RUNX1::RUNX1T1 (AML1-ETO), t(8;21)(q22;q22)
also called AML1-ETO · AML1/ETO · RUNX1-RUNX1T1 · AML1-MTG8 · t(8;21) AML · CBF-AML · AML1-ETO9a
A swap between chromosomes 8 and 21 takes the part of a master blood-cell switch that finds its target genes and bolts it onto a protein that silences genes and glues four copies of itself together. The result parks a silencing machine on exactly the genes that tell a cell to grow up, so the cells stay immature - but this is one of the better-outcome childhood leukaemias.
The same thing, for a scientist
t(8;21)(q22;q22) juxtaposes the 5-prime sequences of **RUNX1** (Q01196) to the 3-prime sequences of **RUNX1T1/ETO/MTG8** (Q06455), producing a 752-residue chimera containing the RUNX1 N-terminus **including the Runt DNA-binding domain** fused to **almost the entire ETO protein** [E1][E2]. The fusion therefore retains the full **RUNX1-CBFB heterodimerisation and DNA-binding surface** (the Runt domain, solved with CBFB on DNA as a DNA-induced molecular clamp, PDB 1H9D/1E50/1IO4) and adds ETO's **NHR2 oligomerisation domain** (a tetramer, PDB 1WQ6, whose integrity is critical for AML1-ETO activity) and **NHR4/MYND corepressor-binding domain** (bound to SMRT, PDB 2ODD) [E3]. Functionally it is the paradigm of **core-binding-factor corruption**: it occupies CBF target sites with wild-type affinity but delivers NCOR/SMRT and HDAC instead of coactivators, converting CBF from an activator of myeloid differentiation into a repressor, and the NHR2 tetramer makes that repression multivalent and high-avidity. Full-length AML1-ETO alone does not cause leukaemia; the alternatively spliced **AML1-ETO9a** isoform, a C-terminally truncated 575-residue protein, causes rapid leukaemia in mice and co-expression with the full-length protein accelerates onset and blocks differentiation at a more immature stage [E2]. Clinically it is ~15% of all AML, 40-50% of FAB M2 [E2], and a **favourable-risk** paediatric AML with 5-year relapse-free survival of 61.9-87.4% depending on MRD-guided risk assignment and transplant [E4].
This is real experimental data — atoms placed by crystallography or cryo-EM, deposited by the people who did the experiment.
I have never read one of these pictures before
A protein is one long chain of amino acids that folds up. The ribbon traces that chain from one end to the other; it is not a wire, it is a simplification of where the backbone runs. Drag to rotate, scroll to zoom.
Domains are the stretches of chain that do a particular job, and they are what the coloured blocks above the picture mark out. Click one and the view flies to it. In this project the important question about any domain is usually whether the fusion still has it — the labels say lost where it does not.
Anything in yellow sticks is a bound small molecule, which is usually the drug.
What is kept and what is lost2 deeper
Kept from RUNX1 (5-prime partner): the N-terminal region including the entire Runt domain 12. This is the module that (i) contacts the TGYGGT consensus DNA and (ii) heterodimerises with CBFB. Both functions are intact in the fusion.
Lost from RUNX1: the C-terminal transactivation domain and the VWRPY / TLE-Groucho motif. That is the whole activating half of RUNX1.
Kept from RUNX1T1/ETO (3-prime partner): almost the entire ETO protein 2, comprising:
- NHR1 (nervy homology region 1, TAF110-like);
- NHR2 — the oligomerisation domain, which forms a tetramer; the PDB entry 1WQ6 states in its own title that the NHR2 tetramer structure is critical for AML1-ETO's activity 3;
- NHR3;
- NHR4 / MYND — binds the corepressors NCOR and SMRT; PDB 2ODD is the AML1-ETO MYND domain complexed with SMRT 3.
Lost from ETO: only the short N-terminus.
The arithmetic is the cleanest of any fusion in this beat. RUNX1 contributes only targeting (DNA + CBFB). ETO contributes only repression (corepressor docking) and avidity (tetramerisation). Every activating element of RUNX1 is deleted; every repressive element of ETO is kept.
How the CBF complex is corrupted, precisely (PI depth request)
The core-binding factor is a heterodimer: RUNX1 (the alpha subunit, CBFalpha2) provides DNA contact through its Runt domain; CBFB (the beta subunit) does not contact DNA but binds the Runt domain and allosterically increases its DNA affinity. The published structural description of the complex is a 'DNA-induced molecular clamp' (PDB 1H9D) — DNA binding and CBFB binding are cooperative, each stabilising the other 3.
The heterodimerisation interface itself (the surface the Queen needs for the hypothesis node): CBFB binds a face of the Runt domain on the opposite side from the DNA-contacting loops. That geometry is the reason the same Runt domain can simultaneously hold DNA and CBFB, and it is why the two binding events are allosterically coupled rather than competitive. Structures 1H9D, 1E50 and 1IO4 describe this interface from different angles; 1CMO is a solution-NMR structure of the isolated Runt domain with no CBFB chain and no DNA, and is listed only as a fold reference (see the correction section dated 2026-09-19); 1IO4 additionally places the Runt-CBFB heterodimer alongside a C/EBPbeta bZIP homodimer on the CSF1R promoter, i.e. CBF working combinatorially with a partner factor at a real myeloid enhancer 3.
