KMT2A::AFF1 (MLL-AF4), t(4;11)(q21;q23)

This is real experimental data — atoms placed by crystallography or cryo-EM, deposited by the people who did the experiment.

• Resistance: acquired MEN1 mutations at the revumenib-binding site (M327I and neighbours) restore menin-KMT2A binding in the presence of drug and drive clinical relapse; base-editor scans predict a broad allelic spectrum, so this is a class liability rather than a revumenib quirk.
• Compensation: the target output is HOXA9/MEIS1, not menin. Any route to sustained HOXA9 expression - a second chromatin lesion, an AFF1-SEC interaction that does not need menin-mediated targeting, or enhancer rewiring - bypasses the whole strategy while leaving the fusion intact.
• Essential-function toxicity: menin is a genuine tumour suppressor (MEN1 syndrome) with required roles in normal haematopoiesis and islet biology, and wild-type KMT2A is under extreme human loss-of-function constraint (LOEUF 0.07; heterozygous loss causes Wiedemann-Steiner syndrome). Chronic menin blockade, or any degrader that also hits wild-type KMT2A, carries real developmental and endocrine risk in an infant.
• On-target hazard: grade >=3 differentiation syndrome occurred in 16% on AUGMENT-101. Releasing a large differentiation-blocked blast burden is intrinsically dangerous, and the risk scales with the very tumour burden that predicts benefit.
• Immunotherapy escape: because the cell of origin is lineage-plastic, CD19-directed therapy (blinatumomab, CAR-T) is met by myeloid lineage switch as well as antigen loss - an escape route this fusion enables by design.
• Delivery: the disease presents in infants under 12 months with frequent CNS involvement. An oral small molecule requiring strong CYP3A4 inhibition and QTc surveillance in a neonate is a pharmacology problem before it is a biology problem.

1. Menin inhibition works but caps out near a 23% CR+CRh rate in relapsed disease. Is the residual disease menin-independent from the outset (a pre-existing subclone with a menin-independent HOXA9 program), or does it become independent under drug pressure? The answer determines whether combination or sequencing is the right strategy.
2. Is there any surface unique to the fusion - the junction itself, or a composite AT-hook/CXXC/ALF conformation absent from either parent - that could be targeted with real selectivity rather than by borrowing the menin pocket?
3. Why does AFF1 essentially never partner KMT2A in AML (0.8% of KMT2A-r AML) while MLLT3 does so constantly? If that is a property of the cell of origin rather than of the protein, then the fusion's lineage output is dictated by the fetal progenitor and a faithful infant model must start from a fetal cell.
4. No structure exists of the intact chimera or of the AFF1 pSER region on chromatin. Would a predicted model of the retained KMT2A half docked on menin/LEDGF plus the AFF1-CHD:AF9 interface reveal a second, non-menin interface worth drugging?

1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   KMT2A::AFF1 is the commonest KMT2A rearrangement (1262/3401, 37.1%), represents 48.3% of infant ALL and 82.7% of adult KMT2A-r ALL but is almost absent from AML, and its KMT2A breakpoint shifts from intron 11 in infants to introns 9-10 in adults.

   The KMT2A recombinome of acute leukemias in 2023. · Meyer C, Larghero P, Almeida Lopes B, et al. · Leukemia 2023
   PMID 37019990DOI
   ▸What this evidence cannot show

   A single-diagnostic-centre referral cohort (DCAL, 2003-2022), so partner frequencies reflect which centres send samples rather than a true population distribution, and ascertainment shifted mid-cohort from LD-PCR to targeted NGS, which changes the detectable breakpoint spectrum. Exon numbering follows the Meyer/Marschalek convention and differs from older papers by three exons.

   ▸Evidence that argues against this (2)

   • These proportions come from a diagnostic REFERRAL series, not a population registry, and the denominator is whoever was sent for KMT2A analysis. That ascertainment shapes every percentage in the claim: partner distribution depends on which assays the referring centres ran, and cryptic events are systematically under-counted - this graph's own atlas records that KMT2A::SEPTIN11 is cytogenetically indistinguishable from KMT2A::AFF1 because SEPTIN11 lies within 250 kb of AFF1. Population-based infant cohorts are the comparator, and Interfant reports its own distribution on consecutively enrolled patients rather than referred ones. Journal of Clinical Oncology 2019
   • 'Almost absent from AML' is the weakest part of the claim, because absence in a referral series is partly a referral decision. A B-lineage-predominant partner is less likely to be sent for molecular KMT2A characterisation from an AML workup, so the AML denominator is not the AML population. The direction of that bias is to exaggerate lineage specificity, which is the claim being made. Leukemia 2023
2. E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   Menin is an essential oncogenic cofactor for KMT2A-fusion leukemogenesis and acts by linking the fusion to LEDGF/PSIP1 on cancer-associated target genes, so the menin-binding motif is required for transformation and for HOXA9 expression.

   Menin critically links MLL proteins with LEDGF on cancer-associated target genes. · Yokoyama A, Cleary ML · Cancer Cell 2008
   PMID 18598942DOI
   ▸What this evidence cannot show

   Mechanism established largely in murine transformation assays and human cell lines; the LEDGF requirement was mapped with domain deletions rather than with a selective LEDGF ligand, so its therapeutic tractability is unproven. Nothing here demonstrates that menin inhibition is safe in a developing infant.

   ▸Evidence that argues against this (1)

   • Menin has bona fide tumour-suppressor functions (MEN1 syndrome) and is required in normal haematopoiesis and pancreatic islets, so 'menin as oncogenic cofactor' is context-dependent, not a property of menin itself. Yokoyama A et al. 2005
3. E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   AFF1/AFF4 scaffold the super elongation complex containing AF9/ENL, ELL-family proteins and the P-TEFb kinase, and AFF4 is a shared subunit of MLL chimeras that links transcription elongation to leukemia.

   AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia · Lin C, Smith ER, Takahashi H, et al. · Molecular Cell 2010
   PMID 20159561DOI
   ▸What this evidence cannot show

   Biochemical purification and cell-line work; AFF4 rather than AFF1 was the primary subject, and AFF1 and AFF4 are partly redundant paralogues, so the exact stoichiometry of an AFF1-containing SEC on a KMT2A::AFF1 fusion in a patient blast is inferred rather than measured.

   ▸Evidence that argues against this (1)

   • This is accurate for AFF1 and should not be read as a statement about KMT2A fusions generally, which is how the phrase 'a shared subunit of MLL chimeras' invites it to be read. The SEC account is strongest exactly here - AFF1 IS the SEC scaffold - and weakest for partners that have no elongation function at all. Keeping the claim scoped to AFF1 costs this entry nothing and stops it being cited as the universal. Blood 2004
4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   Clonotypic KMT2A fusion sequences are detectable in neonatal blood spots from children who later developed leukemia, establishing a prenatal origin for the translocation.

   Backtracking leukemia to birth: identification of clonotypic gene fusion sequences in neonatal blood spots · Gale KB, Ford AM, Repp R, et al. · Proceedings of the National Academy of Sciences USA 1997
   PMID 9391133DOI
   ▸What this evidence cannot show

   A small number of retrospectively retrieved Guthrie cards with PCR-based detection and real contamination risk for the era. It establishes prenatal presence of the fusion, not the identity of the cell in which it arose; the 'fetal liver HSC / lympho-myeloid primed progenitor' cell of origin is an inference from transcriptional and xenograft studies, not from this paper.

   ▸Evidence that argues against this (1)

   • Detecting the clonotypic fusion sequence in a neonatal blood spot establishes when the translocation happened and that the clone was already present; it does not establish that the translocation was the whole of the initiating lesion, which is how the observation is usually deployed. Whole-genome, exome and transcriptome sequencing of 2,754 children with ALL found a median of four putative somatic driver alterations per sample despite a generally low overall mutation burden, 376 putative driver genes with prevalence varying by subtype, and most samples carrying at least one rare gene alteration - including 70 putative driver genes in classes that an exome non-silent-mutation count does not reach, such as ubiquitination and SUMOylation pathway genes and non-coding transcripts. Prenatal origin and single-hit sufficiency are separate claims, and only the first is supported by backtracking. Brady SW et al. 2022
5. E5established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   In relapsed/refractory KMT2A-rearranged acute leukemia the menin inhibitor revumenib achieved a CR+CRh rate of 22.8% and an overall response rate of 63.2% among 57 efficacy-evaluable patients, with grade >=3 differentiation syndrome in 16.0%.

