Oncofusion

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Experimentspeculative confidence 1 of 5: Our own inference or analogy. Not shown to be true.Q50-prc1-myc

Is BENC even on in the disease this project is about? A module-resolved accessibility and deletion map in KMT2A::AFF1 B-lineage cells

also called BENC in infant B-ALL · does the MYC blood enhancer cluster operate in the index disease

Everything known about this MYC control region comes from myeloid leukaemia. The disease at the centre of this project is a B-cell leukaemia of infants, and nobody has checked whether the region is even switched on there. This is the experiment that checks.

The same thing, for a scientist

Every functional result on BENC in leukaemia is myeloid: the deletion phenotype and the leukaemia-maintenance requirement are in MLL-AF9 mice, and the human stem-cell-versus-blast accessibility gradient is in AML [E1]. The only B-lineage evidence is recurrent copy-number amplification of the cluster in BCP-ALL **cell lines**, framed by its own authors as *acquired* during immortalisation [E2]. A PubMed search on 2026-09-20 for `BENC[tiab] AND (infant[tiab] OR "acute lymphoblastic"[tiab])` returns **1** record, that cell-line paper. **The index disease of this project has no BENC data at all.** Design: (1) **ATAC-seq and H3K27ac CUT&RUN across the +1.7 Mb cluster** in KMT2A::AFF1 B-lineage models and, critically, in primary infant patient material, with module-level resolution; (2) **Micro-C or Capture-C from the MYC promoter** to test whether the contacts that exist in myeloid cells exist here [E3]; (3) **CRISPR deletion of individual modules**, sized to the RUNX1/GFI1B/MYB motifs, with MYC expression and viability as readouts, following the precedent that single-module deletion produced measurable effects in inv(16) [E4]; (4) **copy-number assessment of the cluster in primary infant samples** to test whether the cell-line amplification has any counterpart in patients. The experiment is worth running even if the answer is negative, because a negative would mean **MYC in this disease is controlled from somewhere else**, and no alternative has ever been proposed.

Go deeper
Why the myeloid result cannot simply be assumed to transfer

Three specific reasons, not general caution.

1. BENC is defined by lineage-selective modules. Bahr et al. describe modules with selective activity recruiting GFI1B, RUNX1 and MYB, and show that Myc levels across the haematopoietic hierarchy are set by their combinatorial and additive activity 1. A cluster whose whole design principle is module-level lineage selectivity is precisely the kind of element whose behaviour should differ between a myeloid blast and a pro-B blast. The germline deletion also caused loss of B cells as well as myeloid cells, so the cluster is required for the B lineage in normal development - which makes its status in a B-lineage leukaemia an open and interesting question rather than a formality.

2. The infant disease's chromatin is not adult myeloid chromatin. This graph's own entries place KMT2A::AFF1 infant B-ALL in a fetal-progenitor context with a distinctive enhancer landscape. mechanism-enhancer-usage-and-hijacking-kmt2a-r and genome-enhancer-promoter-contacts-kmt2a-r record the disease-specific enhancer biology; neither names this element, because until this cycle the graph had no word for it.

3. The SWI/SNF precedent is a direct warning. The one time a mouse myeloid MYC-enhancer result was tested in human MLL-rearranged cells, the MYC arm did not transfer 5. Assuming transfer here would be repeating the error this beat spent a whole entry documenting.

What each arm would settle, and the order to run them in

Arm 1 - is it open? (cheapest, run first). ATAC-seq plus H3K27ac CUT&RUN over the +1.7 Mb region in two or three KMT2A::AFF1 B-lineage models and in cryopreserved primary infant blasts. Module-level resolution is the requirement; a bulk 'the region is accessible' answer is not useful given the cluster's modular design. If no module is open, arms 2-4 are unnecessary and the finding is already important: it would mean MYC in this disease is not controlled from BENC and would send the field looking for the element that does control it.

Arm 2 - is it connected? Capture-C or Micro-C from the MYC promoter. The inv(16) study established physical connection between its three enhancers and the promoter by enhancer-interaction analysis 4, so there is a method precedent. Accessibility without contact would be a distinct and informative state.

Arm 3 - does it matter? CRISPR deletion of individual modules, with MYC expression and viability. Sizing from the inv(16) precedent: 41-275 bp deletions around the transcription-factor motifs were sufficient, and single-module deletion gave 40-50% MYC reduction and 60-70% viability reduction there 4.

Arm 4 - is it amplified in patients? Copy number over the cluster in primary infant KMT2A-rearranged samples. This is the arm that could be run today on existing data - whole-genome sequencing from infant ALL cohorts exists, and the question is a focal copy-number query over a defined interval. It requires no new material.

Arm 4 first if the data are accessible; otherwise arm 1.

