Myeloid-primed blasts are already present at diagnosis of KMT2A-rearranged B-ALL and expand under immunotherapy — the single-cell demonstration this graph recorded as not existing
also called preexisting lymphomyeloid primed progenitors · myeloid blasts at B-ALL diagnosis · competitive release, shown at single-cell resolution · lineage switch is selection not transdifferentiation
When a baby's B-cell leukaemia turns into a myeloid leukaemia after antibody or CAR-T treatment, the myeloid cells were not created by the treatment — reading single cells shows they were already sitting in the marrow on the day of diagnosis, in small numbers, and the treatment simply cleared away their competition. In the two patients where this was tracked before and after the switch, the myeloid-capable cells were found in the original diagnostic sample both times.
The same thing, for a scientist
This graph's hypothesis `hyp-lineage-switch-is-competitive-release-of-preexisting-clone` states in its own summary that **'no single-cell demonstration exists in KMT2A-rearranged disease'**. It does exist, and has since 2022. Chen et al. profiled 18 treatment-naive KMT2A-r patients clinically diagnosed as B-cell precursor ALL by scRNA-seq and scATAC-seq and report that *'several had substantial blast subpopulations that mapped to myeloid fates'*; for the two patients whose leukaemia subsequently underwent lineage switch, *'in both patients, we identified a preexisting blast population with myeloid potential before lineage switch in our scRNA-Seq and scATAC-Seq data, which expanded under the pressure of immunotherapy'* [E1]. That is the competitive-release model observed directly rather than reconstructed phylogenetically, in the index disease, at the resolution the claim requires. The magnitude is age-dependent and quantified: developmental heterogeneity scored by **Shannon entropy was significantly higher in blasts from patients under 6 months at the transcriptomic level (P = .007)**, with the chromatin-accessibility arm in the same direction but **not significant (P = .07)**, and *'a significantly higher proportion of cells aberrantly coexpressed B and myeloid lineage genes in younger infants'* [E1]. **Bulk data cannot make this observation in principle**: co-expression of B and myeloid lineage genes *in the same cell* is the entire claim, and a bulk transcriptome of a mixed population produces the identical profile whether one cell is bi-lineage or two cells are each uni-lineage. The competing account is not eliminated — epigenetic reprogramming of a multipotent precursor remains supported in the MLL/AF4 switch literature [E2] — but the two are no longer symmetric, because only one of them has been seen cell by cell.
The correction this entry makes, stated plainly
hyp-lineage-switch-is-competitive-release-of-preexisting-clone is a good hypothesis, carefully evidenced from phylogeny (E2 there, PMID 37474833), shared breakpoints (E3 there, PMID 35839448) and a ClonoSEQ immunoglobulin archaeology case (E4 there, PMID 33749383), and it closes with an honest statement of what is missing: no single-cell demonstration exists in KMT2A-rearranged disease.
That statement is wrong, and PMID 34864916 is the paper that makes it wrong. The hypothesis entry is not mine and I have not edited it; the correction is reported in this beat's hand-back to the standard the brief requires — the entry id, the exact sentence, what it should say, and the citation, read at the abstract and at the PMC full text (Results, lineage-switch section), not from recall.
The reason the gap survived is mechanical and is written up separately: ana-the-citation-index-reads-prose-not-the-pmid-field. A corpus-wide instrument built to answer what does this project cite could not see the pmid field, reported 8 single-cell papers where there are 18, and this paper is cited zero times here.
What competitive release predicts that transdifferentiation does not
The two models are distinguishable and the distinguishing tests are cheap on existing samples:
| competitive release of a pre-existing clone | therapy-induced reprogramming | |
|---|---|---|
| myeloid-capable cell at diagnosis | required | not required |
| switch after a chemotherapy-only relapse | possible | should be rarer |
| switch from documented MRD-negative remission | expected (the surviving clone is not B-lineage, so a B-lineage MRD panel does not see it) | requires a cell to be reprogrammed from nothing detectable |
| abundance at diagnosis | should predict switch risk | should not |
The last row is the one worth an experiment, and the single-cell data now makes the predictor concrete: the proportion of diagnostic blasts that map to myeloid fates, or that co-express B and myeloid lineage genes. That is measurable from a diagnostic aspirate that is already taken, and this corpus's clinical entries record that 64.3% of post-immunotherapy lineage switch cases carry a KMT2A rearrangement, at a median 1.5 months from therapy, most often from documented MRD-negative remission — a timing that fits selection far better than it fits reprogramming.
Why the MRD panel is blind to exactly this cell, and what that costs
A flow MRD panel for B-ALL gates on the B-lymphoblast immunophenotype. A blast that maps to a myeloid fate, or an HSPC-like CD34+CD19− blast 1, is outside the gate by construction. So the sequence deep MRD-negative remission → lineage switch at a median of 1.5 months is not a paradox; it is the expected reading of an assay that was never asked about those cells.
This corpus already has concept-mrd-flow-cytometry-and-the-lineage-switch-blind-spot for the general point. What the single-cell data adds is that the blind cell has now been counted at diagnosis, so the blind spot has a measurable size per patient rather than being an argument.
