AK_7_3, a KMT2A::AFF1-derived fusion circRNA that holds down mitochondrial respiration and ROS in t(4;11) B-ALL - the only mitochondrial mechanism in this beat measured in the index fusion
also called AK_7_3 · KMT2A::AFF1 fusion circRNA · f-circRNA AFF1 exon 7 to KMT2A exon 3 · MLL-AF4 f-circRNA
The t(4;11) translocation does not only make a fusion protein; it also makes a small circular RNA that joins the two genes back to front. Removing that circle from leukaemia cells makes their mitochondria work harder, produce more damaging oxygen radicals, become misshapen, and the cells start dying - so the circle is normally keeping the mitochondria quiet and the cells alive.
The same thing, for a scientist
A recurrent back-splicing junction joining **AFF1 exon 7 to KMT2A exon 3 (AK_7_3)** was identified in SEM, RS4;11 and ALL-PO, all t(4;11)/KMT2A::AFF1 lines, and detected in **12/18 paediatric and 17/24 adult t(4;11)-positive B-ALL patients, including three paired diagnosis/relapse samples, while absent in 23 t(4;11)-negative B-ALL patients** [E1]. Whole-transcriptome analysis of AK_7_3-knockdown SEM cells showed upregulation of genes in oxidative stress response and regulation of apoptosis; cell-death analysis confirmed a pro-apoptotic effect of silencing; and confocal imaging, **Seahorse bioenergetic profiling** and electron microscopy showed overproduction of reactive oxygen species, increased mitochondrial membrane potential, increased mitochondrial respiration and dysmorphic mitochondria after knockdown in KMT2A::AFF1 lines [E1]. **This is the only entry in this beat whose mitochondrial phenotype was measured in the index fusion, in the index lineage, with patient-level recurrence data.** It is also the only one whose direction is restraint rather than demand: the fusion product here *limits* respiration, and removing it is what damages the cell.
Why the direction matters more than the molecule
Almost every metabolic finding in this beat says: the leukaemia needs more of something, so take it away. This one says the opposite. AK_7_3 knockdown increases mitochondrial respiration, membrane potential and ROS, and that increase is accompanied by apoptosis 1. The fusion-derived product is holding the mitochondria down, and the cell dies when it is released.
That is a therapeutically attractive shape, because it means the intervention is to remove a leukaemia-specific molecule rather than to inhibit a housekeeping enzyme. AK_7_3 is absent from all 23 t(4;11)-negative patients tested 1, so unlike IMPDH2, MAT2A, PHGDH or MCL1 it is not present in normal tissue at all. An antisense or siRNA approach against a junction that exists only in the tumour has a selectivity argument that none of the enzyme targets in this beat can make.
It also reframes the OXPHOS literature this graph carries. cell-state-oxphos-dependence records that OXPHOS inhibition in MLL-rearranged B-ALL blunts blasts while promoting leukaemia-initiating cells. If the fusion's own circRNA product is already restraining respiration, then pharmacologically restraining it further is pushing in a direction the leukaemia has chosen for itself - which is a plausible reason why that intervention helps the initiating compartment.
What is and is not established
Established by this paper: the junction exists, it is recurrent at both diagnosis and relapse, it is specific to t(4;11) in the tested cohorts, and knocking it down in three fusion-positive lines produces a reproducible mitochondrial and apoptotic phenotype measured by three independent methods (confocal, Seahorse, electron microscopy) 1.
Not established: any in vivo result; any causal molecular mechanism connecting the circRNA to mitochondria - the transcriptome result is an association between knockdown and upregulated oxidative-stress and apoptosis gene sets, not a demonstrated target; the abundance of AK_7_3 relative to the linear fusion transcript; and whether the phenotype survives an off-target-controlled knockdown, which for circRNA work is the standard objection because a junction-spanning siRNA can also hit the linear transcript that contains the same exons in the other order.
A specific caution the paper itself invites: the abstract records the translocation as t(4;11)(q24;q23). The cytoband conventionally written for KMT2A::AFF1 in this graph and in the WHO literature is t(4;11)(q21;q23). This beat has not resolved which is intended; it is recorded as an unresolved discrepancy in the source and not propagated into data.
| molecule | AK_7_3, a fusion circular RNA with a back-splicing junction from AFF1 exon 7 to KMT2A exon 3 |
|---|---|
| direction | the fusion-derived product RESTRAINS mitochondrial respiration; removing it kills the cell - the inverse of every other mechanism in this beat |
| selectivity argument | absent from all 23 t(4;11)-negative B-ALL patients tested, so unlike an enzyme target it has no normal-tissue counterpart |
| unresolved discrepancy | source abstract writes t(4;11)(q24;q23); this graph and WHO use (q21;q23) |
| evidence lineage | INFANT-ADJACENT AND LYMPHOID: paediatric and adult t(4;11) B-ALL, the index fusion of this graph |
cell lines
[ "SEM", "RS4;11", "ALL-PO" ]
patient detection
{
"paediatric_t411_positive": "12/18",
"adult_t411_positive": "17/24",
"t411_negative_controls": "0/23",
"paired_diagnosis_relapse": 3
}phenotype on knockdown
[ "increased reactive oxygen species", "increased mitochondrial membrane potential", "increased mitochondrial respiration", "dysmorphic mitochondria", "apoptosis" ]
methods
[ "whole-transcriptome sequencing", "confocal microscopy", "Seahorse bioenergetic profiling", "electron microscopy" ]
not established
[ "in vivo activity", "molecular target of the circRNA", "abundance relative to the linear chimera", "off-target-controlled knockdown" ]
- Raising mitochondrial respiration and ROS is a pro-mutagenic manoeuvre. Doing it deliberately in a leukaemia that already has a high relapse rate risks selecting a more damaged, more resistant clone rather than killing the disease.
