iALL-IRX1 — the HOXA-negative, IRX1-high state of infant KMT2A::AFF1 ALL
About half of babies with this leukaemia have cells in a different state: the HOXA genes are off and IRX1 is on instead. These children are diagnosed younger and do worse, and almost nothing in the lab models this half.
The same thing, for a scientist
One of two transcriptional states of infant t(4;11)/KMT2A::AFF1 ALL, defined by **absence of the HOXA signature with reciprocal IRX1 overexpression** [E1]. Clinically it is the adverse half: higher relapse rate, worse outcome, and diagnosis at a younger age (the age difference did not reach significance in the cohort tested) [E1][E2]. Its transcriptome is enriched for **MYC targets, oxidative phosphorylation, G2M checkpoint, E2F targets, MTORC1 signalling, IL2/STAT5 and late oestrogen response** — a proliferative profile — and depleted for the interferon-gamma/allograft-rejection immune signature that marks iALL-HOXA9 [E1]. It expresses **less PROM1 (CD133)** than iALL-HOXA9 while CSPG4 (NG2) is comparable [E1]. This beat adds the first chromatin description: in the HOXA-dead primary states the IRX1 locus carries the oncoprotein, ENL and H3K4me3 while HOXA9/HOXA10 carry none of the three [E3].
What state it is, and what is not known about it
The cell of origin is genuinely open. Symeonidou argues for a developmentally earlier cell than iALL-HOXA9, because IRX1 is mesodermal in mouse gastrulation and barely detectable in haematopoietic scRNA-seq, and because MLL-AF4 has been reported in bone-marrow mesenchymal stromal cells of infant patients 1. Nagel's TALE-code says the opposite — IRX1 is a normal pro-B gene 4. The contradiction is unresolved and is recorded in dispute-is-irx1-expressed-in-normal-b-cell-development. Until it is settled, "developmentally earlier" is a hypothesis this graph should not repeat as fact.
The chromatin state, measured here for the first time
In p318 and p454 — the two deep, HOXA-dead primary states — the oncoprotein sits at IRX1 (2.7-6.4x mean promoter at the gene body), ENL at 4.4-6.5x, H3K4me3 at 0.71-0.97x, while HOXA9/HOXA10 carry H3K4me3 at 0.004-0.068x and ENL at 0.000-0.109x 3. Notably the IRX1 H3K4me3 is only about an average promoter: this is not a hyper-active locus, it is an ordinary active one in a cell where the alternative is dead.
Crucially, HOXA-negative does not imply IRX1-positive. TB920488 is HOXA-low and IRX1-zero at adequate depth. So the chromatin state described here is one of at least two ways to be HOXA-negative 3.
Why it is unmodelled, and why that is the practical problem
SEM — the line on which most of what is known about t(4;11) rests — is iALL-HOXA9, and has zero AFF1 signal at IRX1 3. Symeonidou calls explicitly for models mirroring iALL-IRX1 1 and Kühn had to engineer IRX1 into SEM by transgene to study it 2. So the subgroup with the worse prognosis has effectively no preclinical model, and every therapeutic optimised on existing models was optimised against the better-prognosis state.
| location | bone marrow; cell of origin disputed (mesoderm-proximal vs pro-B) |
|---|---|
| prognosis | adverse: higher relapse rate, worse outcome, younger at diagnosis (age difference not statistically significant in the cohort tested) |
| model systems | none; SEM and standard mouse models are iALL-HOXA9 |
markers
[ "IRX1 high", "HOXA9/HOXA10 low or absent", "PROM1/CD133 lower than iALL-HOXA9" ]
enriched programs
[ "MYC targets", "oxidative phosphorylation", "G2M checkpoint", "E2F targets", "MTORC1 signalling", "IL2/STAT5 signalling", "oestrogen response late" ]
depleted programs
[ "interferon gamma response", "allograft rejection" ]
chromatin q145
{
"irx1_gene_kmt2a_n": [
6.076,
2.684,
6.35
],
"irx1_h3k4me3": [
0.705,
0.969
],
"hoxa9_h3k4me3": [
0.004,
0.008
]
}- Menin inhibitors are assessed pharmacodynamically by HOXA9/MEIS1 collapse. In a blast where HOXA is already epigenetically dead there is no such readout, so the drug could be working or failing and the biomarker would look the same.
- CD133-directed CAR-T, proposed for KMT2A-r ALL, has lower target expression in exactly this adverse subgroup.
- If the IRX1 state is more proliferative (MYC, E2F, G2M) it may respond better to cytotoxic chemotherapy in the short term while relapsing more - which is the clinical picture described.
- Is iALL-IRX1 a cell of origin, a differentiation stage, or an acquired state? Nothing distinguishes these and the three imply different therapies.
- TB920488 is HOXA-low and IRX1-negative. Is there a third state, and what is its oncoprotein address?
- Do iALL-IRX1 blasts respond to menin inhibition? No KMT2A::AFF1 sample in this deposit is menin-inhibitor treated and no trial reports the subgroup.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
iALL-IRX1 is defined by absent HOXA signature with reciprocal IRX1 overexpression, is enriched for MYC/OxPhos/G2M/E2F/MTORC1/IL2-STAT5 programs, expresses less PROM1, has worse outcome, and lacks a representative model line.