   Menin Inhibition With Revumenib for KMT2A-Rearranged Relapsed or Refractory Acute Leukemia (AUGMENT-101) · Issa GC, Aldoss I, Thirman MJ, et al. · Journal of Clinical Oncology 2025
   PMID 39121437DOINCT04065399
   ▸What this evidence cannot show

   Single-arm registration cohort with mixed ALL/AML and a wide age range (1.3-75 years, median 37), so the infant KMT2A::AFF1 subgroup is small and not separately powered; response was read at a prespecified interim analysis and CR+CRh is a surrogate, not survival. Dosing required strong CYP3A4-inhibitor co-administration and QTc monitoring.

   ▸Evidence that argues against this (1)

   • Acquired MEN1 mutations at the drug-binding site (e.g. M327I, G331R/D) arise on therapy and cause clinical relapse, showing the interface is drugged but not durably so. Perner F et al. 2023
6. E6established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   On Interfant-06 (n=651 infants with ALL) the 6-year EFS was 46.1% and OS 58.2%, with 6-year EFS of only 20.9% in the KMT2A-rearranged high-risk stratum, and KMT2A rearrangement was the strongest prognostic factor for EFS.

   Outcome of Infants Younger Than 1 Year With Acute Lymphoblastic Leukemia Treated With the Interfant-06 Protocol: Results From an International Phase III Randomized Study · Pieters R, De Lorenzo P, Ancliffe P, et al. · Journal of Clinical Oncology 2019
   PMID 31283407DOI
   ▸What this evidence cannot show

   The reported survival is for all infant ALL, not KMT2A::AFF1 specifically; roughly a fifth of infants are KMT2A-germline and do much better, so the AFF1-only figure is worse than the headline 46.1%. Outcomes differed by 10-12% between West European/North American groups and other participating countries, so this is partly a health-systems number.

   ▸Evidence that argues against this (1)

   • Adding blinatumomab to the same chemotherapy backbone markedly improved short-term outcomes in infant KMT2A-r ALL, so 46.1% is no longer the current standard-of-care benchmark. van der Sluis IM et al. 2023
7. E7moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

   The bacterially expressed MLL AT-hook domain binds cruciform DNA in a gel mobility shift assay, recognising the structure rather than the sequence of the target DNA; the same study maps a transcriptional activation domain 3' and a repression domain 5' of the MLL breakpoint region, so 11q23 translocations retain the repression domain and the AT-hook DNA-binding region while discarding the activation domain.

   11q23 translocations split the "AT-hook" cruciform DNA-binding region and the transcriptional repression domain from the activation domain of the mixed-lineage leukemia (MLL) gene · Zeleznik-Le NJ, Harden AM, Rowley JD · Proceedings of the National Academy of Sciences USA 91(22):10610-4 1994
   PMID 7938000DOI
   ▸What this evidence cannot show

   ABSTRACT ONLY for the binding experiment's details - the wording 'recognizing structure rather than sequence of the target DNA' is the authors' own, quoted from the PubMed abstract; the PMC full text was not read, so the substrate panel, competitor set and affinities behind that conclusion were not independently inspected. 1994 gel-shift biochemistry with a bacterially expressed AT-hook fragment, not the full-length protein and not in cells. This is the ONLY direct binding assay on MLL's own AT-hooks; the much larger literature describing AT-hooks as AT-rich minor-groove binders is about the motif class (Reeves & Nissen consensus peptide, HMGA proteins), not about MLL. Structure preference and AT-richness are also confounded, because AT-rich tracts are the sequences that most readily bend and extrude cruciforms.

   ▸Evidence that argues against this (1)

   • The generic AT-hook motif is defined as an A.T-rich minor-groove binder, so a class-level prior runs against the structure-recognition reading, and the 1994 result has not been independently replicated with modern methods. Reeves R et al. 1990
8. E-alf-loststrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   The AFF1 ALF/N-terminal homology module and the AFF1 cyclin T1-binding sequence both lie N-terminal to the KMT2A::AFF1 junction at AFF1 residue 347, so neither is present in the fusion protein; this entry previously recorded ALF/NHD as a retained 3' domain.

   UniProtKB P51825 (AFF1_HUMAN) canonical sequence, 1,210 aa, FASTA, with the KMT2A::AFF1 junction peptide QTYSNEVH located by string match · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
   ▸What this evidence cannot show

   The junction position is established by string match against the fetched canonical sequence [E-junction-347 in `interface-aff4-ptefb-ccnt1-n-terminal`]. **Graded `strong` rather than `established` because the ALF/NHD boundary itself was not fetched** - the inference is that any published boundary for it falls before 347, which is true of every coordinate this project holds but is not the same as having read the defining paper's numbers. A boundary extending past 347 would overturn this.

   ▸Evidence that argues against this (1)

   • The DDX6 paper could not be read in full - `fullTextXML` returned HTTP 500 and `efetch db=pmc` returned front matter only, 2,828 characters with no body - so the AF4N coordinates quoted in discussions of this module were not verified here. The correction rests on the junction position alone, which is the part that was measured. Mück F et al. 2016

• ← regulatesHDAC3 - the only HDAC in this disease whose requirement was established genetically rather than by a drug, and the same experiment shows it is not fusion-specific

  combined HDAC1-3 inhibition abrogates the dominant transcriptional effect of MLL-AF4

• regulates →HDAC7 - the eraser the index fusion silences, where the proposed therapy is to INDUCE the HDAC, and two 2024-2025 papers point in opposite directions

  KMT2A::AFF1 with EZH2 epigenetically silences HDAC7 in t(4;11) infant B-ALL

• ← related toHDAC2 - the buffering half of the class I pair, and the one class I enzyme a drug result in acute leukaemia has actually been pinned to, in AML rather than in a KMT2A fusion

  MV4-11, a KMT2A::AFF1 line, is in the chidamide/cladribine panel but no KMT2A-versus-non-KMT2A comparison was made

• ← treated byRomidepsin - the HDAC inhibitor with the best preclinical case in KMT2A-rearranged INFANT ALL specifically, and a mechanism that is not about histones at all

  the connectivity-mapping route nominated this class for t(4;11) infant ALL and reported downregulation of the MLL-AF4 fusion product

• ← testsCatalytic-dead versus degrader: a four-arm test that resolves the HDAC7 direction conflict and supplies the pharmacodynamic marker this drug class has never had

  the experiment is designed in KMT2A::AFF1 infant ALL lines with a lineage-matched non-KMT2A comparator

• ← related toExperiment: combinatorial dose-titration of the HOXA9/MEIS1 program to find its minimal cut set

  missing control arm: titrate the shared upstream node (the fusion, or menin) across the same effort range, because the proposed cut-set members are co-regulated rather than independent channels

• ← related toSeverability (contract law) — what survives when a clause is struck, and what survives a KMT2A break

  the severed agreement under analysis

• ← related toHypothesis: the reciprocal AFF1::KMT2A product protects only when it is structurally complete, so its prognostic effect is a breakpoint class in disguise

  concerns the reciprocal AFF1::KMT2A product of t(4;11)

• ← refutesThe reciprocal fusion (AFF1::KMT2A and friends): a second oncoprotein that opens chromatin for the first

  Counter-evidence to the reciprocal-required model: MLL fused to Af4 ALONE in human CD34+ cells generates a pro-B ALL recapitulating the immunophenotypic and molecular features of t(4;11), with no reciprocal present (Lin 2016, PMID 27846391); and in patients the reciprocal AF4-MLL transcript is expressed in only about half of t(4;11) cases (Bueno 2019, PMID 30679325).

• ← related toWhich partner, in which patient: KMT2A partner frequencies across six age-lineage strata

  Counter-evidence (Hartmann 2026, PMID 41743263): an RNA-seq cohort spanning all ages puts adult+elderly AFF1 at 71%, twelve points below the 82.7% recorded here. Denominators differ (321 in the cross-tabulation; 18-54 and 55+ strata), so this qualifies rather than refutes -- but any argument that an adult KMT2A-r ALL trial is effectively a single-fusion trial should carry the range, not the point estimate.

