monocytic-audit",
  "field": "control_arm_disqualifications / Mono-Mac-1 'retained as the only clean comparator'",
  "issue": "Mono-Mac-1 (CVCL_1425) is autologous with Mono-Mac-6 (CVCL_1426), which Cellosaurus annotates KMT2A-MLLT3 citing PMID 7833491; Mono-Mac-1's fusion-negative status is an absence of annotation, not an assay",
  "suggested_text": "the only comparator not positively disqualified; its KMT2A fusion status is unannotated rather than negative, in a line autologous with the KMT2A::MLLT3-positive Mono-Mac-6",
  "source": "Cellosaurus CVCL_1425 and CVCL_1426 fetched 2026-09-20; PMID 7833491",
  "read": "records read in full; PMID 7833491 read as title and curation only"
}
catalogue lag
{
  "line": "SDEY-AML1",
  "pmid": "41656387",
  "cellosaurus": "no accession as of 2026-09-20",
  "effect": "panel is 11 lines by Cellosaurus and at least 12 by the literature",
  "title": "A novel human acute myeloid leukemia cell line SDEY-AML1 with KMT2A: MLLT3, IKZF1: EVX1 fusions exhibits high tumorigenicity in NSG mice.",
  "authors": "Yang C, Zhang W, Wu Y, et al.",
  "venue": "Sci Rep",
  "year": 2026,
  "title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
}
How this could bite us back
  • Nine of the eleven lines are monocytic and seven of the ten patients are adults, so a drug prioritised on this panel is prioritised against adult monocytic disease and read across to a partner population that is 42% lymphoid and heavily infant.
  • Three of the ten patients carry an activating RAS-pathway lesion (THP-1 NRAS G12D, NOMO-1 KRAS G13D, YCU-AML2 KRAS G12A) and two carry FLT3-ITD, so RAS and FLT3 co-mutation - a documented menin-inhibitor resistance route - is over-represented in the panel relative to a de novo patient population.
  • MOLM-13 and MOLM-14 are one patient; any panel-wide statistic that counts them separately overweights that individual's genotype, and this graph has 138 entries quantifying a DepMap panel that does exactly that.
Still open
  1. Does Mono-Mac-1 carry KMT2A::MLLT3? It is in DepMap (ACH-001129) and an RNA-seq fusion call would settle a control-arm assumption this graph currently relies on.
  2. Why has no published study used KOPB-26 or YACL95 to model t(9;11) B-ALL, when 42% of this partner's patients have ALL?
  3. What are the MLLT3 breakpoints in the other ten lines? Only YCU-AML2 has a published intron-level structure, so the panel cannot currently be stratified by YEATS retention even though the whole beat turns on it.
  4. How many other human KMT2A::MLLT3 lines exist in establishment papers without a Cellosaurus accession? SDEY-AML1 was found incidentally.
Every source behind this entry (6)
  1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    Eleven human parent cell lines carry a Cellosaurus-annotated KMT2A + MLLT3 gene fusion: THP-1 (CVCL_0006, M, 1Y, childhood acute monocytic leukemia), MOLM-13 (CVCL_2119, M, 20Y), MOLM-14 (CVCL_7916, M, 20Y, OI with MOLM-13), NOMO-1 (CVCL_1609, F, 31Y), Mono-Mac-6 (CVCL_1426, M, 64Y, OI with Mono-Mac-1 CVCL_1425), IMS-M1 (CVCL_A623, M, 33Y), UG3 (CVCL_5382, F, 26Y), YBT-5 (CVCL_YJ20, M, 63Y), YCU-AML2 (CVCL_E7AL, M, 5Y), KOPB-26 (CVCL_7972, F, 1Y1M, childhood B-ALL) and YACL95 (CVCL_D4A3, sex unspecified, <1Y, childhood B-ALL); Mono-Mac-1 (CVCL_1425) carries no gene-fusion comment.

    What this evidence cannot show

    Cellosaurus annotation reflects what has been published and curated, not what is present: an absent fusion comment is an absence of annotation, not a negative assay, which is exactly the point made about Mono-Mac-1. The sweep depends on the structured comment text `KMT2A + HGNC; HGNC:7136; MLLT3`, so a line whose fusion is described only in free text would be missed. Ages and diseases are as submitted by the depositing laboratory. And the catalogue lags the literature: SDEY-AML1, a human KMT2A::MLLT3 line reported in 2026 (PMID 41656387), returns numFound 0 on a Cellosaurus search of 2026-09-20 and is therefore absent from this panel. An accession-database sweep is complete against the database, not against the field.