What t(8;21) does to that complex — four distinct corruptions:
- Targeting is preserved. The fusion's Runt domain binds DNA and CBFB normally. So the fusion goes exactly where CBF goes. There is no neomorphic address change (contrast CBFA2T3::GLIS2 or TCF3::HLF, which import foreign specificities).
- The output is inverted. RUNX1's transactivation domain is replaced by ETO's corepressor-docking NHR4/MYND, so genes that CBF should activate are actively repressed 3. CBF's normal job is driving myeloid differentiation genes; the fusion silences them.
- Avidity is amplified. The NHR2 tetramer means one DNA-bound fusion brings three more with it, each carrying its own corepressor-binding surface. Repression becomes multivalent and much harder to out-compete than a monomeric repressor would be. The PDB entry's own framing is that this tetramer is critical for activity 3.
- Wild-type CBF is sequestered. Because the fusion retains the CBFB-binding surface, it competes with wild-type RUNX1 for the limited CBFB pool. This is the same competitive logic that CBFB::MYH11 exploits from the other side of the heterodimer (see fusion-cbfb-myh11), and it is why the two CBF fusions are usefully read as a matched pair attacking opposite subunits of the same dimer.
The comparative payoff. RUNX1::RUNX1T1 corrupts the alpha subunit; CBFB::MYH11 corrupts the beta subunit. Both produce favourable-risk CBF-AML. Both keep the heterodimerisation interface. But only CBFB::MYH11 has yielded a protein-protein-interaction inhibitor (AI-10-49), because in that fusion the pathological event is a quantifiable change in affinity at the interface that a small molecule can shift, whereas in AML1-ETO the interface is functionally normal and the pathology lives in the recruited corepressor. Same complex, same interface, different druggable step. That single contrast is the most useful thing in this node for a mechanism-class or hypothesis node.
AML1-ETO9a: the fusion needs a splice variant to be a leukaemia
One of the most important and under-appreciated facts about this fusion is that the canonical full-length product is not sufficient. Although full-length AML1-ETO (752 aa) alters gene expression and haematopoietic proliferation, its expression does not lead to the development of leukaemia in mouse models 2.
What does cause leukaemia is AML1-ETO9a: an alternatively spliced isoform that includes an extra ETO exon (exon 9a) and encodes a C-terminally truncated 575-residue protein. Expression of AML1-ETO9a alone leads to rapid development of leukaemia in a retroviral transduction-transplantation model, and co-expression of AML1-ETO with AML1-ETO9a produces substantially earlier AML onset and blocks myeloid differentiation at a more immature stage than either alone 2.
Three consequences worth carrying into other nodes:
- Splice isoforms of a fusion can be the actual driver. Any comparative programme that models 'the fusion' from a single canonical cDNA may be modelling the wrong protein. This is a concrete methodological warning for the whole beat.
- The truncation removes ETO's C-terminus, including NHR4/MYND. So the more leukaemogenic isoform has less corepressor-binding capacity, which complicates the simple 'corepressor recruitment is the mechanism' story and is an unresolved tension the graph should record rather than smooth over.
- Two isoforms cooperating is a different genetic architecture from one driver plus secondary mutations, and it may partly explain why t(8;21) AML needs relatively few cooperating lesions.
Clinical phenotype, age and prognosis
Disease: AML, classically FAB M2 with Auer rods and abnormal eosinophils; also rare M0, M1 and M4 cases 2. Frequently presents with extramedullary disease (myeloid sarcoma, skin, CNS), and extramedullary infiltration at diagnosis is an independent adverse factor in children 4.
Frequency: identified in 15% of all cases of AML, including 40-50% of the FAB M2 subtype 2. It is proportionally commoner in children and adolescents than in older adults.
Age: children, adolescents and young adults predominate; it is one of the commonest paediatric AML fusions.
Cytogenetically visible — unlike most fusions in this beat, t(8;21)(q22;q22) is a balanced translocation detectable on routine karyotype. That is worth noting explicitly: the cryptic fusions in this beat (ETV6::RUNX1, NUP98::NSD1, NUP98::KDM5A, CBFA2T3::GLIS2) were all discovered decades later precisely because karyotype could not see them.
Prognosis: favourable-risk, and MRD-stratified. In a paediatric cohort of 129 newly diagnosed t(8;21) AML patients stratified by RUNX1-RUNX1T1 transcript level after two consolidation cycles:
- high-risk patients treated with chemotherapy alone: 5-year relapse-free survival 61.9%;
- high-risk patients receiving allogeneic transplant: 5-year RFS 87.4% (p = 0.026), with 5-year OS 82.8% versus 71.4% (p = 0.26, not significant);
- extramedullary infiltration at diagnosis predicted relapse in high-risk patients (cumulative incidence 50% vs 18.4%, p = 0.004), and transplant improved RFS in that group;
- patients with a c-KIT mutation in the high-risk transplant group trended better than high-risk chemotherapy patients (82.9% vs 75%, p = 0.40, not significant) 4.
The honest reading: t(8;21) is a favourable-risk AML on average, but molecular MRD identifies a high-risk subset in whom transplant adds benefit, and KIT mutation and extramedullary disease are the two features that pull cases out of the favourable group.