Facts and figures
designFour arms, gated. Arm 1: ATAC-seq plus H3K27ac CUT&RUN across the +1.7 Mb cluster at module resolution in KMT2A::AFF1 B-lineage models and in cryopreserved primary infant blasts. Arm 2: Capture-C or Micro-C from the MYC promoter to test contact. Arm 3: CRISPR deletion of individual modules sized to the GFI1B/RUNX1/MYB motifs, with MYC expression and viability as readouts. Arm 4: focal copy-number assessment over the cluster in primary infant KMT2A-rearranged samples - runnable on existing whole-genome sequencing with no new material.
readoutmodule-level accessibility and H3K27ac; promoter-enhancer contact frequency; MYC transcript and viability after single-module deletion; copy number over the interval in primary samples
controlsa myeloid KMT2A-rearranged line as a positive control for cluster activity, since all published activity is myeloid; the N-ME (+1.4 Mb NOTCH-dependent T-cell) enhancer as a lineage-inappropriate negative locus; normal B progenitors for the accessibility comparison, because the cluster is required for normal B-cell output and a leukaemia-versus-normal difference is the interesting quantity
cost tiermed
timelinearm 4 in weeks if cohort data are accessible; arm 1 in 2-3 months; arms 2-3 in 6-9 months
statusplanned
run orderarm 4 first if existing cohort sequencing can be queried; otherwise arm 1, which gates the rest
why a negative is valuableif no BENC module is active in KMT2A::AFF1 B-lineage cells, then MYC in the index disease is controlled from an element nobody has identified, and that is a larger and more interesting finding than confirming the myeloid result
bounded absence motivating it
{
  "claim": "no BENC data exist for infant or KMT2A-rearranged acute lymphoblastic leukaemia",
  "query": "BENC[tiab] AND (infant[tiab] OR \"acute lymphoblastic\"[tiab])",
  "count": 1,
  "record": "PMID 38923173, BCP-ALL cell lines, acquired amplification",
  "positive_control": "the same query form returns that record; the instrument returns ones",
  "name_scope": "BENC only - see concept-a-noncoding-element-has-no-symbol-and-three-names; a paper using BDME or a coordinate description would be missed",
  "tool": "NCBI E-utilities esearch db=pubmed",
  "date": "2026-09-20"
}
tests
[
  "hyp-menin-inhibition-swaps-brg1-for-ring1b-at-benc"
]
How this could bite us back
  • If BENC is active and required in this disease, any intervention aimed at it is aimed at an element required for normal B-cell development - and the patients are infants whose B-lineage output is still being established.
  • A negative result would be reported as 'BENC is not relevant to infant ALL' when what it would actually show is that the element is not active in the models tested, which for a disease with few faithful models is a materially weaker statement.
  • Arm 4 uses existing cohort sequencing, which means it inherits whatever coverage and copy-number-calling limitations those cohorts have over a non-coding interval - regions like this are exactly where standard pipelines are least reliable.
  • Confirming BENC activity here would make MYC look more actionable in infant disease than it is, given that no direct MYC inhibitor exists and the enhancer is required for normal haematopoiesis.
Still open
  1. Is any BENC module accessible in a KMT2A::AFF1 B-lineage blast? Nobody has looked, and the answer gates everything else on this beat that concerns the index disease.
  2. Which modules are lineage-selective for B cells? Bahr et al. demonstrate module-level selectivity exists; the B-lineage assignment has not been published and would be needed before a deletion is designed.
  3. Is the cluster focally amplified in any primary infant KMT2A-rearranged sample? This is answerable from existing cohort sequencing today.
  4. If BENC is inactive here, what does control MYC in this disease? No alternative element has ever been proposed for KMT2A::AFF1 B-lineage leukaemia.
Every source behind this entry (5)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    BENC comprises multiple enhancer modules with selective activity recruiting GFI1B, RUNX1 and MYB whose combinatorial and additive activity sets Myc levels across the haematopoietic hierarchy; deletion in mice abolishes Myc in HSC/progenitors with accumulation of differentiation-arrested multipotent progenitors and loss of myeloid AND B cells; the cluster is essential for maintenance of MLL-AF9-driven leukaemia; and one module shows greater chromatin accessibility in human AML stem cells than blasts, correlating with MYC expression and patient outcome.

    A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. · Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, et al. · Nature 2018
    PMID 29342133DOI
    What this evidence cannot show

    Mouse genetics with a human accessibility association; the leukaemia arm is MLL-AF9 myeloid only. Abstract-level reading - Europe PMC returns no PMCID - so module identities, coordinates and which module carries the AML stem-cell signal are not known to this beat and would have to be recovered from the paper before an experiment is designed.