    Evidence that argues against this (1)
    • Drexler and colleagues reported seven cell lines with t(9;11)(p22;q23) in 2004 and stated that of 36 lines with 11q23 translocations, 17 were available to them and confirmed at chromosomal or gene level - so a substantial fraction of historical 11q23 line assignments were never independently re-confirmed, and this panel inherits that. Drexler HG et al. 2004
  2. E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

    MOLM-13 and MOLM-14 were established from the same patient - two acute monocytic leukaemia (AML-M5a) cell lines with interclonal phenotypic heterogeneity showing MLL-AF9 fusion resulting from an occult chromosome insertion, ins(11;9)(q23;p22p23).

    What this evidence cannot show

    The founding report describes both lines from one patient; the insertion rather than reciprocal translocation architecture means these lines may not carry a reciprocal allele in the usual configuration, a point relevant to any reciprocal-status work and not examined here.

    Evidence that argues against this (1)
    • The ins(11;9) architecture of MOLM-13/14 is not a standard t(9;11), so the panel's two best-used myeloid lines are not reciprocal-configured like the patient majority; this graph's reciprocal work should not assume they are. Matsuo Y et al. 1997
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    YCU-AML2 is a newly established high-risk paediatric AML line with KMT2A::MLLT3 in which KMT2A intron 8 is fused to MLLT3 intron 4, together with MECOM overexpression and KRAS p.Gly12Ala, and it is sensitive to MEK inhibitors and to L-asparaginase with glutaminase activity.

    What this evidence cannot show

    A single newly reported line, 2025, with drug sensitivities measured in vitro and in one xenograft. The KRAS G12A and MECOM overexpression are confounders for any fusion-attributed phenotype, and the MEK sensitivity is most simply read as a KRAS result.

    Evidence that argues against this (1)
    • The same report attributes the line's therapeutic vulnerabilities to a genotype that includes KRAS G12A and MECOM overexpression alongside the fusion, so nothing measured in it can be attributed to KMT2A::MLLT3 without an isogenic comparison the paper does not have. Ikeda J et al. 2025
  4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Molecular analysis of the Mono Mac 6 cell line detected an MLL-AF9 fusion transcript.

    What this evidence cannot show

    A 1995 Blood report with no abstract in the PubMed record; this claim is taken from the title and from the Cellosaurus curation that cites it, not from the full text, which was not retrieved. It concerns Mono Mac 6 only; Mono-Mac-1, from the same patient, is not examined in it.

    Evidence that argues against this (1)
    • Because the report covers Mono Mac 6 and not Mono-Mac-1, it cannot be used to assert the fusion in Mono-Mac-1 either - which is why this entry recommends an assay rather than an inference. Drexler HG et al. 2004
  5. E5moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    KOPB-26 appears in a phenotypic and genotypic characterisation of 14 leukaemia and lymphoma cell lines with 11q23 translocations.

    What this evidence cannot show

    1992, pre-dating routine molecular fusion assignment; cited here as a provenance record for the line rather than as the source of its KMT2A::MLLT3 assignment, which Cellosaurus attributes to the 2004 Drexler review.

    Evidence that argues against this (1)
    • A 1992 cytogenetic characterisation cannot distinguish MLLT3 from other 9p partners; the line's partner assignment rests on later curation. Drexler HG et al. 2004
  6. E6moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    A reverse transcriptase-polymerase chain reaction survey detected heterogeneous chimeric mRNAs in leukaemias with 11q23 abnormalities, and is one of the records Cellosaurus cites for both KOPB-26 and IMS-M1.

    What this evidence cannot show

    1994 RT-PCR on a small series; cited as provenance for the lines rather than as an independent confirmation of partner identity in either.

    Evidence that argues against this (1)
    • RT-PCR designed around a limited primer set returns negative for every partner it was not designed around, so a 1994 survey is weak evidence about which partner a line carries. Drexler HG et al. 2004
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