Druggability: undrugged fusion, two genuine handles
Status: undrugged for the fusion itself, but this is a case where the disease is largely curable by other means and the co-mutation is targetable.
Why the fusion resists direct targeting:
- The Runt-DNA and Runt-CBFB surfaces are wild-type. Anything that blocks them hits normal CBF, which is required for definitive haematopoiesis. This is the identical constraint noted for ETV6::RUNX1, which also retains the Runt domain.
- The NHR4/MYND-corepressor interface is a protein-protein interaction shared with wild-type ETO family proteins and with the broader NCOR/SMRT machinery, used across the transcriptome.
- No enzyme active site anywhere. HDAC inhibition is the obvious inference from corepressor recruitment and has been tried extensively without a subtype-specific approval — the same dead end as for ETV6::RUNX1.
Handle 1: the NHR2 tetramer interface. This is the most interesting untapped target in the node. The tetramer is required for AML1-ETO activity 3, it has a solved structure (1WQ6), and — crucially — a tetramerisation interface is a defined, stoichiometric protein-protein interaction, unlike the interchangeable multivalent disorder of NUP98 fusions. Peptide and small-molecule NHR2 dimerisation inhibitors have been reported preclinically. Nothing is clinical. Because CBFA2T3 (ETO2) is a paralogue with the same NHR2 architecture and also appears as a paediatric AML fusion partner (see fusion-cbfa2t3-glis2), an NHR2 inhibitor would be a rare cross-fusion agent.
Handle 2: KIT. KIT mutations are frequent in CBF-AML and adverse; KIT is an approved-drug target. In the paediatric series above, KIT-mutant high-risk patients trended better with transplant 4. KIT inhibition (dasatinib, avapritinib) in CBF-AML has been studied clinically. As with FLT3 in NUP98::NSD1, this is co-mutation pharmacology, not driver-directed therapy.
What actually cures these children is chemotherapy plus MRD-guided transplant 4, and — in adults and increasingly in children — gemtuzumab ozogamicin, which CBF-AML responds to particularly well. The graph records that as an empirical, not mechanism-derived, therapeutic fact.
Correction 2026-09-19: 1CMO is not a clamp structure
Evidence item E3 and the PDB note previously listed 1CMO alongside 1H9D, 1E50 and 1IO4 as structures of the RUNX1 Runt domain with the CBFB core domain on DNA, i.e. as one of the entries describing the 'DNA-induced molecular clamp'. That is withdrawn.
Fetched from RCSB on 2026-09-19, 1CMO is IMMUNOGLOBULIN MOTIF DNA-RECOGNITION AND HETERODIMERIZATION FOR THE PEBP2/CBF RUNT-DOMAIN, experimental method SOLUTION NMR, with one polymer entity of 127 residues mapping to UniProt Q01196 (RUNX1), zero non-polymer entities. There is no CBFB chain and no DNA in the deposited coordinates. It is a structure of the isolated Runt domain in solution; it cannot evidence a DNA-induced heterodimeric clamp.
The clamp claim itself is unaffected - 1H9D, 1E50 and 1IO4 are genuine crystal structures of the Runt-CBFB(-DNA) assembly and carry it. What is withdrawn is the count and the method: the node previously implied four crystallographic views of the same assembly and there are three. The same error appears in fusion-cbfb-myh11#E5 and is corrected there.
This is the structural failure mode the brief for this beat names: a PDB id collected because it maps to the right protein, with the experimental method and the chain composition never re-read.
| gene5 | RUNX1 |
|---|---|
| gene3 | RUNX1T1 |
| cytoband | t(8;21)(q22;q22) |
| frequency note | 15% of all AML and 40-50% of FAB M2 [E2]; we record 45 as the midpoint of the stated 40-50% range. These are literature figures quoted in [E2]'s introduction rather than values measured in that study. |
| prognosis | Favourable-risk AML overall, but MRD-stratified. In 129 paediatric t(8;21) cases risk-assigned by RUNX1-RUNX1T1 transcript level after two consolidation cycles, high-risk patients had 5-year relapse-free survival of 61.9% with chemotherapy versus 87.4% with allogeneic transplant (p=0.026), and 5-year OS 71.4% versus 82.8% (p=0.26, non-significant). Extramedullary infiltration at diagnosis predicted relapse (50% vs 18.4%, p=0.004) [E4]. KIT mutation and extramedullary disease are the two features that pull cases out of the favourable group. |
| uniprot5 | Q01196 |
| uniprot3 | Q06455 |
| PDB note | No structure of the intact AML1-ETO protein exists, and none shows the Runt domain and the NHR2 tetramer in the same molecule. 1H9D / 1E50 / 1IO4 are the RUNX1 Runt domain with the CBFB core domain on DNA (1CMO, also listed, is a SOLUTION NMR structure of the Runt domain alone - no CBFB, no DNA - and cannot support the clamp statement) - the retained 5-prime targeting module and the 'DNA-induced molecular clamp' geometry the Queen needs for the heterodimerisation-interface hypothesis; 1IO4 additionally shows CBF acting combinatorially with a C/EBPbeta bZIP homodimer on the CSF1R promoter. 1WQ6 is the ETO NHR2 tetramer, described in its own primary citation as critical for AML1-ETO activity, and is the most promising untapped drug interface in this node. 2ODD is the AML1-ETO MYND domain bound to the corepressor SMRT. The assembled picture is a composite of fragments [E3]. |
