The apoptotic priming state — KMT2A-rearranged infant ALL is the one childhood ALL subgroup that is BCL-2-dependent rather than BCL-XL-co-dependent, and BH3 profiling is how that was measured
also called apoptotic priming · BH3 profiling state · mitochondrial priming · BCL-2 dependence · anti-apoptotic dependence
Every cell sits somewhere on a scale between ready to die and hard to kill, and a test called BH3 profiling reads that position directly by dripping death signals onto isolated mitochondria. Infant KMT2A-rearranged leukaemia sits in an unusual place on that scale: it leans on one survival protein, BCL-2, where most childhood leukaemias lean on two.
The same thing, for a scientist
Apoptotic priming is a measurable cell state, not an inference, and it is one of the few states in this graph with a functional assay that works on primary patient material in hours. Three results define it here. (1) In a panel of childhood ALL xenografts, effective antileukaemic activity generally required **concurrent inhibition of both BCL-2 and BCL-XL**, with BCL-XL expression the key predictor of poor venetoclax response — **with one named exception, MLL-rearranged infant ALL, where venetoclax largely recapitulated the activity of navitoclax** [E1]. That is a lesion-specific statement about which anti-apoptotic protein the cell is addicted to, and it is the reason venetoclax entered this disease. (2) **BH3 profiling of MLL-ALL identified BCL-2 dependence as a mechanism of treatment resistance**, and cells surviving SFK/FLT3 inhibition were dependent on BCL-2; a triple combination of glucocorticoid, RK-20449 and ABT-199 completely eliminated MLL-ALL cells in vivo [E2]. (3) **Dynamic BH3 profiling** — the version that measures how priming *moves* under a drug — showed that in a KMT2A-rearranged line and in KMT2A-rearranged PDX cells, targeted agents raise priming acutely and then provoke an **MCL-1-dependent anti-apoptotic adaptation**, which sequential MCL-1 inhibition overcomes [E3]. The state is therefore not fixed: it is a position that moves within days of treatment, and the direction it moves in is the clinically relevant quantity.
What BH3 profiling measures, and why it is the right instrument for this beat
Most cell-state claims in this graph are transcriptional. Apoptotic priming is not: BH3 profiling exposes permeabilised cells or isolated mitochondria to synthetic BH3 peptides and reads cytochrome c release, so it measures how close the mitochondrion is to the death threshold and which anti-apoptotic protein is holding it back. The answer comes as a dependence — BCL-2, BCL-XL, MCL-1 — not as an expression level.
That distinction does real work here. E1 found that BCL-XL expression predicted poor venetoclax response while sensitivity did not follow BCL-2 expression, and this project's own MCL-1 entry independently found that S63845 sensitivity did not correlate with BCL-2 or MCL1 levels. Expression is a bad proxy for dependence twice over in this disease.
Dynamic BH3 profiling adds a time axis: prime the cells with a drug for a few hours, then profile. It answers 'did this drug move the cell toward death, and what moved to stop it', which is the question a combination strategy actually needs 3.
The exception that made venetoclax a paediatric ALL drug
The Khaw result is worth stating precisely because it is usually compressed to 'KMT2A-rearranged ALL is venetoclax-sensitive'. What the study found was a general rule with one exception 1:
- Across the majority of childhood ALL xenografts, venetoclax alone was insufficient and effective killing required concurrent BCL-2 and BCL-XL inhibition.
- BCL-XL expression was the key predictor of poor venetoclax response.
- Dual inhibition was synergistic in the majority of xenografts.
- MLL-rearranged infant ALL was the notable exception, in which venetoclax largely recapitulated navitoclax activity — so the BCL-XL arm was contributing little.
- The authors' own conclusion was therefore that MLL-rearranged infant ALL patients are candidates for venetoclax trials, while navitoclax should progress ahead of venetoclax in the other subgroups.
That last clause is the part that gets lost, and it means the selectivity argument for venetoclax in this disease is a statement about BCL-XL's irrelevance here rather than about BCL-2's importance here.
This graph's target-mcl1-with-bcl2-and-dexamethasone-infant-kmt2a-all entry supplies the same conclusion from the opposite direction: KMT2A-rearranged cells had significantly lower BCL-XL protein, and BCL-XL mRNA correlated positively with MCL1-inhibitor IC50.