• ← related toSeparation-of-function test: does KMT2A::AFF1 need its C-terminal homology domain to dimerise?

  Naming trap worth propagating: the AFF1/AFF4 C-terminal dimerisation module is called CHD in one structural paper and THD ('TPRL with Handle Region Dimerization Domain') in another. This node was built on the CHD literature alone and missed the published interface mutants for exactly that reason. Search both names.

• ← part ofAFF1 / AF4 — domain architecture and residue coordinates

  domain architecture of the 3' partner; ALF/NHD lost, pSER/TAD/motif/CHD retained

• ← related toKMT2A::AFF1 oligomerises through the retained AFF1 CHD, putting the commonest fusion in the oligomerisation class

  predicts an additional, menin-independent interface in the commonest KMT2A fusion

• ← analogous toCBFB — domain architecture and residue coordinates

  both fusions preserve a wild-type protein-protein interface intact, leaving no fusion-specific epitope on that side

• ← related toCyclophosphamide - where the KMT2A literature reports two different activated oxazaphosphorines and only one of them is this drug's metabolite

  t(4;11) blasts are 4.4-fold more resistant to activated IFOSFAMIDE than other 11q23 - a class-level result for the isomer, not for this drug

• ← related toProgrammed DNA breaks - V(D)J and class switching - and the verdict on whether either one breaks KMT2A

  V(D)J recombination is proximally biased in 121 KMT2A::AFF1 cases across all age classes, up to 50% using IGHV6-1

• ← related toExperiment: measure KMT2A-AFF1 spatial proximity in the human fetal progenitor, in the cell and at the time the translocation actually happens

  pre-translocation geometry of the two loci that make this fusion

• ← part ofThe other half of the break: what is actually known about the AFF1 breakpoint region, and the negative-control gene nobody cites

  the 4q21 half of the t(4;11) break

• ← causesTOP2A - the proliferation isoform, the one the drugs are actually measured against, and the only one with a germline association in this disease

  cleaves the normal homologues of a therapy-related t(4;11) patient's MLL and AF-4 junctions in vitro, etoposide-enhanced

• ← depends onATR - the replication-stress kinase with the best preclinical case in this disease and the best published reason not to inhibit it

  MEK+ATR synergy in Mll-Af4/N-Ras G12D mouse and patient-derived xenografts

• ← depends onWEE1 - the one checkpoint target with a KMT2A::AFF1-specific result, and the paper that also found the escape route

  KMT2A-rearranged ALL cells show the highest failure to recover proliferation under WEE1 inhibition; RS4;11 KMT2A-RUNX1-MYC network disrupted

• ← analogous toPICALM::MLLT10 (CALM-AF10), t(10;11)(p13;q14) - the DOT1L-dependent HOXA fusion that contains no KMT2A

  the index fusion's natural control: same HOXA/MEIS1 output, no KMT2A and no menin interface

• causes →The non-synchronisable state: five KMT2A-rearranged lines refuse mimosine, double thymidine and nocodazole, and the fusion protein does not fluctuate through the cycle

  SEM and RS4;11 could not be synchronised by mimosine, double thymidine or nocodazole, and endogenous MLL-AF4 protein did not fluctuate across elutriated cell-cycle fractions

• ← expressed inDiagnosis versus relapse in the same child: relapse comes from a subclone that was already there and already quiescent, shown twice, seven years apart, by two unrelated methods

  paired diagnosis and relapse samples in MLL-AF4-positive infant ALL; branching subclonal architecture already present at diagnosis

• causes →The innate-immune-rewired state — LAMP-5 is a direct fusion target that routes signalling away from interferon and toward NF-kB, and the cell depends on that routing

  LAMP5 reported as a direct target of the oncogenic MLL fusion, expressed highly and specifically in MLL-rearranged leukaemia across lineages

• ← testsSettle the monocytic confound isogenically: degrade the fusion, read haem-gene dependency before lineage has time to move

  degron-tagged MV4-11 KMT2A-AFF1 as arm 1 model

• ← arises inMonoblast — the immature monocyte that names FAB M5a, the dominant morphology of congenital KMT2A leukaemia

  t(4;11)/KMT2A-AFF1 is the commonest lesion in neonatal leukaemia, which is usually monoblastic myeloid

• ← related toThe G1 state in KMT2A-rearranged leukaemia — where CDK6 does a job that is not about the cell cycle at all

  CDK6 is a direct transcriptional target of MLL-AF4 and MLL-ENL

• ← supportsRetained fetal programme — the infant-versus-adult stem cell difference, and the reason KMT2A::AFF1 needs no second mutation

  LIN28B is required for KMT2A::AFF1 to transform human fetal liver CD34+ cells

• arises in →Fetal liver haematopoietic stem and progenitor cell — the leading candidate cell of origin for t(4;11) infant ALL

  leading candidate cell of origin; transcriptome of 124 infant cases matches most immature fetal liver HSPC and CRISPR t(4;11) in primary fetal liver cells reproduces the disease

• arises in →Fetal CD19+CD34+CD10-negative PreProB progenitor — a cell that exists before birth and almost not at all after

  fetal-restricted CD10-negative committed B-progenitor; shares transcriptomic signature with CD10-negative infant ALL blasts

• arises in →Lymphoid-primed multipotent progenitor (LMPP) — the bi-potent cell that explains how one fusion makes two lineages

  fetal liver LMPP supplies the prerequisites for t(4;11) initiation in murine Mll-AF4 models

• arises in →Haemogenic endothelium — the vessel-wall cell that gives birth to blood

  possible site of the translocation event rather than of transformation; MLL-AF4 in hESC skews hemato-endothelial specification but does not transform

• causes →The differentiation block — what it actually is, operationally, in KMT2A::AFF1 leukaemia

  actively maintained arrest with grafted self-renewal

• causes →The stem-like self-renewal state — a limited stem-cell module grafted onto a committed cell

  re-activation of a limited HSC self-renewal module; measurable in normal cord blood CD34+ cells before any leukaemia

• causes →The pro-B arrest state — what a KMT2A::AFF1 blast is actually doing while it sits there

  CD10-negative immature, oligoclonal Ig/TCR rearrangement with IL7R/KIT co-expression and NG2-driven glucocorticoid resistance

• causes →The primed chromatin state — what is actually established, and why the word 'bivalent' should be used carefully here

  spreading of fusion and menin with H3K79me2/3 at unmethylated CpG, plus subtype-specific promoter hypermethylation

• ← related toWhere KMT2A and its fusions sit inside the nucleus — SNL1/SNL2, nuclear speckles and the condensate question

  the punctate subnuclear distribution directed by the SNLs is retained in ALL-1/AF-4 and other MLL fusions

• ← related toIs KMT2A::AFF1 leukemia epithelial or endothelial? No — it is haematopoietic. But the question is a good one

  answers the origin-tissue question for this fusion: haematopoietic, not epithelial or endothelial

• causes →Where KMT2A-rearranged leukemia physically sits — marrow niche, CNS, blood, liver/spleen and skin

  hyperleukocytosis, organomegaly, CNS and extramedullary involvement as the presenting anatomical picture

• ← testsCell type or the fusion? MV4-11 LOOSENS the confound the graph's own lineage split was built on - but its founding paper calls it biphenotypic

  MV4-11 (myeloid) against SEM, SEMK2 and RS4;11 (B-lineage) holds this fusion constant while varying cell type

• ← related toLEDGF/p75 is required in the leukaemic cell and dispensable in ADULT MOUSE HAEMATOPOIESIS - not in the normal organism, which its germline knockout does not survive

  the requirement is conditional on the presence of a KMT2A fusion rather than on a cell type

• causes →The CD24-positive pre-leukaemic state — what the index fusion makes before it makes leukaemia

  ontogeny-specific induction of the fusion produces this distinct CD24-positive pre-leukaemic state

• ← testsPut the same fusion in two cell types and degrade it, rather than cutting the gene

  an endogenous degron on the fusion allele in MV4-11 and SEM

• ← related toWhy PML::RARA became curable — and what KMT2A::AFF1 does not share with it

  Decisive disanalogy (Liu 2007, PMID 17908926): the APL cure works by destroying the oncoprotein, and KMT2A fusions are specifically degradation-RESISTANT -- wild-type MLL is cleared by SCF(Skp2)/APC(Cdc20), degradation initiates in the N-terminal ~1400 aa every fusion retains, and the prevalent fusions tested resist it. The APL strategy is aimed at the worst possible substrate.