| mechanism class note | The archetype of the class, and the cleanest example in this beat: targeting (Runt domain, DNA + CBFB) is fully preserved and wild-type, while the transcriptional output is inverted from activation to NCOR/SMRT-mediated repression, with the NHR2 tetramer amplifying avidity. No foreign DNA-binding specificity is imported, unlike CBFA2T3::GLIS2 or TCF3::HLF - and this fusion is correspondingly much less aggressive. |
| druggability class | undrugged |
| druggability note | The fusion is undrugged. Two genuine handles: (1) the NHR2 tetramerisation interface, which is required for activity, has a solved structure (1WQ6) and - unlike NUP98 FG-repeat disorder - is a defined stoichiometric interaction; an NHR2 inhibitor would also potentially hit CBFA2T3::GLIS2 through the paralogous domain [E3][E6]; (2) KIT, frequently co-mutated and an approved-drug target [E4]. Empirically, CBF-AML responds well to chemotherapy plus gemtuzumab ozogamicin, which is not mechanism-derived. |
| stage of hematopoiesis | Bone-marrow haematopoietic stem / early myeloid progenitor (CD34+), with differentiation arrest at the myeloblast-promyelocyte boundary producing FAB M2 morphology with Auer rods. The fusion is detectable in cord blood at roughly 100-fold the incidence of the corresponding leukaemia, indicating - as for ETV6::RUNX1 - a prenatal or early preleukaemic origin with a long latency requiring further hits |
| stage of hematopoiesis note | The cord-blood detection point comes from the same study cited for ETV6::RUNX1 in-utero origin (Mori et al. 2002, PMID 12048236), which screened for both TEL-AML1 and AML1-ETO; it is recorded here for the developmental argument but is not among this node's evidence items. |
| age peak | children, adolescents and young adults; proportionally commoner in paediatric than in older-adult AML |
| developmental order rank | 3 |
diseases
[ "pediatric AML (FAB M2 predominant)", "adult AML", "AML with myeloid sarcoma / extramedullary disease", "rare FAB M0, M1, M4" ]
frequency
{
"all_aml_pct": 15,
"fab_m2_aml_pct": 45
}breakpoints
[
{
"id": "bp-runx1-exon5-runx1t1-exon2",
"gene5_exon_last": 5,
"gene3_exon_first": 2,
"frequency_pct": 95,
"population": "pediatric and adult t(8;21) AML",
"domains_retained_5": [
"RUNX1 N-terminus",
"Runt domain (DNA binding + CBFB heterodimerisation)",
"nuclear matrix targeting signal"
],
"domains_lost_5": [
"RUNX1 transactivation domain",
"C-terminal VWRPY / TLE-Groucho motif",
"RUNX1 C-terminus"
],
"domains_retained_3": [
"NHR1 (TAF110-like)",
"NHR2 (oligomerisation domain - tetramerises; critical for activity)",
"NHR3",
"NHR4 / MYND domain (NCOR/SMRT corepressor binding)"
],
"domains_lost_3": [
"ETO N-terminus (short)"
],
"phenotype_notes": "The canonical full-length product is 752 amino acids: RUNX1 N-terminus including the DNA-binding domain plus almost the entire ETO protein [E2]. Exon numbers are convention labels; the reliable statement from [E1] and [E2] is the domain-level architecture. Note that full-length AML1-ETO alone does NOT produce leukaemia in mouse models [E2]."
},
{
"id": "bp-runx1-runx1t1-exon9a-aml1eto9a",
"gene5_exon_last": 5,
"gene3_exon_first": 2,
"frequency_pct": null,
"population": "t(8;21) AML (alternatively spliced isoform, co-expressed with full-length)",
"domains_retained_5": [
"RUNX1 N-terminus",
"Runt domain (DNA binding + CBFB heterodimerisation)"
],
"domains_lost_5": [
"RUNX1 transactivation domain",
"VWRPY motif"
],
"domains_retained_3": [
"NHR1",
"NHR2 (oligomerisation)"
],
"domains_lost_3": [
"NHR3",
"NHR4 / MYND corepressor-binding domain",
"ETO C-terminus"
],
"phenotype_notes": "AML1-ETO9a: an alternatively spliced isoform including ETO exon 9a, encoding a C-terminally truncated 575-residue protein. THIS is the isoform that causes rapid leukaemia in mice, and co-expression with the full-length protein accelerates onset and blocks differentiation at a more immature stage [E2]. Note the paradox the graph records rather than resolves: the MORE leukaemogenic isoform has LESS corepressor-binding capacity, because NHR4/MYND is truncated away.",
"frequency_pct_note": "Left null: this is a splice isoform co-expressed with the full-length transcript rather than a distinct genomic breakpoint, and we did not verify a published transcript-ratio distribution across patients."
}
]PDB IDS
[ "1H9D", "1E50", "1IO4", "1CMO", "1WQ6", "2ODD" ]
mechanism class
[ "tf-repression-corruption" ]
- Any agent aimed at the Runt-DNA or Runt-CBFB surface will inhibit wild-type RUNX1 and CBFB, which are required for definitive haematopoiesis - predictable on-target marrow failure. This is the same constraint that blocks ETV6::RUNX1, and it is why the NHR2 tetramer (present only in the fusion's ETO moiety) is the strategically better interface.
