Does a menin inhibitor break homologous recombination? Test the menin - SETD2 - LEDGF - CtIP chain in a blast, before the next genotoxic combination is designed
also called menin inhibitor HR competence · CtIP resection under revumenib · menin gamma-H2A.X motif V371-Q400
A menin inhibitor might block the DNA repair that keeps a cell alive, and nobody has checked that with the drugs children actually receive. One study has checked a tool compound given together with a second drug, and found the repair was disrupted.
The same thing, for a scientist
Lian et al. 2026 report a chain in which **menin binds gamma-H2A.X through a Val371-Gln400 motif, recruits SETD2, SETD2 writes H3K36me3, LEDGF reads it and recruits CtIP** to perform end resection and activate RPA2/RAD51 [E1]. This graph independently holds the LEDGF-CtIP half as a mechanism entry citing Daugaard et al. 2012 [E2]. **The clinical question nobody has asked: do revumenib, ziftomenib and bleximenib impair this?** The drugs occupy the MBM cavity that accepts KMT2A residues 4-15, which cycle 63 MEASURED as overlapping the Val371-Gln400 surface at its first residue - ziftomenib sits 2.3 A from Val371 and revumenib 4.4 A, while bleximenib is 10.7 A away - so the prediction is NOT no, and it differs between compounds - but they also reduce menin protein, which would remove the scaffold regardless of where the contact sits. **The two routes make opposite predictions and the experiment separates them.** Every patient in the pivotal trials received cytotoxics, so the question is live in banked material and in every combination protocol now being written.
Design
Arm 1, the direct readout. KMT2A-rearranged lines (SEM, RS4;11, MV4-11) +/- revumenib at clinically achievable exposure, irradiated or etoposide-treated. Score RAD51 foci, RPA2 phosphorylation, and 53BP1:RAD51 ratio at fixed times. An HR reporter (DR-GFP) gives the quantitative arm.
Arm 2, the chain. ChIP for H3K36me3 at a defined DSB (AsiSI/DIvA system) +/- menin inhibitor, and CtIP recruitment by immunofluorescence or ChIP. This distinguishes 'HR is impaired' from 'HR is impaired through this chain'.
Arm 3, pocket versus protein. Compare an agent that predominantly occupies the pocket against one that predominantly degrades menin, at matched target engagement, and against MEN1 knockdown as the ceiling. If pocket occupancy alone does nothing and degradation does, the liability is drug-specific and not class-wide - which changes which agent belongs in a genotoxic combination.
Arm 4, the motif. Menin Val371-Gln400 deletion or substitution, re-expressed in MEN1-null cells, as the separation-of-function control. This also tests whether that region overlaps the FANCD2-binding region IntAct records as menin 214-390.
Arm 5, the clinical sensitiser readout. PARP-inhibitor and etoposide sensitivity +/- menin inhibitor. A positive result here is simultaneously the toxicity signal and the combination rationale.
Why it matters which way this comes out
- If menin inhibition impairs HR: every menin-inhibitor-plus-genotoxic combination carries an unquantified genomic-instability risk in a largely curable paediatric disease, and the class becomes a rational partner for PARP inhibition. Both follow from one result.
- If it does not: the menin-HR scaffold function is pocket-independent, which is a useful and reassuring structural statement about the drug class, and it means the Val371-Gln400 surface is a separate druggable site that could be targeted without touching the KMT2A contact.
There is no outcome of this experiment that is uninformative, which is unusual and is the main argument for running it.
What makes this runnable rather than aspirational
The DIvA/AsiSI system, DR-GFP reporters, RAD51 and RPA2 antibodies, and all three menin inhibitors are standard reagents. The only novel construct is the Val371-Gln400 menin mutant, and the source paper made it. The menin fractionation experiment this graph already proposes - chromatin-bound menin after UV, +/- menin inhibitor, +/- ATR inhibitor - shares its cells, its damage protocol and its timepoints with arm 1, so the two should be run together.