• ← related toKMT2A::AFDN (MLL-AF6), t(6;11)(q27;q23)

  Dispute recorded rather than resolved: the RA1 self-association model (Liedtke 2010, PMID 20395419) and the AF6-sequestration/RAS-activation model (Manara 2014, PMID 24695851) make different predictions for an RA1 interface mutant and neither tests the other's construct. Meanwhile revumenib was approved across KMT2A translocations without partner restriction (PMID 37019990), so the actionable interface for this partner is menin, not RA1.

• ← related toMechanism class 1 — chromatin and elongation hijack (KMT2A-r, NUP98-r)

  Bound on the PDX result (Mahdavi 2025, PMID 41027490): heavily pretreated KMT2A::AFF1 samples from the same patients resist menin inhibition with no prior exposure, while on-target repression of canonical menin targets is sustained. Efficacy and on-target chromatin action are separable.

• ← related toHypothesis — the menin lesson generalises: every non-enzymatic fusion has an obligate partner interface that is more druggable than the fusion

  Obligate-for-program is not obligate-for-survival (Mahdavi 2025, PMID 41027490): pretreated KMT2A::AFF1 samples resist menin inhibition with on-target repression of canonical targets intact and no prior drug exposure.

• ← related toNUP98 fusions share the menin dependency (confirmed preclinically) — and the partner-supplied reader/writer module is not why

  Prior therapy beats genotype in the only serial data (Mahdavi 2025, PMID 41027490): multiply relapsed KMT2A::AFF1 samples resist menin inhibition with no prior exposure and preserved on-target repression.

• related to →Ordering the fusions developmentally — which stage of blood formation each one hijacks, and at what age the child presents

  Prenatal origin is not single-hit sufficiency (Brady 2022, PMID 36050548): a median of four putative driver alterations per sample across 2754 paediatric ALL cases, with 70 putative drivers in classes an exome non-silent count does not reach.

• ← co-occurs withKRAS - the commonest co-mutation in a disease that has almost none, and it is usually in a minority of the cells

  KRAS(G12V) does not cooperate with MLL-AF4 to initiate leukaemia; it confers dissemination

• ← supportsSubclonal cooperating lesions lost at relapse - what was actually measured, and why 'lost' is the wrong word

  the genomic argument that the fusion is close to sufficient: its partners are dispensable at relapse

• ← related toThe reciprocal ChIP: is chromatin-bound XPO1 present in a KMT2A-rearranged cell, and does a menin inhibitor move it?

  SEM and RS4;11, the B-lineage arm no XPO1 experiment has ever used

• ← related toKMT2A rearrangement creates a requirement for the FA ubiquitin-transfer module — the claim, its prior, and the four results that would kill it

  three of the four B-lineage index lines carry KMT2A::AFF1 (RS4;11, SEM, SEMK2), per Cellosaurus

• ← testsIn-silico digest of 81 modelled KMT2A fusion junctions: the peptide that would prove the fusion protein exists

  computes the junction-spanning peptide (VDFKQTYSNEVHCVEEILK, [M+H]+ 2281.12) that would attribute a measurement to this protein

• ← related toNo KMT2A fusion junction peptide has ever been reported - the one measurement that would prove the protein exists has not been published

  no protein-level sequence-resolved identification of this fusion exists in the literature

• ← testsTargeted PRM for the KMT2A::AFF1 junction peptide - the experiment that makes every other attribution claim testable

  absolute copies per cell of the fusion protein, never measured

• ← related toAnti-AFF1 antibodies: attributable on a gel, not attributable in a microscope, and the classic localisation result shows exactly why

  detected at 240 kDa on a blot, unattributable in microscopy and in IP

• ← testsAttribution audit 1 of 5 - who co-purifies with KMT2A::AFF1: the inventory does not survive, the individual partner blots mostly do

  audits every published claim about which proteins co-purify with this fusion, by reagent class

• ← testsAttribution audit 2 of 5 - post-translational modifications on KMT2A::AFF1: nothing survives at peptide level, and the one strong PTM result is explicitly about the wild-type protein

  audits every published PTM claim about this protein by reagent, and finds no attributable one

• ← testsAttribution audit 3 of 5 - where KMT2A::AFF1 sits in the nucleus: the endogenous image does not survive, the overexpression images do and say something different

  audits every published localisation claim about this protein by reagent class

• ← testsAttribution audit 4 of 5 - the half-life and turnover of KMT2A::AFF1: this class SURVIVES, and it is the only endogenous fusion-attributable protein measurement this beat found

  audits turnover claims and finds the only endogenous fusion-attributable protein measurement in this literature

• ← testsAttribution audit 5 of 5 - where KMT2A::AFF1 sits on chromatin: the field's standard attribution heuristic is invalidated by the paper that founded it, but two real survivors exist

  audits every published occupancy claim about this fusion, and grades the two attribution heuristics the field uses

• ← related toThe experiment nobody has done: an epitope tag knocked into the endogenous KMT2A fusion allele in a patient-derived line

  the single construct that would make five classes of claim about this protein attributable

• ← testsJunction RT-PCR is the one routine assay in this disease that IS fusion-specific - and it is structurally blind to KMT2A*

  the one routine assay in this disease that attributes to this fusion by construction

• ← related toBounded unreadable: the only affinity purification of a SET-retaining KMT2A-derived fusion complex fails all four routes, and the molecule is the reciprocal product

  the paper is routinely cited for this fusion's complex and is about the reciprocal product instead

• ← testsKnock a tag-plus-degron cassette into the endogenous KMT2A::AFF1 allele in SEM - one construct that makes five claim classes attributable

  makes five claim classes about this protein attributable with one construct

• ← related toExperiment: does MLL-AF4 transform a staged fetal progenitor when it cannot transform cord blood?

  Counter-evidence (Barabe 2007, PMID 17463288): primary human haematopoietic cells expressing an MLL fusion DID generate serially transplantable myeloid or lymphoid acute leukaemia in mice, so the cord-blood refractoriness to MLL-AF4 is partner-specific, not source-specific -- the design needs an MLL-ENL positive-control arm before the fetal-window interpretation is admissible

• ← related toExperiment: long-hold degron depletion of endogenous KMT2A::AFF1, to ask whether the leukaemic program recovers without the fusion

  Counter-evidence (Liu 2007, PMID 17908926): prevalent MLL fusions resist the SCF(Skp2)/APC(Cdc20) degradation that clears wild-type MLL, so the 28-day maintained-depletion arm needs quantitative fusion-protein measurement at every timepoint and a pre-specified depletion floor, or a drifting partial depletion will be misread as programme recovery

• ← related toIn-utero origin, proven: clonotypic KMT2A::AFF1 junctions found in the patient's own newborn blood spot

  clonotypic KMT2A::AFF1 genomic junctions recovered from the patient's own newborn blood spot

• ← related toTwin concordance: near-total for infant KMT2A-rearranged leukaemia, about 5% for childhood ALL overall

  near-total concordance argues the fusion is close to sufficient in the fetal target cell

• ← related toAre the fusions temporary? No: the KMT2A fusion is the one thing that does not change between diagnosis and relapse

  the fusion is truncal and retained through relapse and lineage switch

• ← depends onHypothesis: KMT2A::AFF1 is continuously required, not a hit-and-run initiator whose job is done once the epigenome is set

  hypothesis is about continuous requirement for this fusion specifically

• ← inhibitsCorrecting the fusion with genome editing: verdict NOT FEASIBLE for infant leukaemia, though intron-targeted disruption is a real published strategy

  intron-targeted double cut would disrupt the fusion specifically in rearranged cells