Priming moves, and MCL-1 is where it moves to
Dynamic BH3 profiling of B-cell precursor ALL found that the MEK inhibitor trametinib and the multi-target TKI sunitinib sharply increased apoptotic priming in an NRAS-mutant line and in a KMT2A-rearranged, FLT3-high line respectively; profiling after treatment then identified anti-apoptotic changes in the BCL-2 family involving MCL-1, and sequential addition of the MCL-1 inhibitor S63845 was synergistic and more effective than single agents. KMT2A-rearranged PDX cells responded to sunitinib with an analogous profile to the SEM cell line 3.
This is the mechanism that makes the state a state rather than a biomarker: the cell has a reserve. Knock out its primary dependence and it shifts to MCL-1 within the timescale of an assay. Any single-agent BH3 mimetic in this disease is therefore operating against a system with a designed-in escape, which is what resistance-adaptive-nongenetic-menin describes for a different drug class.
The sequencing detail matters and is easy to lose: the combination was metronomic and sequential, S63845 added after the kinase inhibitor, not concurrently.
Where the state connects to menin inhibition
Two links, one supported and one absent.
Supported. TP53 inactivation in KMT2A-rearranged AML produces de novo revumenib resistance with impaired induction of TP53 targets and deregulated BCL-2 and MCL-1, and an MCL-1 inhibitor — but not venetoclax — preferentially sensitised TP53-mutant cells to revumenib. That is recorded in resistance-tp53-apoptotic-priming-menin and it is an apoptotic-priming explanation of a menin-inhibitor failure: the transcriptional effect happens and the execution step does not.
Absent. Nobody has run BH3 profiling, static or dynamic, before and after menin inhibition in KMT2A-rearranged cells. That is a one-week experiment on primary material with an established assay, and it would say directly whether a menin inhibitor primes cells for death, de-primes them, or shifts their dependence — and therefore whether venetoclax is the right partner, the wrong one, or partner-dependent on TP53 status. This graph holds several menin-plus-venetoclax combination entries that all rest on an unmeasured assumption about priming.
| state definition | The proximity of a cell's mitochondria to the apoptotic threshold and the identity of the anti-apoptotic protein maintaining that threshold; measured functionally by BH3 profiling (static) or by BH3 profiling after short drug exposure (dynamic), not by expression of BCL-2 family members |
|---|---|
| negative predictor | BCL-XL expression predicts poor venetoclax response in childhood ALL generally; KMT2A-rearranged cells have comparatively low BCL-XL, which is the stated basis of their relative BCL-2 dependence |
| expression is not dependence | venetoclax sensitivity did not follow BCL-2 expression, and MCL1-inhibitor sensitivity did not follow BCL-2 or MCL1 levels; both required a functional assay |
| not yet measured | BH3 profiling before and after menin inhibition in KMT2A-rearranged cells; no published study, static or dynamic |
assay
{
"static_bh3_profiling": "synthetic BH3 peptides applied to permeabilised cells; readout is cytochrome c release or mitochondrial depolarisation",
"dynamic_bh3_profiling": "short in vitro drug exposure then profiling; readout is the CHANGE in priming and the anti-apoptotic protein the cell shifts to"
}dependencies reported in kmt2a rearranged disease — the numbers behind the chart
[
{
"protein": "BCL-2",
"setting": "MLL-rearranged infant ALL xenografts; venetoclax recapitulates navitoclax",
"pmid": "27343252",
"title": "Venetoclax responses of pediatric ALL xenografts reveal sensitivity of MLL-rearranged leukemia.",
"authors": "Khaw SL, Suryani S, Evans K, et al.",
"venue": "Blood",
"year": 2016,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"protein": "BCL-2",
"setting": "MLL-ALL resistant to SFK/FLT3 inhibition, by BH3 profiling",
"pmid": "33581643",
"title": "Targeting critical kinases and anti-apoptotic molecules overcomes steroid resistance in MLL-rearranged leukaemia.",
"authors": "de Groot AP, Saito Y, Kawakami E, et al.",
"venue": "EBioMedicine",
"year": 2021,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"protein": "MCL-1",
"setting": "adaptive shift after targeted therapy, KMT2A-rearranged line and PDX, by dynamic BH3 profiling",
"pmid": "34568318",
"title": "MCL-1 Inhibition Overcomes Anti-apoptotic Adaptation to Targeted Therapies in B-Cell Precursor Acute Lymphoblastic Leukemia.",