| design | Arm 1: KMT2A-rearranged lines (SEM, RS4;11, MV4-11) +/- revumenib at clinically achievable exposure, with ionising radiation or etoposide; RAD51 foci, phospho-RPA2, 53BP1:RAD51 ratio, DR-GFP HR reporter. Arm 2: H3K36me3 ChIP and CtIP recruitment at a defined DSB using the AsiSI/DIvA system, +/- menin inhibitor. Arm 3: pocket-occupancy-dominant versus degradation-dominant agent at matched target engagement, with MEN1 knockdown as ceiling. Arm 4: menin Val371-Gln400 deletion/substitution re-expressed in MEN1-null cells as the separation-of-function control, also testing overlap with the IntAct-curated FANCD2 region 214-390. Arm 5: PARP-inhibitor and etoposide sensitivity +/- menin inhibitor. |
|---|---|
| readout | HR competence (DR-GFP), RAD51 and phospho-RPA2 foci, H3K36me3 and CtIP at a defined break, and drug-combination sensitivity |
| primary endpoint | DR-GFP HR efficiency, menin inhibitor versus vehicle, in a KMT2A-rearranged line at clinically achievable exposure |
| discriminating arm | arm 3 - if pocket occupancy alone does nothing and menin degradation does, the liability is agent-specific rather than class-wide, which changes which drug belongs in a genotoxic combination |
| no uninformative outcome | a positive result gives both a toxicity signal and a PARP-combination rationale; a negative result establishes that the scaffold function is pocket-independent and identifies Val371-Gln400 as a separate site |
| shares protocol with | the chromatin-fractionation experiment this graph already proposes (menin chromatin pool after UV, +/- menin inhibitor, +/- ATR inhibitor) - same cells, same damage protocol, same timepoints |
| status | proposed, not run |
| CORRECTION cycle 63 the pocket DOES touch the motif | This entry predicted that a pocket-binding menin inhibitor would not disturb the gammaH2A.X motif, because the MBM cavity 'is not obviously the Val371-Gln400 surface'. Measured from coordinates: three of four clinical menin inhibitors contact Val371, the motif's first residue. VERIFIED BY THE KING FROM PDB COORDINATES, 2026-09-22: in 8VA6 ziftomenib sits 2.5 A from menin 363, 2.6 A from 366, 2.7 A from 367 and 2.3 A from 371; in 7UJ4 revumenib sits 3.4, 2.9, 3.9 and 4.4 A from the same residues. In both structures the SUV39H1 functional residues are far away - D418 at 16.1 and 16.6 A, W436 at 10.0 and 11.2 A. UniProt independently curates menin E366A/D370A as reducing KMT2A binding. Bleximenib is the exception at 10.7 A, so this is now a question that DISTINGUISHES the compounds rather than one with a single answer - which makes arm 3 of this experiment more informative, not less. |
reagents novel
[ "menin Val371-Gln400 mutant (made by the source paper)" ]
reagents standard
[ "DIvA/AsiSI", "DR-GFP", "RAD51 and phospho-RPA2 antibodies", "revumenib, ziftomenib, bleximenib" ]
PARTLY ANSWERED cycle 62
{
"what_this_entry_used_to_say": "Nobody has checked whether the drug blocks the repair. That is no longer exactly true and the summary is corrected.",
"what_has_been_checked": "PMID 31590682, Clinical Epigenetics 2019, doi 10.1186/s13148-019-0723-0 - verified by the king at abstract level. Chidamide (an HDAC inhibitor) combined with the menin-MLL interaction inhibitor MI-3 in human MLL-rearranged AML disrupts the DNA damage checkpoint at CHK1/CHK2 rather than at ATR/ATM, and disrupts 'DNA repair likely via homologous recombination (HR), but not non-homologous end joining (NHEJ)'.",
"why_the_experiment_is_still_worth_doing": "Three reasons, each stated rather than implied. It is a COMBINATION, so HR disruption cannot be attributed to menin inhibition - HDAC inhibition independently impairs HR. It uses MI-3, a TOOL COMPOUND, not revumenib or ziftomenib. And it is ADULT MLL-r AML, not infant KMT2A::AFF1 ALL.",
"for_the_clinical_agents_the_original_sentence_is_exactly_right": "revumenib[tiab] AND \"DNA repair\"[tiab] returns 0 against a 135-record drug-name operand",
"found_by": "Q32; PMID verified independently by the king before this edit"
}- A positive result would complicate every menin-inhibitor-plus-chemotherapy protocol now in design. It would also identify a PARP combination. Reporting only one half would be a distortion in either direction.
