Oncofusion

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Explainermoderate confidence 3 of 5: One strong study, or several smaller consistent ones.Q24-reciprocal-product

Half of all KMT2A::MLLT1 patients make no reciprocal product at all - a ready-made control arm of about 240 people

also called spliced KMT2A-MLLT1 fusions · MLLT1 upstream breaks · 241 of 460

In the second commonest version of this leukaemia, half the patients break the chromosome in a place that produces no mirror-image gene at all. That means there is already a large group of patients with and without it, with the partner gene held constant.

The same thing, for a scientist

In the KMT2A recombinome, 241 of 460 KMT2A::MLLT1 cases break upstream of MLLT1 exon 1 [E1]. Those are spliced fusions: the breakpoint lies in the region 5' of the partner's first exon, so the direct fusion transcript is generated by splicing into MLLT1 exon 1 and no in-frame reciprocal fusion gene is produced. That gives a natural experiment of roughly 241 reciprocal-negative against roughly 219 reciprocal-positive patients, **with the partner gene held constant** - the design feature that makes it interpretable and that the t(4;11) comparison lacks, because there reciprocal status is entangled with breakpoint position, HOXA status and possibly with the direct product's own composition. The analysis has never been published. What makes it more valuable still is that the same recombinome reports KMT2A has a gene-internal promoter upstream of exon 12, so even out-of-frame reciprocal alleles can express a 5'-truncated KMT2A protein [E1] - meaning 'no reciprocal fusion transcript' and 'no KMT2A C-terminal protein from the der allele' are different statements, and the spliced-fusion class is the cleaner of the two.

Go deeper
Why this is the best available test of whether the reciprocal product matters clinically

Every other comparison confounds. In t(4;11), reciprocal-positive and reciprocal-negative patients differ in breakpoint position 2, in HOXA expression 3 and possibly in the composition of their direct fusion. In the MLLT1 spliced-fusion class, the partner is fixed, the direct product is a canonical KMT2A::MLLT1, and the difference is the presence or absence of a reciprocal allele. If reciprocal status carries prognostic information there, it is much harder to explain away; if it does not, the t(4;11) association is probably a proxy for something else.

The gene-internal promoter, which complicates every reciprocal-negative claim

KMT2A carries a gene-internal promoter upstream of exon 12, so an out-of-frame reciprocal allele can still express a 5'-truncated KMT2A protein - essentially the reciprocal product without its partner N-terminus 1. A patient scored reciprocal-negative because the join is out of frame may therefore still make a menin-blind, SET-containing KMT2A fragment. Only the spliced-fusion class, where no reciprocal allele exists at all, is unambiguously negative.

Facts and figures
partnerMLLT1 (ENL)
spliced fusion cases241
total mllt1 cases460
reciprocal negative arm n241
reciprocal positive arm n219
design advantagepartner gene held constant
analysis statusnever published
complicationKMT2A gene-internal promoter upstream of exon 12 allows a 5'-truncated KMT2A protein from out-of-frame reciprocal alleles
How this could bite us back
  • If reciprocal status turns out to carry no prognostic weight when the partner is held constant, the clinical case for reciprocal-status stratification of menin-inhibitor therapy weakens sharply.
  • The gene-internal promoter means a patient can be reciprocal-fusion-negative and still carry a menin-blind KMT2A fragment, so a binary reciprocal biomarker would misclassify them.
Still open
  1. Do spliced KMT2A::MLLT1 patients differ in outcome, HOXA signature or menin-inhibitor sensitivity from reciprocal-expressing KMT2A::MLLT1 patients? The cohort exists and the analysis does not.
  2. Is the 5'-truncated KMT2A protein from the gene-internal promoter ever detected? It would be a menin-blind, SET-containing KMT2A species present in patients scored reciprocal-negative.
  3. Does the spliced-fusion class exist in t(4;11)? AFF1 breakpoints cluster in introns 3-4, which are internal, so probably not - which is why MLLT1 and not AFF1 is the place to run this test.
Every source behind this entry (3)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Read in full text (PMC10169636): spliced fusions arise when the 5' portion of KMT2A lies upstream of an intact partner gene, so transcription from the KMT2A promoter splices into the partner's exon 2; they are rare except for MLLT1, where of n = 460 cases about 50% (n = 241) of breakpoints localise upstream of MLLT1 exon 1 and only KMT2A::MLLT1 transcripts and no reciprocal one are expressed. The same mechanism occurs for EPS15 (12 of 51), ELL (10 of 119), PRPF19 (3 of 3), AFDN (2 of 138), MLLT3 (2 of 612), AFF1 (1 of 1,262), MYO1F (1 of 5), and single cases of DCPS, SEPTIN5 and CT45A2 - 275 cases in total. Of 426 complex KMT2A rearrangements analysed, 40 reciprocal fusions were in frame and 386 were non-functional or out of frame at the genomic DNA level, but the majority of the out-of-frame ones may still be transcribed and encode a 5'-truncated KMT2A protein termed KMT2A*, from a gene-internal promoter upstream of KMT2A exon 12.

    The KMT2A recombinome of acute leukemias in 2023. · Meyer C, Larghero P, Almeida Lopes B, et al. · Leukemia 2023
    PMID 37019990DOI
    What this evidence cannot show

    Read in full text via Europe PMC fullTextXML (86,330 characters), not abstract only. Counts come from a single diagnostic centre's referral series of 3,401 patients accumulated 2003-2022, so partner denominators reflect referral patterns. The 241/460 split is a count of breakpoint positions with the transcript consequence inferred from gene structure and attributed to a prior reference, not a per-patient RT-PCR measurement. Note the number that matters most for this beat's index fusion: AFF1 has 1 spliced case out of 1,262, so t(4;11) has effectively no spliced-fusion class.

    Evidence that argues against this (1)
    • The functional premise behind the framing is contested: removal of the reciprocal transcript from human t(4;11) lines produced no growth, cell-cycle or apoptotic phenotype. Kumar AR et al. 2011
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    KMT2A breakpoints in t(4;11) cluster in introns 9-11 with intron 11 commonest in infant ALL, and the position of the break determines the composition of both the direct and the reciprocal product.

    PMID 34489550DOI
    What this evidence cannot show

    Distributional and construct-level statement rather than a per-patient analysis; the clinical consequence of breakpoint position in t(4;11) has never been measured.

    Evidence that argues against this (1)
    • No cohort analysis has tested breakpoint position against outcome in t(4;11), so its status as a confounder is inferred from mechanism rather than demonstrated. Agraz-Doblas A et al. 2019
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In the Interfant cohort HOXA cluster genes were expressed exclusively in the reciprocal-expressing t(4;11) patients, who also had markedly better event-free and overall survival.

    PMID 30679323DOI
    What this evidence cannot show

    n = 43 for the t(4;11) subgroup; the cross-tabulation behind 'exclusively' is not in the abstract.

    Evidence that argues against this (1)
    • A partner-stratified paediatric cohort that reported outcome by KMT2A partner measured neither HOXA status nor reciprocal status, so the collinearity has no independent check. Qiu KY et al. 2022
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