• ← inhibitsRNA-targeting the fusion transcript: verdict THE LEAST HOPELESS of the three fusion-level routes, blocked by delivery rather than by biology

  junction-directed siRNA or ASO eliminates the fusion transcript

• ← analogous toSET / TAF-I beta - a histone chaperone that binds the retained N-terminus of MLL, co-activates HOXA with it, and is itself a HOXA-activating fusion partner that recruits DOT1L

  SET-NUP214 activates HOXA in paediatric T-ALL; same output, different machine

• ← related toDoes KMT2A::AFF1 change histone turnover at its target genes, or does it read a chromatin state it did not make?

  asks whether the fusion sets or inherits the turnover rate at its targets

• ← testsDoes KMT2A::AFF1 bind the histone chaperone SET/TAF-I beta, and does that contact overlap the menin-binding motifs? A co-IP and a peptide competition

  whether the fusion retains the 2005 MLL N-terminus/TAF-I beta contact

• ← supportsThe trans-histone crosstalk H2Bub → DOT1L → H3K79me: modulatory for me1, effectively required for me2/me3

  DOT1L ubiquitin-binding and acidic-patch mutants fail to support proliferation of the KMT2A::AFF1 line MV4;11

• ← related toPAF1C couples transcription to H2B ubiquitination - but the RTF1 half of that coupling is yeast-specific and contested in human cells, and PAF1C is one of the few complexes that genuinely binds the retained KMT2A fragment

  PAF1C binds sequences flanking CxxC, retained in every KMT2A fusion; whether that contact delivers the ubiquitination machinery is untested

• ← regulatesH2BK120ub (H2Bub1) — the ubiquitin tag on histone H2B that licenses H3K79 methylation, and the mark this graph was missing

  enriched across the bodies of MLL-fusion target genes and required for H3K79me there

• regulates →CDK6 - the kinase the KMT2A-r rationale actually rests on, and the pan-essentiality flag and the selectivity are both true

  CDK6 mRNA falls on siRNA knockdown of MLL-AF4; CDK6 is a transcriptional output of the fusion

• ← expressed inICOSLG on infant t(4;11) blasts converts T cells into regulatory T cells - the one immune-evasion route measured in this exact disease, in this exact age group

  ICOSLG elevated at diagnosis in 43 t(4;11) infants and strongly raised at relapse in 18

• regulates →CSPG4 / NG2 - the flow-cytometry surrogate for a broken KMT2A, and a direct target gene of the fusion that makes it

  NG2/CSPG4 is an epigenetically regulated DIRECT target gene of MLL-AF4; it suppresses NR3C1 via FLT3/AP-1 and confers glucocorticoid resistance

• ← related toCD34 - named in 132 entries of this graph and written in none, and it does not mean what the graph has been using it to mean

  CD34 does NOT fractionate the leukaemia-initiating compartment in MLL-AF4: both CD34+CD38+CD19+ and CD34-CD19+ cells initiate, while CD34+CD38-CD19-CD33- is enriched for NORMAL HSC

• regulates →PROM1 / CD133 - a direct MLL-AF4 target switched on by an intragenic H3K79me2/3 enhancer, and the one surface target in this disease with a published human-relevant kill

  direct MLL-AF4 binding at PROM1 via an intragenic H3K79me2/3 enhancer element (KEE); PRC2-repressed when off

• ← related toKMT2A-rearranged acute leukemia across all ages: infants are 4% of it

  AFF1 is one of 107 in-frame KMT2A fusion partners catalogued

• ← related toPER-490 (CVCL_W986) — a KMT2A::AFF1 B-ALL line from a nine-day-old infant

  carries the index fusion; t(4;11) by karyotype and KMT2A break-apart FISH

• ← related toPER-494 (CVCL_A8JU) — infant t(4;11;7) line, and the one whose AFF1 was never demonstrated

  t(4;11;7); AFF1 inferred not demonstrated

• ← related toPER-485 (CVCL_W984) — the relapse half of a matched infant t(4;11) pair, and it has lost CD19

  der(11)t(4;11)(q21;q23) at relapse

• ← related toPER-785 (CVCL_IZ03) — infant t(4;11) line from a child who survived

  t(4;11)(q21;q23) confirmed by directed metaphase KMT2A FISH

• ← related toALL-PO (CVCL_1069) — an infant KMT2A::AFF1 line that is already in DepMap and has never been screened

  Cellosaurus KMT2A-AFF1 gene-fusion annotation

• ← related toBLIN-3 (CVCL_QW47) — a three-month-old's KMT2A::AFF1 line used to show the pro-B to pre-B block can be pushed

  Cellosaurus KMT2A-AFF1 annotation; 3-month-old donor

• ← related toSCMC-L1 (CVCL_7125) — a four-month-old's KMT2A::AFF1 line carrying NSD2 E1099K

  Cellosaurus KMT2A-AFF1 annotation; 4-month-old donor

• ← related toThe KOCL series (CVCL_3993, CVCL_6867, CVCL_3994, CVCL_3995) — four Japanese infant KMT2A::AFF1 lines, all under one year

  four Japanese infant lines annotated KMT2A-AFF1

• ← related toSEM (CVCL_0095) — the workhorse, from a five-year-old, and microsatellite unstable

  the most-used human KMT2A::AFF1 model; donor aged 5 years

• ← related toRS4;11 (CVCL_0093) — an ADULT KMT2A::AFF1 line, MSI-high, carrying NSD2 E1099K

  in-frame KMT2A::AFF1 from a 32-year-old; NCIt term is adult B-ALL

• ← related toMV4-11 (CVCL_0064) — KMT2A::AFF1, yes, but a ten-year-old's acute monocytic leukaemia with FLT3-ITD

  carries KMT2A::AFF1 in a monocytic AML background

• ← related toThe 'infant ALL' PDX panel with four KMT2A::AFF1 models — one of which the full text calls adult

  four infant PDX models carrying the index fusion

• ← related toCRISPR-engineered t(4;11) in human fetal liver — the only model that reproduces infant-specific biology

  endogenous t(4;11) engineered in primary human fetal liver cells

• ← related toMll-AF4 mouse genetics — B-lineage tumours, long latency, and never infant pro-B ALL

  conditional mouse systems for the index fusion

• ← related toMLL fused to MURINE Af4 in human CD34+ cells — the model that works, and the swap that makes it work

  human MLL fused to MURINE Af4; recapitulates pro-B ALL

• ← related toThe pluripotent stem-cell route has failed from both ends, and the failures are informative

  MLL-AF4 in human ESCs; and failed iPSC reprogramming of MLL-r B-ALL

• ← related toIMSUTi002-A-2 (CVCL_C9HE) — a doxycycline-inducible KMT2A::AFF1 iPSC line, and the isogenic design nobody in this graph has used

  doxycycline-inducible KMT2A-AFF1 in a healthy-donor iPSC

• ← depends onFLT3 / CD135 — the strongest non-tether co-dependency, and a target the field may have written off on a badly executed trial

  KMT2A::AFF1 lines SEM, SEMK2 and MV4-11 are among the most FLT3-depleted in DepMap

• regulates →BCL2 — the one co-dependency in this beat that already has an approved drug pointed at it

  MLL/AF4 upregulates BCL2 specifically via DOT1L-dependent H3K79me2/3

• ← refutesRBBP5 — a WRAD subunit that binds the one part of KMT2A every fusion throws away

  correction: RBBP5 is not a direct interactor of the fusion; its contact surface is not retained

• ← refutesASH2L — the WRAD subunit that has DPY30's essentiality profile and none of its co-dependency signal

  correction: ASH2L binds the SET domain, lost at every KMT2A breakpoint

• ← refutesKDM6A / UTX — a commonly asserted KMT2A partner that belongs to a different complex and points the opposite way

  correction: UTX belongs to MLL3/MLL4 COMPASS-like, not to MLL1 or the fusion complex

• regulates →HOXA9 — required for survival of established MLL-rearranged leukemia, and dispensable for starting it

  canonical transcriptional output at the HOXA locus

• ← testsSeparate positioning from catalysis: an ASH2L mutant that keeps RBBP5 and loses DPY30

  run in SEM and SEMK2, both KMT2A::AFF1

• ← supportsKMT2A / MLL1 — the gene that breaks

  the intact allele is not a bystander: MLL1 fusion proteins lack the PHD fingers and require a prebound wild-type MLL1 complex for stable HOXA9 association