- HDAC inhibition is the obvious inference from NCOR/SMRT recruitment and has repeatedly failed to deliver a subtype-specific therapy; corepressor complexes are used across the transcriptome, so the therapeutic window is poor. The AML1-ETO9a paradox [E2] additionally suggests corepressor recruitment may not even be the essential activity.
- KIT co-mutation is adverse and the natural response is to add a KIT inhibitor, but KIT inhibition in CBF-AML is co-mutation pharmacology with the usual consequences: on-target resistance mutations, and KIT's essential roles in normal haematopoiesis, mast cells and germ cells.
- MRD-guided transplant is the current answer for the high-risk subset [E4], and transplant in a child carries graft-versus-host disease, infertility, endocrine failure and secondary malignancy. Because the comparison in [E4] was non-randomised and by treatment choice, the true benefit may be smaller than 87.4% versus 61.9% suggests, meaning some children may be transplanted for a gain that is partly selection artefact.
- The leukaemia has a prenatal or early preleukaemic reservoir detectable in cord blood at far above disease incidence (see the stage_of_hematopoiesis note), so as with ETV6::RUNX1 the fusion-positive founder clone can survive therapy and seed a genetically distinct relapse.
- Modelling risk: any preclinical programme that expresses only the canonical full-length AML1-ETO cDNA may be studying a protein that is not sufficient to cause the disease [E2]. Negative results from such models should not be trusted, and this is a general warning for every fusion in this beat where splice isoforms have not been catalogued.
- RUNX2 compensates for RUNX1 loss in this system, so a RUNX1-directed strategy in t(8;21) has a paralogue escape route already documented -- the same failure mode this project recorded for KDM4C in `hyp-paralogue-buffering-hides-dependencies`.
- Is the NHR2 tetramerisation interface a real drug target? It is required for activity, structurally defined (1WQ6) and stoichiometric rather than diffuse [E3], which makes it far more tractable than the NUP98 FG-repeat disorder. Peptide inhibitors have been reported preclinically but nothing is clinical. Because CBFA2T3/ETO2 carries the same domain and is itself a paediatric fusion partner [E6], an NHR2 inhibitor would be one of very few genuinely cross-fusion agents - worth a dedicated target node.
- Why does AML1-ETO9a, which LOSES the NHR4/MYND corepressor-binding domain, cause leukaemia when full-length AML1-ETO does not [E2]? If corepressor recruitment were the core mechanism, the truncated isoform should be less oncogenic, not more. Either MYND-mediated repression is not the essential activity, or the full-length protein carries a C-terminal restraint that the truncation removes. Resolving this would change how the whole tf-repression-corruption class is understood.
- Do human t(8;21) blasts express AML1-ETO9a at a consistent ratio to the full-length transcript, and does that ratio predict MRD kinetics or relapse? Given that MRD by RUNX1-RUNX1T1 transcript level is already the paediatric risk-stratification tool [E4], isoform-resolved MRD is a cheap, immediately clinical question.
- RUNX1::RUNX1T1 and CBFB::MYH11 attack opposite subunits of the same heterodimer and both give favourable-risk AML, yet only the beta-subunit fusion produced a PPI inhibitor [E5]. Is that because the alpha-subunit fusion's interface is functionally normal, or simply because nobody has run the equivalent screen? A direct attempt to find an AML1-ETO/CBFB interface modulator would settle it.
- Both this fusion and ETV6::RUNX1 retain a wild-type Runt domain and are detectable prenatally in cord blood, yet one gives myeloid and the other lymphoid disease. What determines that, given an identical DNA-binding module?
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
t(8;21)(q22;q22) juxtaposes 5-prime sequences of AML1/RUNX1 on chromosome 21 to 3-prime sequences of ETO on chromosome 8, producing a fusion transcript; AML1 shares 69% amino-acid identity with the Drosophila segmentation gene runt over the DNA-binding region.
Identification of breakpoints in t(8;21) acute myelogenous leukemia and isolation of a fusion transcript, AML1/ETO, with similarity to Drosophila segmentation gene, runt · Erickson P, Gao J, Chang KS, Look T, Whisenant E, Raimondi S, Lasher R, Trujillo J, Rowley J, Drabkin H · Blood 1992What this evidence cannot show
Nine t(8;21) cases analysed by restriction mapping and cDNA cloning; the protein product's function was inferred from the runt homology rather than measured, and no DOI is registered for this 1992 Blood article so the PubMed record is the citable anchor.
Evidence that argues against this (1)
- Detecting the fusion transcript is not detecting the disease, and this is the clearest published demonstration of it for t(8;21). Miyamoto et al. found AML1/ETO mRNA by RT-PCR in the marrow and/or blood of ALL 18 patients in continuous complete remission for 12-150 months (median 45) after chemotherapy or peripheral-blood stem-cell transplantation, and 51 of 2469 colonies (2.1%) grown from their clonogenic progenitors expressed it - across granulocyte-macrophage, mixed, erythroid AND megakaryocyte colonies - carrying the same X-inactivation allele as the diagnostic blasts, while constitutive haematopoiesis was polyclonal. Only the four allogeneic BMT recipients were negative. The translocation therefore sits in a multipotent progenitor that can persist benignly for over a decade in cured people; the fusion is a clonal marker, not a disease state. Miyamoto T et al. 1996
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
Full-length AML1-ETO is a 752-residue protein containing the RUNX1 N-terminus including its DNA-binding domain plus almost the entire ETO protein; t(8;21) occurs in 15% of all AML and 40-50% of FAB M2; full-length AML1-ETO expression does NOT cause leukaemia, whereas the alternatively spliced C-terminally truncated 575-residue AML1-ETO9a isoform causes rapid leukaemia in mice, and co-expression of both accelerates AML onset and blocks differentiation at a more immature stage.