"authors": "Manzano-Muñoz A, Alcon C, Menéndez P, et al.",
"venue": "Front Cell Dev Biol",
"year": 2021,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"protein": "MCL-1",
"setting": "TP53-mutant KMT2A-rearranged AML resistant to revumenib; MCL-1 inhibitor but not venetoclax sensitises",
"pmid": "40196700",
"title": "TP53 Inactivation Confers Resistance to the Menin Inhibitor Revumenib in Acute Myeloid Leukemia.",
"authors": "D'Souza J, Leung CJ, Ballapuram AC, et al.",
"venue": "bioRxiv",
"year": 2025,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
}
]atlas refs — the numbers behind the chart
[
{
"label": "MLL-rearranged infant ALL as the BCL-XL-independent exception in paediatric ALL xenografts",
"pmid": "27343252",
"title": "Venetoclax responses of pediatric ALL xenografts reveal sensitivity of MLL-rearranged leukemia.",
"authors": "Khaw SL, Suryani S, Evans K, et al.",
"venue": "Blood",
"year": 2016,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"label": "BCL-2 dependence identified by BH3 profiling as a resistance mechanism in MLL-ALL",
"pmid": "33581643",
"title": "Targeting critical kinases and anti-apoptotic molecules overcomes steroid resistance in MLL-rearranged leukaemia.",
"authors": "de Groot AP, Saito Y, Kawakami E, et al.",
"venue": "EBioMedicine",
"year": 2021,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"label": "MCL-1 anti-apoptotic adaptation detected by dynamic BH3 profiling in KMT2A-rearranged cells",
"pmid": "34568318",
"title": "MCL-1 Inhibition Overcomes Anti-apoptotic Adaptation to Targeted Therapies in B-Cell Precursor Acute Lymphoblastic Leukemia.",
"authors": "Manzano-Muñoz A, Alcon C, Menéndez P, et al.",
"venue": "Front Cell Dev Biol",
"year": 2021,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
}
]- BCL-2 dependence in this disease is real at baseline and universally lost under selection in preclinical models, with escape through BAX and TP53 rather than through BCL2 — so resistance will not be detectable by sequencing the drug target and will confer cross-resistance to other BH3 mimetics.
- MCL-1 inhibition rescues the adaptive shift in vitro but caused lethal tumour lysis in the majority of mice when combined with venetoclax above a threshold dose; the in vitro synergy and the in vivo toxicity are properties of the same mechanism.
- BCL-2 and MCL-1 are both required by normal haematopoietic cells, and MCL-1 additionally by cardiomyocytes; an infant on a BH3-mimetic combination has little marrow reserve and a lifetime of cardiac follow-up ahead.
- Every priming measurement in this disease was made outside a human marrow, and dormancy-associated resistance is documented to reverse on removal from the niche, so the assay that defines the state may be systematically measuring the wrong state.
- Does menin inhibition increase, decrease or redirect apoptotic priming in KMT2A-rearranged cells? Dynamic BH3 profiling before and after revumenib would answer in a week on primary material, would tell you whether venetoclax is the right partner, and has never been published despite several combination trials being open.
- Is the priming difference between KMT2A-rearranged ALL and AML as large as the metabolic and differentiation differences are? Menin inhibition kills KMT2A-rearranged ALL rapidly and differentiates AML slowly; if priming explains that, it is measurable.
- Does the BCL-2 dependence of infant KMT2A-rearranged ALL survive contact with the human marrow niche? Every measurement supporting it was made in a murine xenograft or ex vivo, and dormancy-associated drug resistance is documented to reverse on removal from the niche.
- Why do venetoclax-resistant KMT2A-rearranged models acquire BAX and TP53 variants but not BCL2 variants? Escape downstream of the target means the resistance is invisible to target sequencing and predicts cross-resistance to every BH3 mimetic, not just to venetoclax.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
In childhood acute lymphoblastic leukaemia xenografts, effective antileukaemic activity in the majority of models required concurrent inhibition of both BCL-2 and BCL-XL, with BCL-XL expression identified as a key predictor of poor venetoclax response and dual inhibition synergistic in most xenografts; mixed lineage leukaemia-rearranged infant ALL was a notable exception in which venetoclax largely recapitulated the activity of navitoclax, identifying that subgroup as candidates for venetoclax trials while supporting navitoclax ahead of venetoclax in other subgroups.