• ← related toHCFC1 (HCF-1) — a founding member of the wild-type KMT2A complex that the fusion cannot bind

  NOT an interactor: the HBM at aa 1799-1802 lies beyond the breakpoint cluster region and is deleted from the fusion

• ← related toPPIE (CyP33) — the off-switch the fusion throws away, and the reason PHD3 reinsertion kills transformation

  NOT an interactor: PHD3 is deleted from all KMT2A translocation products, and reinserting PHD3 abrogates transformation

• ← related toKAT8 (MOF) — a genuine KMT2A partner that binds the half of KMT2A the fusion discards

  NOT an interactor: the mapped contact is C-terminal to every clinical breakpoint

• ← related toCREBBP (CBP) — binds the KMT2A transactivation domain, which no fusion keeps

  NOT an interactor: the TAD is deleted, so the fusion has no activation domain of its own

• ← related toUSP22 — a KMT2A-rearranged dependency that works through MEIS1 protein stability, and is not an interactor of the fusion

  downstream dependency, NOT a demonstrated interactor: no published test of binding to any KMT2A fusion

• ← related toSIAH1 — the E3 ligase that degrades AFF1, and that the reciprocal AF4::KMT2A fusion escapes

  NOT an interactor of the der(11) product: the AFF1 N-terminus is carried by the reciprocal AFF1::KMT2A, not by KMT2A::AFF1

• ← related toSIAH2 — the second AFF1 E3 ligase, reported only alongside SIAH1 and never separated from it

  NOT an interactor of the der(11) product

• regulates →RUNX1 — activated by KMT2A::AFF1 and then bound by the reciprocal fusion, in the one published two-oncoprotein circuit in t(4;11)

  RUNX1 is a direct transcriptional target of MLL-AF4 in t(4;11)

• ← related toMLLT6 (AF17) — the fourth KMT2A fusion partner inside DotCom, and the only one no cell needs

  NOT an interactor: DotCom and the AF4/P-TEFb assembly are alternatives, and DOT1 does not bind AF9-AF4-P-TEFb complexes

• ← bindsRTF1 — the PAF1C subunit the graph was missing, on a complex that does bind the retained KMT2A fragment

  PAF1C binds sequences flanking the CxxC domain, which the fusion retains (complex-level claim, shown for MLL-AF9)

• ← related toThe little elongation complex (ELL + ICE1 + ICE2 + ZC3H8) — the other place ELL works, and why ELL's pan-essentiality is probably not about the fusion

  NOT an interactome member: no KMT2A or AFF1 contact; entered to reinterpret ELL's essentiality

• ← testsFirst systematic enumeration of the KMT2A fusion interactome, and the diff against this graph

  first systematic enumeration of the fusion interactome from primary complex-composition sources

• ← testsProximity-labelling map of KMT2A::AFF1 — the experiment nobody has run in twenty years of interactome work

  no proximity-labelling map of any KMT2A fusion exists in the indexed literature

• ← related toPCGF1 — the PRC1.1 scaffold whose LOSS causes menin-inhibitor resistance, so it is a restraint on the leukaemia rather than a dependency of it

  NOT a demonstrated interactor: no co-IP, proximity or structural evidence of PCGF1 contacting any KMT2A fusion; the relationship is promoter-level antagonism

• ← related toRNF2 (RING1B) — the one catalytic subunit shared by every PRC1 flavour, which is why the genetics point two ways at once

  NOT a demonstrated interactor: no experiment places RING1B on a KMT2A fusion protein

• ← related toBCORL1 — the BCOR paralogue that is in the only crystal structure of the PRC1.1 core, and is the one PRC1.1 subunit nobody has tested in KMT2A-rearranged leukaemia

  NOT an interactor and entirely untested: 7 PubMed records for (MLL OR KMT2A) AND (BCORL1 OR CXXC10), none a functional test

• ← related toSKP1 — a pan-essential housekeeping adaptor that is also a structural subunit of PRC1.1, which makes it the one PRC1.1 member that can never be a target

  NOT an interactor: pan-essential (-1.281), zero KMT2A selectivity, 1 PubMed record across four symbol spellings

• ← related toPRC1.1 — the complex this graph has been leaning on, now enumerated subunit by subunit, and the enumeration changes the conclusion

  NOT an interactome member: the documented relationship is promoter-level antagonism; no PRC1.1 subunit has been shown to contact a KMT2A fusion

• ← related toSUPT5H (SPT5) — the pausing factor the KMT2A field has never studied, and the counted absence that undercuts 'the fusion hijacks pause release'

  NOT an interactor: 1 PubMed record across all aliases co-occurring with MLL/KMT2A; no functional test in any KMT2A-rearranged model

• ← related toSUPT4H1 (SPT4) — zero papers linking it to KMT2A, and the 138th most KMT2A-selective gene out of 17,728

  NOT an interactor: 0 PubMed records with MLL/KMT2A, yet rank 138/17,728 for KMT2A selectivity - an unexplained lead

• ← related toNELF — the brake that has to come off for elongation, absent from the KMT2A literature, and less required in KMT2A-rearranged lines than in any other leukaemia

  NOT an interactor: 1-2 records across all subunit aliases, all reviews; no functional test in KMT2A-rearranged disease

• ← testsMeasure the pausing index at KMT2A::AFF1 target genes — the one number the whole pausing argument turns on, and it has never been reported

  measures directly what the fusion does to promoter-proximal pausing at its own target genes - never published for any KMT2A fusion

• ← related toEAF1 — the interactor with an actual subnuclear phenotype: an MLL fusion evicts it from Cajal bodies, and the bodies themselves fall apart

  NOT a demonstrated interactor: EAF1's contacts are with ELL and ELL2, and the fusion phenotype is MLL-ELL, a different partner

• ← related toEAF2 (U19) — the EAF paralogue whose ELL-binding domain is a mapped tumour-suppressor module, described entirely in prostate cancer

  NOT an interactor and untested in leukaemia: 5 PubMed records with MLL/KMT2A, all functional work in prostate cancer

• ← related toICE1 — the 2,266-residue scaffold of the little elongation complex, the subunit that acts at initiation, and zero papers connecting it to leukaemia of any kind

  NOT an interactor: 0 PubMed records against MLL, KMT2A or leukaemia across both symbol spellings

• ← related toICE2 — the fourth LEC subunit, the one with no assigned step, no structure, and no leukaemia literature

  NOT an interactor: 0 PubMed records against MLL, KMT2A or leukaemia across three symbol spellings

• ← related toEP300 — the acetyltransferase whose paralogue split is the finding: p300 is the 108th most KMT2A-selective gene, CBP is the 16,950th

  NOT a demonstrated interactor: the evidence is genetic requirement and pharmacology, with no experiment placing p300 on a KMT2A fusion protein

• ← related toKDM1A (LSD1) — acts at the loci the fusion binds, spares normal stem cells, and still has never been shown to touch the fusion protein

  NOT a demonstrated interactor: co-occupancy at fusion-bound loci plus functional dependence is not a protein-protein interaction

• ← related toMYB — rank 17 of 17,728 for KMT2A selectivity, and the only node in this beat where partial, transient suppression eradicated leukaemia without stopping normal blood production

  NOT an interactor: MYB is a downstream effector enforced BY the fusion programme, shown by transcriptional profiling and inducible RNAi

• ← related toBRD9 — dispensable in the average cell, rank 39 of 17,728 in KMT2A-rearranged lines, and with an on-target proof most epigenetic targets never get

  NOT a demonstrated interactor: rank 39/17,728 for KMT2A selectivity comes from an unbiased scan, and (MLL OR KMT2A) AND BRD9 returns 3 records

• ← related toSUPT16H (SPT16) - the large FACT subunit: pan-essential, an anti-dependency in KMT2A-rearranged lines, and drugged in MLL-r leukaemia by a compound that works through p53

  No published physical link: FACT-versus-SEC/AFF1 queries return zero relevant records and the DepMap difference is an anti-dependency.