- The mechanism rests on one 2026 paper that this graph found this cycle and has not replicated. Designing a clinical combination on it would be premature; designing a cell experiment on it is not.
- Menin inhibitors are among the few effective agents in relapsed KMT2A-rearranged leukaemia. A genomic-instability finding would need a quantified effect size before it changed anything, because the alternative to the drug is worse.
- Does Val371-Gln400 overlap the menin surface that binds FANCD2 (IntAct: residues 214-390)? Arm 4 answers it as a by-product and would turn two separate DNA-damage partner claims into one surface.
- Do the three clinical menin inhibitors differ in how much they lower menin protein at equivalent target engagement? Arm 3 depends on that difference existing and it has not been measured head to head.
- Is the menin-HR function present in a lymphoid blast at all? Everything published is in solid-tissue models, and menin's abundance and chromatin distribution differ substantially between lineages.
- E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
Menin directly recognises gamma-H2A.X via a Val371-Gln400 motif with the interaction promoted by DNA damage, recruits SETD2 to damage sites to write H3K36me3, and LEDGF then reads that mark and recruits CtIP as the end-resection effector activating RPA2/RAD51; Men1 ablation caused spontaneous lung carcinogenesis with severe genomic instability and pharmacological restoration of H3K36me3 rescued the HR defect.
The tumor suppressor menin is a key scaffold mediator for homologous recombination repair. · Lian A, et al. · Nucleic Acids Res 2026What this evidence cannot show
Abstract read this session; full text not retrieved. Published 2026, not independently replicated, and new to this graph. Lung carcinogenesis model and cell lines - no haematopoietic system, no KMT2A fusion (brief rule 73). The motif is given without the mapping method, and no structure exists.
Evidence that argues against this (1)
- IntAct records menin residues 214-390 as the sufficient region for FANCD2 binding from a 2003 co-IP, so the same broad menin surface has already been assigned to a different DNA-damage partner. Coarse deletion mapping cannot distinguish a genuine hub from construct-boundary artefacts, and a Val371-Gln400 mutant would perturb both assignments at once. EMBL-EBI IntAct 2026
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
The downstream half of the chain is independently established: LEDGF/p75 promotes homologous recombination, its depletion impairs CtIP recruitment to breaks and CtIP-dependent end resection, and LEDGF binds CtIP in a DNA-damage-dependent manner.
LEDGF (p75) promotes DNA-end resection and homologous recombination. · Daugaard M, et al. · Nat Struct Mol Biol 2012What this evidence cannot show
Human cancer cell lines, not haematopoietic, no KMT2A fusion (brief rule 73). Abstract-level in this graph; no PMCID available. Already cited three times here, which is why this experiment adds the menin arm rather than re-establishing the LEDGF arm (brief rule 82).
Evidence that argues against this (1)
- A CRISPR knockout series found untreated LEDGF-null cells already carry DNA fragmentation and elevated gamma-H2AX and BRCA1, so LEDGF loss is broader than a resection-recruitment defect and a menin-inhibitor phenocopy would not be expected to look identical. Liedtke V et al. 2021
shares the RPA2 reagent and answers a different question; that entry is the better buy if only one can run
falsifiers 1 and 2 are run in that experiment's system and would settle it
that entry already proposes the measuring experiment; this one supplies the surface map and a compound-level prediction its arm 3 did not have
refutes that entry's stated premise that the drug pocket 'is not obviously the Val371-Gln400 surface' - three of four clinical compounds contact Val371 at 2.3-4.3 A
supplies a sixteen-year-older rationale for that experiment than the one it cites
CtIP recruitment is the readout of the chain
tests whether menin inhibition breaks the LEDGF-CtIP arm
the agent whose HR effect is unmeasured
arm 4 tests whether Val371-Gln400 overlaps the curated FANCD2 region 214-390
the drug pocket, which is NOT obviously the gamma-H2A.X surface - the reason the prediction is uncertain
revives the menin-HR line by a protein-scaffold route after the occupancy-based version failed its own housekeeping control
a third, mechanistic rationale for the menin-PARP combination that does not rest on promoter occupancy