HOXA9/IRX1 expression pattern defines two subgroups of infant MLL-AF4-driven acute lymphoblastic leukemia · Symeonidou V, Ottersbach K · Exp Hematol 2021What this evidence cannot show
Reanalysis of two existing RNA-seq cohorts (n = 22 and n = 27 patients), entirely transcriptional. The younger age at diagnosis did NOT reach statistical significance. GSEA hallmark enrichments at these n are hypothesis-generating. Full text fetched and read this cycle.
Evidence that argues against this (1)
- Nagel & Meyer's survey of TALE-class genes in BCP-ALL assigns MEIS1 to KMT2A fusions and IRX2/IRX3 to TCF3 and ETV6 fusions respectively, and reports no IRX1-KMT2A association at all. Nagel S et al. 2022
- E2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
The HOXA-low/IRX1-high t(4;11) subgroup was independently verified by a second group and correlated with a three-times higher risk of relapse; IRX1 had to be introduced into SEM by transgene to be studied.
The IRX1/HOXA connection: insights into a novel t(4;11)-specific cancer mechanism · Kuhn A, Loscher D, Marschalek R · Oncotarget 2016What this evidence cannot show
The relapse-risk figure is reported by Kuhn as a summary of prior work rather than measured in that paper, so it is a second-hand quantity here. The mechanistic work is HEK293T with a single SEM transgene line.
Evidence that argues against this (1)
- A three-fold relapse risk quoted second-hand without the original cohort's n or confidence interval is not a quantity this graph should propagate as precise. Symeonidou V et al. 2021
- E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
In the HOXA-dead primary states the IRX1 locus carries oncoprotein, ENL and H3K4me3 while HOXA9/HOXA10 carry none; but one HOXA-low patient (TB920488) is also IRX1-negative at adequate depth.
q145 re-analysis of GSE252378: IRX1 and HOXA oncoprotein occupancy across seven KMT2A::AFF1 patients (analyses/q145-irx1-in-hoxa-negative-infants) · Iqbal Lab oncofusion knowledge graph, beat q145 · internal analysis over deposited GSE252378 bigWigs 2026What this evidence cannot show
Seven patients, no RNA-seq in the deposit, so no patient can be assigned to the published EXPRESSION subgroup by the published criterion. Activity tracks exist for only three sample records. Every number is a WITHIN-SAMPLE share: an interval's mean coverage divided by that same library's mean promoter coverage, so 1.0 = an average promoter in that library. **GSE252378 has no spike-in and no drug arm**, so no between-sample absolute statement is licensed; the only cross-sample quantity used is a ratio of two loci measured inside one library, where the unknown per-library scale cancels.
Evidence that argues against this (1)
- One deposit, one lab, one assay; seven patients, no RNA-seq. A second cohort profiled by a different group could reverse any of this. Janssens DH et al. 2024
- E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
IRX1 and MEIS1 are expressed exclusively in pro-B-cells in normal B-cell development.
Normal and Aberrant TALE-Class Homeobox Gene Activities in Pro-B-Cells and B-Cell Precursor Acute Lymphoblastic Leukemia · Nagel S, Meyer C · Int J Mol Sci 2022What this evidence cannot show
Contradicts E1's scRNA-seq observation and Kuhn's statement. Included here because the cell-of-origin claim for this state depends on which is right, and the graph should not choose silently.
Evidence that argues against this (1)
- Symeonidou's interrogation of adult bone marrow and fetal liver scRNA-seq found very little IRX1 in the haematopoietic system, directly opposing this. Symeonidou V et al. 2021
first chromatin description of the state
- ← part ofIRX1 — Iroquois homeobox 1, the gene that names the HOXA-negative half of infant t(4;11) ALL
IRX1 names and defines the state
one of two states of infant KMT2A::AFF1 ALL, the adverse one
- arises in →KMT2A::AFF1 (MLL-AF4), t(4;11)(q21;q23)
a state of t(4;11) blasts
- related to →The differentiation block — what it actually is, operationally, in KMT2A::AFF1 leukaemia
an alternative homeobox program in a blocked progenitor
- related to →iALL-HOXA9 — the HOXA-high state of infant KMT2A::AFF1 ALL, and the one everything is modelled on
the two states of the published split; anti-correlated but NOT mutually exclusive at chromatin
- ← supportsIn the HOXA-dead infant states IRX1 carries H3K4me3 and ENL while HOXA9/HOXA10 carry neither
the chromatin signature of the state
SEM cannot model the IRX1 state; the adverse subgroup has no model line
the switched AML retains the IRX1 address
- ← related toIs IRX1 expressed in normal blood at all? Two of the three papers say no, one says exclusively yes
decides whether the state is an ectopic or a retained program
- ← related toIRX1 is a second address for the KMT2A::AFF1 oncoprotein, not merely the gene that turns HOXA off
proposes the mechanism of the state
the chromatin composition of the adverse state
whether the state is a clone or a cell-intrinsic program
the iALL-IRX1 subgroup is 43.8% of KMT2A::AFF1 infant ALL by this count
19 of 48 KMT2A::AFF1 infant ALL cases are IRX1-only, independently re-derived
the iALL-IRX1 arm is PROM1-depleted: 11 of 13 PROM1-negative AFF1 cases are IRX1-positive