- AK_7_3 was detected in only 12/18 paediatric and 17/24 adult t(4;11) patients, so roughly a third of the target population does not have the molecule at all by the assay used.
- Delivering an RNA-targeting agent to marrow blasts in an infant is an unsolved delivery problem, and the selectivity advantage of a tumour-specific junction is worth nothing without it.
- If the circRNA and the linear fusion transcript cannot be knocked down independently, then any therapeutic effect attributed to the circle is really an effect of reducing the oncogenic fusion protein - a much older idea with a much harder delivery problem.
- Is AK_7_3 present in INFANT t(4;11) disease specifically? The cohorts are described as paediatric and adult; infants under one year are the index population of this graph and are not separately reported.
- What does AK_7_3 bind? Without a target the mechanism is a knockdown phenotype, and circRNA phenotypes have a poor replication record in the absence of an identified interactor.
- Does a junction-spanning knockdown reagent spare the linear KMT2A::AFF1 transcript? This is the control that decides whether the finding is about the circle or about the fusion protein.
- Does releasing mitochondrial restraint kill the leukaemia-initiating compartment, or only the bulk? The published direction of benefit in this lineage runs the other way, so a limiting-dilution transplantation readout is essential before this is called a therapeutic direction.
- E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
A novel recurrent KMT2A::AFF1-derived back-splicing junction joining AFF1 exon 7 to KMT2A exon 3 (AK_7_3) was identified in the t(4;11)/KMT2A::AFF1 B-ALL cell lines SEM, RS4;11 and ALL-PO, observed in RT-PCR products encompassing two splicing variants of KMT2A exon 4 that are also present in the linear KMT2A::AFF1 chimera; AK_7_3 was found in 12/18 paediatric and 17/24 adult t(4;11)-positive B-ALL patients including three paired diagnosis/relapse samples, and was absent in 23 t(4;11)-negative B-ALL patients; whole-transcriptome analysis of AK_7_3-knockdown SEM cells identified upregulated genes involved in oxidative stress response and regulation of apoptosis; cell-death analysis confirmed a pro-apoptotic impact of AK_7_3 silencing; and confocal analyses, Seahorse bioenergetic profiling and electron microscopy revealed overproduction of reactive oxygen species, increased mitochondrial membrane potential, increased mitochondrial respiration and dysmorphic mitochondria after AK_7_3 knockdown in KMT2A::AFF1 cell lines.
A novel KMT2A::AFF1-derived fusion circRNA regulates mitochondrial metabolism in t(4;11) B-cell acute lymphoblastic leukemia. · Tolomeo D, Bardini M, Venuto S, ..., Storlazzi CT · Haematologica 2026What this evidence cannot show
Abstract read this session; full text not retrieved and no PMCID was returned by efetch on 2026-09-20, so the knockdown controls, the off-target analysis and the Seahorse parameters were not checked. **No in vivo data.** The mechanism connecting the circRNA to mitochondria is not identified: the transcriptome result is an enrichment of oxidative-stress and apoptosis gene sets after knockdown, which is a consequence, not a target. Standard circRNA objection applies and is not addressed in the abstract - a junction-spanning knockdown reagent can also affect the linear transcript containing the same exons, and the linear KMT2A::AFF1 chimera is the dominant oncogenic product in these cells, so a phenotype attributed to the circle could belong to the protein. Patient detection is by RT-PCR presence/absence with no quantitation and no normal-tissue control beyond fusion-negative B-ALL. The abstract writes the translocation as t(4;11)(q24;q23) where this graph and the WHO classification use (q21;q23); the discrepancy is unresolved and is not propagated.
Evidence that argues against this (1)
- The graph's established position on this lineage is that inhibiting oxidative phosphorylation blunts MLL-rearranged B-ALL blast proliferation while promoting leukaemia-initiating cell emergence. A model in which the fusion's own product restrains respiration predicts that further restraint should be tolerated or beneficial to the leukaemia, which is consistent - but it also means that the therapeutic move suggested here (releasing the restraint) has never been tested against a leukaemia-initiating-cell readout, where the published direction of benefit runs the other way. Morris V et al. 2022
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
In MLL-rearranged B-ALL, inhibiting oxidative phosphorylation blunts blast proliferation but promotes leukaemia-initiating cell emergence, while inhibiting hypoxia and glycolysis impairs leukaemia-initiating cells and provides therapeutic benefit in xenotransplantation.
Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells. · Morris V, Wang D, Li Z, ..., Rowe RG · Cell Rep 2022What this evidence cannot show
Abstract read this session; identifiers re-fetched from PubMed rather than copied from sibling entries. Cited here to place the AK_7_3 result in the lineage's existing metabolic context, not as evidence about circRNAs. Xenotransplantation engraftment is a proxy for leukaemia-initiating capacity. The specific OXPHOS inhibitor is not named in the abstract.
Evidence that argues against this (1)
- That study measures pharmacological OXPHOS inhibition in bulk and in the initiating compartment; the circRNA study measures the consequence of removing a fusion-derived transcript in cell lines. They are not the same manipulation and a clean reconciliation is not available from either abstract. Tolomeo D et al. 2026
a fusion-derived circular RNA product of the t(4;11) rearrangement
knockdown raises mitochondrial respiration and membrane potential in KMT2A::AFF1 lines
detected in 12/18 paediatric and 17/24 adult t(4;11)-positive B-ALL, absent in 23 fusion-negative
a fusion product that directly sets a mitochondrial set-point, in the index fusion