    Evidence that argues against this (1)
    • The one time a mouse MYC-enhancer result from this locus was tested for SWI/SNF dependence in human MLL-rearranged cells, the MYC arm failed to transfer. Lineage and species transfer at this locus has a documented failure, which is the reason for arm 1 rather than an assumption. Cruickshank VA et al. 2015
  2. E2weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.paper

    Recurrent copy-number alterations of the blood enhancer cluster occur in B-precursor acute lymphoblastic leukaemia cell lines, where BENC acts as a super-enhancer driving MYC expression and possibly contributing to immortalisation and proliferative advantage in vitro; a PubMed search on 2026-09-20 for BENC[tiab] AND (infant[tiab] OR 'acute lymphoblastic'[tiab]) returns this single record.

    Acquired copy number amplification at the MYC enhancer in human B-precursor acute lymphoblastic leukemia cell lines. · Watanabe A, Wang L, Tan TK, Urayama KY, Kizuki T, Komatsu C, et al. · Cancer Sci 2024
    PMID 38923173DOI
    What this evidence cannot show

    Cell lines only, and the authors' own title word is 'Acquired' - their framing is in-vitro immortalisation, not patient disease. No KMT2A-rearranged subgroup is identified in the abstract, and no infant material is involved. The counted absence is bounded by the token BENC and by [tiab]; the naming problem recorded in concept-a-noncoding-element-has-no-symbol-and-three-names means a paper using another name for the element would be missed. Positive control: the identical query form returns this record, so the instrument returns ones.

    Evidence that argues against this (1)
    • Focal amplification of the same region is reported at only about 3% in primary AML, so a recurrent finding in cell lines against a rare finding in primary material is itself an argument that the cell-line result is culture adaptation. Arm 4 exists to settle that in the disease of interest rather than to assume it either way. Shi J et al. 2013
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In MLL-AF9 leukaemia cells, Brg1 is required at the +1.7 Mb enhancer cluster to maintain transcription-factor occupancy and long-range chromatin looping interactions with the Myc promoter - establishing that the element's function in a KMT2A-rearranged context is exercised through physical contact with the promoter.

    Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. · Shi J, Whyte WA, Zepeda-Mendoza CJ, Milazzo JP, Shen C, Roe JS, et al. · Genes Dev 2013
    PMID 24285714DOI
    What this evidence cannot show

    Mouse, myeloid, RN2 model with a cooperating NrasG12D allele. Cited here to justify arm 2's readout - contact with the promoter is the functional currency at this element - not to predict that the contact exists in B-lineage cells.

    Evidence that argues against this (1)
    • The same laboratory group's model is the one in which MYC enhancer usage is documented to re-route under chromatin-drug pressure to a different focal enhancer, so the contact map at this element is not a fixed property even within one cell type, let alone across lineages. Rathert P et al. 2015
  4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Method precedent for module-level deletion: in inv(16) AML cells, CRISPR/Cas9 deletions of 41 bp, 67 bp and 275 bp around the RUNX1 binding sites of three MYC enhancer elements reached 77-99% allele frequency and each single deletion reduced MYC expression by 40-50% and viability by 60-70%; enhancer-interaction analysis confirmed the three elements are physically connected to the MYC promoter.

    CBFbeta-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia · Pulikkan JA, Hegde M, Ahmad HM, Belaghzal H, Illendula A, Yu J, O'Hagan K, Ou J, Muller-Tidow C, Wolfe SA, Zhu LJ, Dekker J, Bushweller JH, Castilla LH · Cell 2018
    PMID 29958106DOI
    What this evidence cannot show

    A different fusion and a myeloid line (ME-1); the deletions target RUNX1 motifs specifically, and the motif set that matters in a B-lineage KMT2A::AFF1 cell may be different - GFI1B and MYB are also named BENC recruits. Read in full from PMC6211564 on 2026-09-20. Cited as a sizing and feasibility precedent, not as a prediction.

    Evidence that argues against this (1)
    • A 40-50% MYC reduction from a single small deletion in one cell line is a larger effect than the combinatorial-and-additive model of the cluster would predict, and the two descriptions of the element's architecture have not been reconciled. An experiment designed around the larger effect could be underpowered if the additive model is right. Bahr C et al. 2018
  5. E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    A mouse MYC-enhancer result at this locus failed to transfer to human MLL-rearranged cells: SMARCA4, SMARCD2 and DPF2 were required for haematopoietic-stem-cell-associated gene expression but, in explicit contrast to the mouse data, not for expression of c-MYC-regulated genes.

    SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance. · Cruickshank VA, Sroczynska P, Sankar A, Miyagi S, Rundsten CF, Johansen JV, et al. · PLoS One 2015
    PMID 26571505DOI
    What this evidence cannot show

    The failure to transfer concerns SWI/SNF dependence, not the element's activity, so it is a warning about assuming transfer rather than evidence that BENC is inactive in human or B-lineage cells. The readout is a gene signature with no enhancer measurement.

    Evidence that argues against this (1)
    • Deletion of the element itself is independently required for MLL-AF9 leukaemia maintenance, so the element's importance in a KMT2A-rearranged context does not rest on the contested SWI/SNF result. The warning is about which factor operates it, not about whether it operates. Bahr C et al. 2018
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