A previously unidentified alternatively spliced isoform of t(8;21) transcript promotes leukemogenesis · Yan M, Kanbe E, Peterson LF, Boyapati A, Miao Y, Wang Y, Chen IM, Chen Z, Rowley JD, Willman CL, Zhang DE · Nat Med 2006What this evidence cannot show
The leukaemogenicity comparison is in a murine retroviral transduction-transplantation model with non-physiological expression levels, so the 'full-length does not cause leukaemia' statement is model-specific - other groups have produced leukaemia from full-length AML1-ETO with added cooperating mutations or different expression systems. The relative abundance of AML1-ETO9a versus full-length transcript in human patient blasts, and whether the ratio predicts anything clinically, is not established here.
Evidence that argues against this (1)
- The differentiation-block framing needs the native factor put back in. t(8;21) Kasumi-1 cells REQUIRE wild-type RUNX1: knockdown attenuates the mitotic checkpoint and causes apoptosis, knockdown of AML1-ETO in those cells rescues them, and an active RUNX1 allele is usually preserved in t(8;21) patients. The fusion and the native factor compete at common sites and the malignant state depends on the ratio. Ben-Ami O et al. 2013
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
The fusion retains the RUNX1 Runt domain, whose complex with CBFB on DNA functions as a DNA-induced molecular clamp (PDB 1H9D, 1E50, 1IO4; 1CMO is a solution-NMR structure of the isolated Runt domain, not of the clamp), and adds the ETO NHR2 oligomerisation domain, whose tetramer structure is critical for AML1-ETO activity (PDB 1WQ6), and the NHR4/MYND corepressor domain, solved in complex with SMRT (PDB 2ODD).
PDB entries 1H9D (AML1/CBF-beta/DNA complex, 'DNA-Induced Molecular Clamp'), 1IO4 (Runt-CBFbeta heterodimer with C/EBPbeta on the CSF1R promoter), 1WQ6 ('The tetramer structure of the Nervy homology two domain, NHR2, is critical for AML1/ETO's activity') and 2ODD ('Solution structure of the MYND domain from AML1-ETO complexed with SMRT') · RCSB Protein Data Bank · RCSB PDB 2006What this evidence cannot show
Verified by fetching each RCSB entry record. Every entry is an isolated domain or domain pair - there is no structure of the intact AML1-ETO protein, and no structure showing the Runt domain and the NHR2 tetramer in the same molecule, so the assembled picture is a composite model. The claim that the NHR2 tetramer is critical for activity is quoted from the entry's own primary-citation title and should ideally be traced to the functional data in that paper.
Evidence that argues against this (2)
- One of the four listed clamp structures is not a clamp structure. Fetched from RCSB on 2026-09-19, 1CMO is a SOLUTION NMR structure with a single 127-residue polymer entity mapping to UniProt Q01196 (RUNX1) and zero non-polymer entities: no CBFB chain, no DNA. It shows the isolated Runt domain in solution and cannot evidence a DNA-induced heterodimeric clamp. The clamp claim survives on 1H9D, 1E50 and 1IO4, which are genuine crystal structures of the assembly; what is withdrawn is the count and the implied method. The claim text and the PDB note have been corrected, and the same error in fusion-cbfb-myh11#E5 is corrected there. RCSB Protein Data Bank 1999
- The NHR2 oligomerisation interface has produced peptides and no drug-like molecule in nearly two decades, and the one clinically used agent anywhere that acts at a fusion oligomerisation module (arsenic at the PML RBCC) is escaped by point mutation at its binding surface with the oncoprotein intact. The NHR2 tetramer being structurally solved is not evidence that it is chemically addressable. Goto E et al. 2011
- E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
In 129 paediatric t(8;21) AML patients stratified by RUNX1-RUNX1T1 transcript level after two consolidation cycles, allogeneic transplant improved 5-year relapse-free survival in high-risk patients (87.4% vs 61.9% with chemotherapy, p=0.026; 5-year OS 82.8% vs 71.4%, p=0.26); extramedullary infiltration at diagnosis predicted relapse (50% vs 18.4%, p=0.004); and c-KIT-mutant high-risk patients trended better with transplant (82.9% vs 75%, p=0.40).
Allogeneic hematopoietic stem cell transplantation can improve the prognosis of high-risk pediatric t(8;21) acute myeloid leukemia in first remission based on MRD-guided treatment · Hu GH, Cheng YF, Lu AD, Wang Y, Zuo YX, Yan CH, Wu J, Sun YQ, Suo P, Chen YH, Chen H, Jia YP, Liu KY, Han W, Xu LP, Zhang LP, Huang XJ · BMC Cancer 2020What this evidence cannot show
Not randomised: transplant versus chemotherapy in the high-risk group was by treatment choice, so selection bias is substantial and the 87.4% versus 61.9% difference cannot be attributed to transplant with confidence. Single-centre Chinese cohort; the KIT subgroup comparison is explicitly non-significant and underpowered. The MRD threshold used to define high risk is protocol-specific and not internationally standardised.