Venetoclax responses of pediatric ALL xenografts reveal sensitivity of MLL-rearranged leukemia · Khaw SL, Suryani S, Evans K, Richmond J, Robbins A, Kurmasheva RT, et al., Lock RB · Blood 2016What this evidence cannot show
Patient-derived xenografts in immunodeficient mice, so the niche influence on priming is murine and the human marrow's contribution is absent; the graph's own quiescence entry records that dormancy and drug sensitivity are reversible on removal from the niche, which bears directly on any ex vivo or xenograft priming measurement. The number of MLL-rearranged infant models in the panel is not given in the abstract, so the 'notable exception' rests on an unstated n. 'MLL-rearranged' is not resolved to fusion partner. Read: abstract only.
Evidence that argues against this (1)
- BCL-2 dependence in KMT2A-rearranged ALL is not durable. In KMT2A-rearranged ALL cell lines and xenograft models all of which initially responded well to venetoclax, secondary resistance developed in every model, with pathogenic variants in TP53 and in the pro-apoptotic effector BAX but notably NOT in BCL2 itself, multifarious gene and protein expression changes with high inter- and intra-model heterogeneity, and single-cell RNA sequencing implicating the tumour microenvironment. A dependence that is real at baseline and universally lost under selection is a poor foundation for single-agent use, and because the escape is not through the drug target it cannot be detected by sequencing BCL2. Read: abstract only. Richter A et al. 2025
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
In MLL-rearranged ALL, Src family kinase and FLT3 signalling pathways were over-represented in patient specimens; patient-derived xenograft models of infant MLL-ALL recapitulated glucocorticoid resistance in vivo and the SFK/FLT3 inhibitor RK-20449 eliminated human MLL-ALL cells in vivo and overcame that resistance; BH3 profiling identified BCL-2 dependence as a mechanism of treatment resistance in MLL-ALL, cells resistant to RK-20449 were dependent on BCL-2 for survival, and the triple combination of glucocorticoid, RK-20449 and ABT-199 resulted in complete elimination of MLL-ALL cells in vivo.
Targeting critical kinases and anti-apoptotic molecules overcomes steroid resistance in MLL-rearranged leukaemia · de Groot AP, Saito Y, Kawakami E, Hashimoto M, Aoki Y, Ono R, et al., Ishikawa F · EBioMedicine 2021What this evidence cannot show
RK-20449 is a tool compound with no clinical development, so the triple combination as tested is not translatable as written; its dual SFK/FLT3 activity also means the BCL-2 dependence identified is a dependence of cells surviving a specific and broad kinase inhibition, not of untreated disease. The BH3 profiling is reported as a finding without the peptide panel or the quantitative dependence values in the abstract. PDX in NSG mice, so glucocorticoid pharmacology and the marrow niche are murine. Read: abstract only.
Evidence that argues against this (1)
- The dependence BH3 profiling reports is the dependence at the moment of profiling, and in this disease it moves. Dynamic BH3 profiling of B-cell precursor ALL showed that after targeted-agent treatment the BCL-2 family shifts toward MCL-1 dependence, in a KMT2A-rearranged cell line and in KMT2A-rearranged PDX cells. A protocol built on a single baseline BCL-2 dependence measurement will therefore be correct at day 0 and wrong by the time resistance emerges, which is the failure mode the venetoclax resistance models display. Read: abstract only. Manzano-Munoz A et al. 2021
- E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
Dynamic BH3 profiling of B-cell precursor ALL showed that the MEK inhibitor trametinib and the multi-target tyrosine kinase inhibitor sunitinib sharply increased apoptotic priming in an NRAS-mutant line and in a KMT2A-rearranged line with high FLT3 expression respectively; profiling after treatment identified anti-apoptotic adaptation in the BCL-2 family particularly involving MCL-1; metronomic sequential addition of the MCL-1-specific BH3 mimetic S63845 was synergistic and more effective than single agents; and KMT2A-rearranged patient-derived xenograft cells responded to sunitinib with a dynamic BH3 profile analogous to the SEM cell line.