The competing account, which is not refuted
Tirtakusuma et al. remains the strongest mechanistic alternative and is already cited 11 times in this corpus. Myeloid relapses after lineage switch in MLL/AF4 leukaemia share oncogene fusion breakpoints with their matched lymphoid presentations — so the clonal continuity is not in dispute — and that study attributes the switch to epigenetic-regulator gene lesions directing the fate of a multipotent precursor of origin, with CHD4 reprogramming as the worked mechanism 2.
Shared breakpoints are compatible with both models. What separates them is whether the myeloid-fated cell existed before the pressure or was made by it, and the single-cell answer — in two patients — is that it existed. Two patients is two patients; that is the honest size of the direct evidence, and it is why this entry is strong and not established. The two accounts are also not exclusive: a pre-existing multipotent cell can be pushed further by an acquired epigenetic lesion, and the deposited data (GSE132396/GSE130142 for E2, HTAN for E1) would support a joint reanalysis.
Epigenetics inside the mechanism
The pre-existing population was identified in both the scRNA-seq and the scATAC-seq modalities 1, which matters: a myeloid-primed chromatin state in a cell whose transcriptome is still B-lineage is priming, and it is the thing bulk ATAC on a sorted B-lymphoblast population would average away.
The entropy result is asymmetric between modalities and the entry should not smooth that over: transcriptome P = .007, accessibility P = .07 1. Read strictly, the significant claim is about transcriptional heterogeneity; the chromatin arm is a consistent trend at n = 18 and no more. Anyone quoting 'increased plasticity at both levels' from the abstract is quoting past the statistics in the paper's own figure.
| mechanism class | clonal selection / competitive release |
|---|---|
| system | human primary KMT2A-rearranged ALL, 18 treatment-naive patients plus 2 with paired pre-/post-lineage-switch samples |
| shown for fusion | KMT2A-rearranged ALL as a class (mixed partners, 18 infants + 7 older in the parent cohort); NOT resolved to KMT2A::AFF1. The competing epigenetic-reprogramming account (E2) IS in MLL/AF4. |
assays
[ "scRNA-seq", "scATAC-seq", "snmC-seq2" ]
quantification
{
"metric": "Shannon entropy of developmental heterogeneity per patient",
"comparison": "blasts from patients <6 months vs older",
"transcriptome_p": 0.007,
"chromatin_accessibility_p": 0.07,
"note": "the accessibility arm does not reach significance; the abstract's 'significantly increased lineage plasticity' is carried by the transcriptomic arm"
}hspc like markers
[ "CD34+", "CD19-", "GATA2", "HMGA2" ]
immunosuppressive ligand receptor pairs
[ "KIRs – MHC class I", "TGFB – TGFBR" ]
- If the myeloid-capable cell is present at diagnosis, then CD19-directed therapy does not fail because it stops working — it fails because it succeeded on the wrong target set. Adding a second B-lineage antigen (CD22) does nothing about this; only an antigen the myeloid-primed cell also carries, or a fusion-directed agent, addresses it.
- This is an argument FOR a menin inhibitor being used earlier rather than later, since it targets the fusion's programme in whatever lineage the cell wears — but it is also a warning, because the same corpus records lineage switch under menin inhibition as a documented resistance route (resistance-lineage-switch-under-menin-inhibition). A fusion-directed agent removes the lineage-specific escape and may not remove the escape.
- A diagnostic assay for myeloid-primed blast abundance would create a new way to be wrong: a patient scored low-risk for switch who switches anyway, treated less aggressively on the strength of a single-cell fraction measured from one aspirate, with all of that fraction's sampling variance unmeasured. Before it stratifies anyone it needs a technical-replicate study on paired aspirates.
- Does the diagnostic abundance of myeloid-mapping blasts predict which patients switch? Two patients switched in this cohort and both had the population; the question needs the patients who did NOT switch as the denominator, and the cohort is large enough to ask.
- Do the myeloid-primed diagnostic blasts carry the fusion transcript, or are they a fusion-negative normal progenitor contaminating the blast gate? This is answerable in the deposited data by scoring fusion-spanning reads per cell and it decides whether the model is selection of a leukaemic clone or outgrowth of normal myelopoiesis after B-cell ablation.
- The chromatin-accessibility entropy P = .07 at n = 18. What n would resolve it, and does any later cohort (the enhancer-heterogeneity snATAC set, GSE297908) supply it?
- Are the myeloid-primed cells and the HSPC-like CD34+CD19- cells the same population, overlapping populations, or distinct? The paper reports both; this entry and cell-state-hspc-like-blast-fraction currently treat them as related but not identical, and the deposited data settles it.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
In 18 treatment-naive KMT2A-rearranged patients clinically diagnosed as B-cell precursor ALL, several had substantial blast subpopulations mapping to myeloid fates; in both patients who later underwent lineage switch, a pre-existing blast population with myeloid potential was identified in the pre-switch scRNA-seq and scATAC-seq data and expanded under immunotherapy pressure. Developmental heterogeneity by Shannon entropy was higher in blasts from patients under 6 months (transcriptome P = .007; chromatin accessibility P = .07), and a significantly higher proportion of cells aberrantly co-expressed B and myeloid lineage genes in younger infants. The HSPC-like blasts are CD34+CD19− and express GATA2 and HMGA2.
Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell-like blasts in KMT2A-rearranged leukemia · Chen C, Yu W, Alikarami F, et al. (senior author Tan K) · Blood 2022What this evidence cannot show
The direct lineage-switch demonstration rests on TWO patients with paired longitudinal samples. The cohort is KMT2A-rearranged ALL with mixed partner genes, not KMT2A::AFF1 specifically, so the entry must not be read as an index-fusion result. The chromatin-accessibility entropy difference is NOT significant (P = .07) and the abstract's phrasing is broader than the figure supports. The paper does not report what fraction of patients had myeloid-mapping subpopulations or at what frequency — 'several had substantial blast subpopulations' is the verbatim precision available, and I read the PMC full text to confirm no number is given. No functional assay (xenograft, colony) was applied to the myeloid-primed population to prove it is the cell that gives rise to the AML; the inference is transcriptomic and epigenomic.
Evidence that argues against this (1)
- Epigenetic reprogramming of a multipotent precursor remains a supported and non-exclusive alternative in the MLL/AF4 switch literature, with shared fusion breakpoints establishing clonal continuity without establishing that the myeloid-fated cell pre-existed the therapy. Tirtakusuma R et al. 2022
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Myeloid relapses after lineage switch in MLL/AF4 leukaemia share oncogene fusion breakpoints with their matched lymphoid presentations and arise from a range of differentiation stages, with epigenetic regulator gene lesions directing the fate of a multipotent precursor of origin.
Epigenetic regulator genes direct lineage switching in MLL/AF4 leukemia · Tirtakusuma R, Szoltysek K, Milne P, et al. (senior author Bomken S) · Blood 2022What this evidence cannot show
Cited here as the competing mechanism, not as support. This paper is already cited in 11 entries of this corpus, so its conclusions are documented elsewhere; what is new here is the comparison with the single-cell observation. Its deposited data (GSE132396, GSE130142) is named in GEO and is not currently referenced anywhere in this graph.
Evidence that argues against this (1)
- Shared fusion breakpoints between the lymphoid presentation and the myeloid relapse are equally predicted by BOTH models, so this evidence does not discriminate. It is included as the competing mechanism precisely because its strongest datum is neutral between the two accounts; what separates them is the timing of the myeloid-fated cell's existence, which only the single-cell data addresses. Chen C et al. 2022
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Whole-genome phylogenetic reconstruction in a child who developed AML after anti-CD19 cellular and antibody therapy showed the AML derived from the initial ALL clone, establishing clonal continuity across the switch independently of any single-cell measurement.
Clonal origin of KMT2A wild-type lineage-switch leukemia following CAR-T cell and blinatumomab therapy · Coorens THH, Collord G, Treger TD, et al. (senior author Behjati S) · Nature Cancer 2023What this evidence cannot show
This case is explicitly KMT2A WILD-TYPE, so it establishes the phenomenon of clonal continuity across a switch but says nothing specific about KMT2A-rearranged disease. Already cited in 9 entries here; included for the contrast between bulk phylogenetic reconstruction (what it does) and direct observation of the pre-existing cell (what E1 does).
Evidence that argues against this (1)
- This case is KMT2A wild-type, so importing it into a KMT2A-rearranged argument is exactly the partner-and-genotype import this corpus's provenance audit warns about. Clonal continuity across a lineage switch in a non-KMT2A leukaemia is evidence that switches are clonal in general; it is not evidence about the index disease, and the entry should not be read as though it were. Coorens THH et al. 2023
the single-cell demonstration that hypothesis records as not existing: a pre-existing myeloid-potential blast population before switch in both switching patients
- supports →Lineage switch in KMT2A-rearranged leukemia — the same clone changes what kind of blood cell it is
selection of a pre-existing myeloid-primed clone rather than therapy-induced transdifferentiation
- supports →Flow-cytometric MRD: the fastest readout, and the one a lineage switch walks straight out of
a CD34+CD19- or myeloid-fated blast is outside a B-ALL flow MRD gate by construction, which is why switch follows MRD-negative remission
- related to →Lineage switch as antigen escape from CD19-directed therapy in KMT2A-rearranged leukemia
the pre-existing population is what CD19-directed pressure releases
- related to →Blinatumomab in infant KMT2A-rearranged ALL — the largest single outcome gain in thirty years
immunotherapy pressure is what the pre-existing myeloid-potential population expanded under
same 25-patient resource; whether the myeloid-primed and HSPC-like populations are the same cells is unresolved
a blast co-expressing B and myeloid lineage genes in one cell is the single-cell reading of mixed phenotype
the deposited resource behind the pre-existing myeloid-primed blast observation, including both lineage-switch patients