Evidence that argues against this (1)
- The c-KIT limb does not replicate, in a larger series from the same country. Qin et al. screened 351 core-binding-factor AML patients at diagnosis for c-KIT exon 17 and exon 8 mutations and followed 250: 36.5% were mutated, and c-KIT was an independent adverse factor for relapse, disease-free and overall survival in ADULT t(8;21) (all p<=0.016) but showed no significant effect in PAEDIATRIC t(8;21) or in adult inv(16) (all p>0.05). If c-KIT carries no prognostic weight in children with t(8;21), a 'c-KIT-mutant high-risk' subgroup trending toward transplant benefit at 82.9% versus 75% (p=0.40) in a 129-patient cohort is describing noise. The transplant comparison itself was not randomised: allocation to transplant requires surviving to transplant, and in the entry's own numbers the relapse-free survival gap (87.4% vs 61.9%, p=0.026) does not carry through to overall survival (82.8% vs 71.4%, p=0.26) - the signature of selection rather than of a treatment effect. Qin YZ et al. 2014
- E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
CBFB::MYH11, the fusion that corrupts the OTHER subunit of the same core-binding-factor heterodimer, outcompetes wild-type CBFB for binding to RUNX1 and has yielded a protein-protein-interaction inhibitor (AI-10-49) that disrupts the fusion-RUNX1 interaction and restores RUNX1 transcriptional activity - demonstrating that the CBF interface is druggable in principle when the pathology is an altered affinity at that interface.
Chemical biology. A small-molecule inhibitor of the aberrant transcription factor CBFbeta-SMMHC delays leukemia in mice · Illendula A, Pulikkan JA, Zong H, Grembecka J, Xue L, Sen S, Zhou Y, Boulton A, Kuntimaddi A, Gao Y, Rajewski RA, Guzman ML, Castilla LH, Bushweller JH · Science 2015What this evidence cannot show
This is evidence about a DIFFERENT fusion (CBFB::MYH11), cited here for the comparative argument about the CBF interface. It is preclinical: mouse survival delay plus selective cell death in primary patient blasts, no clinical trial data, and AI-10-49 has not advanced to an approved agent. The inference that no analogous approach works for AML1-ETO because its interface is functionally normal is our reasoning, not a published result.
Evidence that argues against this (1)
- The AI-10-49 precedent is weaker as evidence for interface druggability than it reads. A ClinicalTrials.gov query in September 2026 finds no registered interventional study of any CBFbeta-SMMHC:RUNX1 inhibitor, eleven years after publication. 'Druggable in principle' has not converted to a trial. US National Library of Medicine 2026
- E6strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
CBFA2T3/ETO2, a paralogue of RUNX1T1/ETO with the same NHR2 and MYND architecture, is itself a recurrent paediatric AML fusion partner (in CBFA2T3::GLIS2), so the ETO-family oligomerisation and corepressor modules appear in at least two distinct paediatric leukaemia fusions.
An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia · Gruber TA, Larson Gedman A, Zhang J, Koss CS, Marada S, Ta HQ, Chen SC, Su X, Ogden SK, Dang J, Wu G, Gupta V, Andersson AK, Pounds S, Shi L, Easton J, et al., Mardis ER, Wilson RK, Downing JR · Cancer Cell 2012What this evidence cannot show
Cited for the paralogue relationship and the existence of a second ETO-family paediatric fusion, not for any statement about t(8;21). Whether CBFA2T3::GLIS2 actually tetramerises through NHR2 as AML1-ETO does is a homology inference and has not, to our knowledge, been demonstrated.
Evidence that argues against this (1)
- The same modules are core machinery in normal blood, which changes what 'appears in two paediatric fusions' licenses. Goardon et al. identified ETO2/CBFA2T3 as a component of the TAL-1/SCL complex in erythroid cells, recruited through E2A/HEB alongside GATA-1, LMO2 and Ldb1; ETO2 actively represses erythroid TAL-1 target genes and governs the expansion of erythroid progenitors, and a change in ETO2 stoichiometry WITHIN that complex is what licenses terminal erythroid maturation, including induction of Gfi-1b and p21(Cip). An oligomerisation-and-corepressor module shared by two leukaemia fusions and by the normal erythroid master complex is a recurrence of physiology, not a leukaemia-specific signature; a drug against it should be expected to hit erythro-megakaryopoiesis, which is exactly the lineage these two fusions arise in. Goardon N et al. 2006
- E7strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
t(8;21) cells require native RUNX1 for survival, and RUNX1 is required for AML1-ETO cell survival through BCL2 with RUNX2 able to compensate.
Transcription factor RUNX1 promotes survival of acute myeloid leukemia cells. · Goyama S, Schibler J, Cunningham L, et al. · Journal of Clinical Investigation 2013What this evidence cannot show
Abstract only. Human cord blood transduction and mouse genetics; RUNX1 overexpression conversely inhibits normal cord blood growth, so the effect is dose-dependent and no therapeutic window is demonstrated. Concordant with PMID 24055056.