MCL-1 Inhibition Overcomes Anti-apoptotic Adaptation to Targeted Therapies in B-Cell Precursor Acute Lymphoblastic Leukemia · Manzano-Munoz A, Alcon C, Menendez P, Ramirez M, Seyfried F, Debatin KM, et al., Montero J · Front Cell Dev Biol 2021What this evidence cannot show
The KMT2A-rearranged arm is a single cell line (SEM) plus PDX cells; n is small and the fusion partner is KMT2A::AFF1 only. Sunitinib is used as an FLT3-directed agent in a FLT3-high context, which is a property of the line as much as of the lesion. Dynamic BH3 profiling measures priming over hours and its relation to durable clinical response is an inference. Neither drug in the pair is in paediatric use for this indication. Read: abstract only.
Evidence that argues against this (1)
- This project's own MCL-1 entry records that the in vitro and in vivo pictures invert for exactly this strategy. S63845 monotherapy gave no significant survival benefit in infant KMT2A-rearranged PDX at any dose tested; S63845 plus venetoclax did not beat venetoclax alone and at 12.5 mg/kg or above with venetoclax induced lethal tumour lysis syndrome in 8 of 12 mice. Only the triple combination with dexamethasone produced durable responses. An MCL-1-directed rescue of an anti-apoptotic adaptation is therefore supported as a mechanism and unsupported as a two-drug regimen. The full text of this paper was retrieved and read by an earlier beat of this project (target-mcl1-with-bcl2-and-dexamethasone-infant-kmt2a-all); the identifiers in this block were re-fetched from PubMed for this entry rather than copied from that entry, and the PubMed record carries no abstract, so the numerical details are quoted from that beat's reading of the full text and not from an abstract. Karsa M et al. 2026
MLL-rearranged infant ALL is the named exception in paediatric ALL xenografts where venetoclax alone recapitulates navitoclax, i.e. BCL-2-dependent without BCL-XL co-dependence
venetoclax acts on the BCL-2 dependence this state defines; BH3 profiling rather than BCL-2 expression is what predicts the response
- depends on →BCL2 — the one co-dependency in this beat that already has an approved drug pointed at it
BH3 profiling of MLL-ALL identified BCL-2 dependence as the mechanism of treatment resistance
the state entry behind that target: dynamic BH3 profiling shows the MCL-1 shift that the triple combination is built to close, and the in vivo tumour-lysis result is its limit
the priming explanation of menin-inhibitor failure: transcriptional effect intact, execution step broken; MCL-1 inhibition but not venetoclax sensitises TP53-mutant cells
no published BH3 profiling, static or dynamic, before and after menin inhibition in KMT2A-rearranged cells — a one-week experiment underpinning several open combination trials
if menin inhibition kills KMT2A-rearranged ALL by apoptosis, its effect on apoptotic priming is the measurement that would choose its BH3-mimetic partner — and it has never been made in lymphoid cells
measures whether menin inhibition raises, lowers or redirects apoptotic priming, and to which anti-apoptotic protein
apoptotic axis: the BCL-2-dependent, BCL-XL-independent exception is lymphoid and the whole priming literature in this disease is lymphoid
MCL1 sets the second axis of apoptotic priming alongside BCL-2
directly represses BIK, HRK, TP63, RASSF6, TP53INP1, AIM2 and EAF2 and supports Bcl-xL - an anti-apoptotic axis that venetoclax does not cover
the venetoclax vulnerability of the stem-like fraction is an apoptotic-priming claim that has not been made at single-cell resolution in KMT2A-r
enitociclib lowers MCL-1 protein and potentiates venetoclax in relatively venetoclax-resistant KMT2A-rearranged infant leukaemia cells - removing the MCL-1 arm of the priming axis
m6A promotes translation of c-MYC, BCL2 and PTEN in KMT2A::MLLT3 MOLM-13, so METTL3 loss lowers BCL2 protein through translation rather than through transcription or BH3 displacement
venetoclax is the most potent agent against CREBBP-mutated B-ALL but kills by FERROPTOSIS rather than apoptosis - a BCL2-inhibitor response that does not run through the priming axis
TP53 status sets which anti-apoptotic protein the cell leans on (MCL-1 rather than BCL-2 in the revumenib-resistance preprint), and p53 has a coded mitochondrial-matrix pool