• ← related toSSRP1 - the small FACT subunit, and the only protein in this beat that binds a confirmed KMT2A-fusion interactor directly (LEDGF/p75, via HMG box to PWWP)

  Two mapped contacts away via LEDGF/p75; no direct evidence and an anti-dependency in the DepMap scan.

• ← related toFACT (SPT16-SSRP1) - the chromatin arm of transcription elongation, and a clean negative result for the KMT2A::AFF1 interactome

  Clean negative: zero title-checked records link FACT to the fusion or the SEC, and both subunits are anti-dependencies.

• ← related toMED23 — rank 16 of 17,728, survives the lineage split with the B-lineage half stronger, and is not absent from the leukaemia literature after all

  Data-driven lead only: rank 16 of 17,728 with a stronger B-lineage than myeloid arm, and zero published records tying MED23 to KMT2A.

• ← related toDoes WDR5 move between complexes? An acute KANSL1 degron with WDR5 co-IP, WDR5 CUT&RUN and H4K5/K8/K16ac readout in a KMT2A-rearranged line

  Run in SEM, a KMT2A::AFF1 B-lineage line, alongside a myeloid line so both halves of the lineage split are represented.

• ← related toThe RNA layer scored for KMT2A-selectivity across 79 genes, lineage-split — PTBP1 is the only menin-shaped hit, and the IGF2BP family shows no co-dependency

  Index arm is 11 KMT2A-rearranged lines, three of the four lymphoid ones KMT2A::AFF1

• ← regulatesKHDRBS1 (Sam68) — an RNA-binding protein that holds the MLL-AF4 message DOWN, a class no dropout screen can find

  Ribosomal stalling at AU-rich sites inhibits MLL-AF4 translation; synonymous escape mutants transform

• ← regulatesRNA-binding proteins set how much KMT2A::AFF1 protein a cell makes from its own fusion transcript

  Sets fusion protein output from the fusion transcript, post-transcriptionally

• ← co-occurs withIGF2BP2 — the paralogue co-over-expressed with IGF2BP3 in MLL/AF4 B-ALL, and the one with an inhibitor in another leukaemia

  Over-expressed in MLL/AF4-positive B-ALL alongside IGF2BP3

• ← testsThe decisive experiment: acute degron removal of IGF2BP3, IGF2BP2 and both, read on self-renewal and xenograft initiation rather than bulk dropout

  Three KMT2A::AFF1 index lines plus a KMT2A-rearranged non-AFF1 comparator

• ← depends onPTBP1 — the strongest RNA-layer dependency in KMT2A-rearranged lines, found by a domain-focused screen and missed by this beat's own gene panel

  KMT2A-rearranged bias in a domain-focused RNA-protein CRISPR screen; reproduced lineage-split in DepMap

• ← related toHNRNPA2B1 — the panel's strongest KMT2A-selective RNA-layer gene after PTBP1, with ZERO records against MLL or KMT2A

  Selectivity signal in KMT2A-rearranged lines with zero published records

• ← treated byI3IN-002 — the first small-molecule IGF2BP3 inhibitor with in vivo activity in an MLL-Af4 model

  Anti-leukaemic activity in a syngeneic MLL-Af4 transplantation model

• ← part ofLEDGF IBD to KMT2A: TWO motifs, not one - IBM1 at 124-133 and IBM2 at 147-152, and the Kd this graph recorded as missing is 14.7 uM

  both motifs retained in the index fusion

• ← related toWDR5 WIN site and KMT2A Arg3765: measured at 1.7 uM, three co-crystals, and absent from every leukaemic fusion - plus the MLL3 peptide that binds it 51-fold tighter

  absent from the index fusion by position

• ← part ofMBM2, the second menin-binding motif of KMT2A (residues 23-40): 26-fold weaker than MBM1, never separately co-crystallised, and the only part of the menin grip a drug is not aimed at

  retained in the index fusion

• ← related toThe AFF-family N-terminus on cyclin T1: Kd 10 nM, a 2.94 A crystal, and every number in it measured on AFF4 rather than on AFF1

  the characterised contact lies N-terminal to the AFF1 breakpoint and is not in the fusion

• ← part ofAFF1-AFF4 heterodimerisation through the C-terminal homology domain: the one SEC interface KMT2A::AFF1 certainly keeps, defined by a 2.2 A structure of the wrong subunit

  the SEC interface with the strongest positional claim to being retained

• ← related toTaspase1 and its two KMT2A cleavage sites: an enzyme-substrate interface with four apo structures, one co-crystal with a small molecule, and no structure with MLL at all

  the index fusion contains neither site and is not a substrate

• ← part ofCXXC to unmethylated CpG DNA: nine mapped contact residues, and an affinity that spans 44 uM to 33 nM depending on the construct, the DNA and the salt

  retained in the index fusion

• ← related toPHD3 reading H3K4me3: Kd 4.3 uM for the PHD3-bromo cassette, 30 uM for PHD3 alone, two co-crystals - and the whole module is thrown away by the breakpoint

  absent from the index fusion

• ← related toThe KMT2A transactivation domain on the CBP KIX domain: a cooperative allosteric site at 2842-2858, solved three times, and thrown away by every breakpoint

  absent from the index fusion; the lost item is a cooperativity, not a function

• ← part ofKMT2A 747-755 on HLA-B*07:02: a phosphoneoantigen from the half of KMT2A every fusion keeps, with seven crystal structures and a cognate TCR

  S750 lies in the retained KMT2A fragment of the index fusion

• ← related toHalf this graph's claims are unopposed; these are the ones that matter

  Highest-load unopposed claim in the graph, at degree 131 on a source shared by 50 entries.

• ← related toKMT2A::AFF1 has had a published affinity-purification interactome since 2018 — in a paper titled for SETD2, uncurated by IntAct, and cited zero times here

  Records that the index fusion was one of seven Strep-HA-tagged AP-MS baits in Skucha 2018 (PMID 29777171), purified from nuclear lysate of isogenic Jurkat cells — a published, bait-specific interactome for KMT2A::AFF1 that this graph had never cited.

• ← related toThree quarters of KMT2A::AFF1's top partners are shared with other MLL fusions — and the two analyses that said otherwise were both artifacts of how the source table was built

  Measures how distinctive the index fusion's protein interactome is against six other MLL fusions in one isogenic system: at equal n it is unremarkable, ranking 3rd, 4th and 5th of seven, with roughly three quarters of its top partners shared.

• ← related toKMT2A::AFF1 retains THD2 by position, so the HBO1 contact can apply to it — but the paper that established that contact tested MLL-ELL, MLL-AF6 and MLL-AF10, never the index fusion

  Answers a domain-retention question positionally: THD2 sits within MLL 869-1124, N-terminal to the CXXC domain at 1147-1195 that every leukaemogenic fusion retains, so the index fusion carries it. Whether it FUNCTIONS there is untested.

• ← related toOne trial, two published analyses, never crossed: gemtuzumab clearly helps KMT2A-rearranged children, and a common CD33 genotype abolishes gemtuzumab benefit — nobody has asked whether it abolishes it in them

  Bears on the rearrangement class rather than on this fusion specifically: AAML0531 is an AML trial, 215 of 1,022 KMT2A-rearranged, and t(4;11) KMT2A::AFF1 is rare in AML cohorts. The entry says so rather than transferring the result across lineage.

• ← analogous toNUP98::KMT2A, inv(11)(p15q23) — the NUP98 fusion that contains KMT2A and is menin-inhibitor RESISTANT

  THE CIS/TRANS NATURAL EXPERIMENT. Both contain KMT2A sequence and they differ in whether the menin-binding motif survives: KMT2A::AFF1 retains MBM1/MBM2 in cis and is menin-sensitive, while NUP98::KMT2A deletes KMT2A exon 1 and removes the MBM from the very MLL1 species the fusion supplies - and is resistant. This pair is the sharpest evidence for hyp-menin-dependency-tracks-available-mbm.