Evidence that argues against this (1)
- The requirement is not specific to this fusion, which turns a putative vulnerability into an essentiality confound. In the very paper cited, a level of RUNX1 activity was required for the growth of MLL-AF9 cells as well as AML1-ETO cells; combined Runx1/Cbfb loss inhibited MLL-AF9 leukaemia development in mice; and the BCL2-mediated survival effect was demonstrated in MLL-fusion leukaemia. The same work shows RUNX1 overexpression INHIBITS normal cord-blood cell growth by inducing myeloid differentiation, so the dependency is dose- and context-dependent in both directions. RUNX1 dependence therefore spans at least two unrelated fusion classes plus a dose window in normal cells; read as a t(8;21)-selective target it is the lineage-essentiality confound this graph tracks elsewhere. Goyama S et al. 2013
5-prime partner in RUNX1::RUNX1T1, t(8;21); same Runt domain, opposite orientation
Class correction (Ben-Ami 2013, PMID 24055056; Goyama 2013, PMID 23979164): 'dominant negative' is withdrawn for the core-binding-factor members. t(8;21) and inv(16) cells REQUIRE native RUNX1 -- knockdown kills them, AML1-ETO knockdown rescues, an active RUNX1 allele is preserved in patients -- so the pathology is a maintained balance, and both source papers propose inhibiting rather than restoring RUNX1.
Published instance of the paralogue-buffering failure mode inside core-binding-factor disease (Goyama 2013, PMID 23979164): RUNX2 compensates for RUNX1 loss in AML1-ETO and MLL-AF9 cells, so a single-gene CRISPR score understates the dependency.
Delivery-assay artefact (Vives 2003, PMID 12678851): apparent energy-independent TAT entry came from fixation redistribution and ionic surface binding; uptake is endocytic, so a TAT-NHR2 competitor is largely endosomal, not nucleoplasmic.
Delivery artefact in the NHR2 peptide evidence (Vives 2003, PMID 12678851): apparent energy-independent TAT entry came from fixation redistribution and surface ionic binding; uptake is endocytic.
Marker-versus-disease bound (Miyamoto 1996, PMID 8639850): AML1/ETO transcripts persisted in all 18 t(8;21) patients in remission for 12-150 months, in 2.1% of clonogenic colonies across four lineages, so the fusion transcript is a clonal marker rather than a disease state.
- related to →Nobody needs to enrol anyone: the PTH question is a regression on data that already exists
Subgroup replication failure (Qin 2014, PMID 25449688): in 351 CBF-AML patients c-KIT mutation was adverse only in ADULT t(8;21) and had no significant effect in paediatric t(8;21) (p>0.05), undercutting the 129-patient c-KIT/transplant subgroup.
Physiology confound (Goardon 2006, PMID 16407974): ETO2/CBFA2T3 is a core component of the normal erythroid TAL-1/SCL complex whose stoichiometry gates terminal maturation, so the shared ETO module is recurrent physiology, not a leukaemia-specific signature.
Essentiality confound (Goyama 2013, PMID 23979164): RUNX1 is also required for MLL-AF9 cell growth and for MLL-AF9 leukaemia development in mice, so native-RUNX1 dependence is not a t(8;21)-selective vulnerability.
- related to →Dataset: PDB and AlphaFold - the structural census, including the two absences that shape every plan
Structural correction (RCSB 1CMO, fetched 2026-09-19): 1CMO is a SOLUTION NMR structure of a single 127-residue RUNX1 Runt domain with no CBFB and no DNA, so it cannot evidence the DNA-induced clamp. Entry corrected.
significantly worse outcomes when EZH2 overexpression co-occurs
same protein, opposite role: 5' partner of a different fusion, and a target-programme node in KMT2A-r
- analogous to →CBFB::MYH11 (CBFbeta-SMMHC), inv(16)(p13;q22)
THE TWO CORE-BINDING-FACTOR LEUKAEMIAS, disrupting the same transcription factor complex from its two subunits. The canonical example in this graph of one complex broken two ways giving one disease class, which is the comparison the KMT2A partner families are measured against.
reference domain coordinates for the RUNX1T1 side of this fusion
RUNX1::ETO converges on the same metabolic enzyme in a RUNX1-dependent manner
- ← related toKMT2A::MAML2, inv(11)(q21q23) - a therapy-related fusion that also causes a solid tumour
one reported patient developed KMT2A::MAML2 T-lymphoblastic lymphoma after RUNX1::RUNX1T1 AML and myeloid sarcoma
RUNX1::RUNX1T1-TurboID labelled nuclear repressor complexes
the family whose NHR2 tetramer has the only small-molecule oncogenic-oligomer disruptor
- analogous to →KMT2A::AFF1 (MLL-AF4), t(4;11)(q21;q23)
partner-contributed self-association module as the obligate, mutation-resistant target - established in one family, hypothesised in the other
RUNX1 K43 acetylation in the retained 5 prime portion
CROSS-FAMILY (PI dimension 5): GFI1's subnuclear partner ETO/MTG8 is RUNX1T1, the 3' partner of t(8;21); GFI1's only compartment is one it shares with a different fusion family's partner protein (Q89 2026-09-21)
AML1-ETO upregulates Zeb2 in the pre-leukemic HSC compartment; Zeb2 knockdown delays leukemia onset