• ← regulatesHMGA2 (P52926) - a direct KMT2A::AFF1 target through the let-7b axis, and a recurrent fusion partner whose own fusions work by escaping a microRNA rather than by making a chimeric protein

  HMGA2 is a TARGET of the index fusion, not a partner: KMT2A fusions suppress MIRLET7B by promoter hypermethylation and also positively regulate HMGA2 directly, and HMGA2 then represses CDKN2A (PMID 26403224, uncited here until now)

• ← bindsMLLT1 / ENL — the reader that beat its own paralogue, with a degrader already in hand

  ENL, the acyl-histone reader that outperformed its own paralogue as a target

• ← bindsMLLT3 / AF9 — a famous fusion partner that is not a dependency, and a hub domain that is

  AF9, a famous partner that is not itself a dependency

• ← bindsCBX8 — the one place in this interactome where two good papers flatly disagree, and DepMap takes a side

  binds the partner side; two good papers disagree about what it does there

• ← bindsKAT7 / HBO1 — an enzyme, a leukaemia-stem-cell dependency, and an inhibitor already in a crystal
• ← co-occurs withKRAS as a co-mutation in KMT2A-r leukemia — the single most frequently co-mutated gene, and it still cannot start the disease

  the single most frequent co-mutation

• ← co-occurs withNRAS as a co-mutation in KMT2A-r leukemia — the one co-lesion that is specifically enriched in t(4;11)
• ← co-occurs withFLT3 in KMT2A-r leukemia — near-universal overexpression, but activating mutation in only ~3% of infants

  near-universal overexpression, but activating mutation is rarer than assumed

• ← testsStep 5: molecular confirmation and naming the partner

  the step that names the partner

• ← regulatesmiR-9 — the most MLL-specific microRNA in AML, encoded at three separate loci nobody has disambiguated

  the most KMT2A-specific microRNA in myeloid leukemia

• ← related toThe reciprocal fusion (AFF1::KMT2A and friends): a second oncoprotein that opens chromatin for the first

  the second oncoprotein made by the same translocation

• ← related toHypothesis: the R-loop landscape of a KMT2A::AFF1 blast is remodelled by the fusion and is both a vulnerability and a source of ongoing genome instability

  an empty cell in the genome-wide sweep

• ← related toHypothesis: transfer-RNA and ribosome biology is a genuinely empty cell in KMT2A-rearranged leukemia, and translational capacity may be the unmeasured dependency

  recorded explicitly as an untouched area

• ← testsCorrecting the fusion with genome editing: verdict NOT FEASIBLE for infant leukaemia, though intron-targeted disruption is a real published strategy
• ← supportsStep 3: the G-banded karyotype and t(4;11)(q21;q23)

  t(4;11)(q21;q23) on the karyotype is the cytogenetic signature of this fusion

• ← part ofKMT2A minor breakpoint cluster region (BCR2): intron 20 - exon 24

  the second, minor breakpoint cluster region of the same gene; relevant to which fusions a PCR assay detects

• ← depends onTERT — telomerase, switched on by the index fusion through HOXA7
• ← analogous toLPP (lipoma-preferred partner) - a KMT2A fusion partner in acute monoblastic leukaemia whose day job is adhesion mechanotransduction, and which is barely expressed in leukocytes

  a KMT2A fusion partner from a different family: contributes two adhesion LIM domains rather than an elongation module, and is barely expressed in leukocytes

• ← related toIn St. Jude paediatric AML, 2 of the 6 ARID1A-mutant cases are KMT2A-rearranged and BOTH ARID1A mutations are TRUNCATING frameshifts in KMT2A::MLLT10 cases - so the exact combination cycle 86 showed the ARID1B dependency is confined to DOES occur in patients, and cycle 88's empty DepMap intersection is a cell-line sampling artefact rather than a fact about the disease. The paediatric ALL cohort returned zero ARID1A mutations, which is panel coverage and not biology

  the fusion this project exists for has ZERO documented truncating-ARID1A co-occurrences: the only B-lineage cohort available could not measure ARID1A at all

• ← related toThe two TARGET B-ALL studies in cBioPortal are 868 of the same patients assayed twice, so joining them DOES answer the question I had just written off as unanswerable: all four ARID1A-mutant B-ALL patients are definitively KMT2A-negative, three of them with truncating calls. The answer is zero of three - and at a 2.7% KMT2A-positive rate an empty overlap has probability 0.92, so it is an upper bound and not a finding

  bounds what can be claimed for the fusion this project exists for: zero of three truncating-ARID1A B-ALL patients is KMT2A-rearranged, at P(empty)=0.92

• ← related toRe-measured against IntAct the interactome is 103/217 (47.5%) covered, up from 41.0%, and the read queue is now ZERO - no partner with two publications or two baits lacks an entry, so the instrument's own ranking criterion has stopped selecting anything. It was also persisting the list of partners that DO have entries while counting and discarding the 105 that do not, which is the exact defect cycle 57 fixed for the other list

  the fusion itself resolves to NO gene symbol and its rows sit in the 116 unresolved row-sides, so this coverage figure cannot answer the PI question as literally posed

• ← related toThe interactome tail is orderable after all, just not by evidence: 62 of the 96 unwritten partners are already DISCUSSED somewhere in this corpus and need only promoting to entries, while 34 have never been read at all. Two cycles looked for a priority order in evidence strength and found none, because the ordering that exists is over how much work is left, not over how good the evidence is

  bounds what saturating the PI priority still costs: 62 promotions and 34 readings

• ← related toGSE299100 supplies the vehicle-versus-vehicle pair that neither GSE260742 nor GSE127507 could - two independent control hairpins, both DMSO, same date, uniformly processed to hg38_rmdup.tdf, for MEN1, MLL1 and input - in MV4-11, which Cellosaurus confirms carries KMT2A::AFF1 though it presents as monocytic rather than the infant B-ALL this project studies. It also holds MEN1 and MLL1 ChIP under five different menin inhibitors in that line, and the six control files total 1.87 GB

  MV4-11 carries KMT2A-AFF1 per Cellosaurus CVCL_0064 - the first deposit reached in this thread that is in the project's own fusion

• ← related toBRINP1 (DBC1/DBCCR1/FAM5A) - the last bait-supported partner of the six core proteins without an entry, a neural-specific BMP/retinoic-acid-inducible protein pulled down with DOT1L as bait in one quantitative AP-MS experiment and nowhere else

  two of the three apparently unwritten bait-supported partners were the fusion proteins themselves - Q8TD98 is submitted to UniProt as 'MLL/AF4 fusion protein' and Q2Q440 as 'MLL/ENL fusion protein', 20 residues - curated as interactors of their own components

• ← supportsThe index fusion DISCARDS the SIAH degron: the junction is at AFF1 residue 347, the degron is at human 282-304, and three entries had it the other way because they measured a murine motif against an exon-numbering junction

  confirms the 2026-09-20 correction to residue 347 by unique peptide match, against a beat that had overridden it

• ← part ofKMT2A / MLL1 — the gene that breaks

  contributes the 5' half: DNA targeting plus the menin grip

• ← part ofAFF1 / AF4 — the 3' half of the fusion, and a target with almost no structural footing

  contributes the 3' half: the elongation engine

• ← bindsMEN1 / menin — the adaptor the fusion cannot work without

  clamps the retained MBM1 motif, which is why partner identity does not matter to the drug

• ← bindsPSIP1 / LEDGF p75 — the tether with the best therapeutic index in the whole interactome

  LEDGF completes the chromatin tether alongside menin

• ← bindsDOT1L — the target where excellent chemistry met an indirect interaction

  recruited through the partner side, deposits H3K79 methylation

• causes →Infant acute lymphoblastic leukaemia (ALL diagnosed under 1 year of age)

  the initiating and usually near-sole driver lesion

• arises in →Fetal CD19+CD34+CD10-negative PreProB progenitor — a cell that exists before birth and almost not at all after

  the fetal progenitor whose transcriptome the disease matches

• arises in →Fetal liver haematopoietic stem and progenitor cell — the leading candidate cell of origin for t(4;11) infant ALL

  fetal liver, in utero, before the marrow takes over

• causes →The differentiation block — what it actually is, operationally, in KMT2A::AFF1 leukaemia

  the phenotype that matters: self-renewal on, maturation off

• causes →The stem-like self-renewal state — a limited stem-cell module grafted onto a committed cell
• ← co-occurs withKinase/PI3K/RAS pathway activation — the only common co-lesion class in KMT2A-r leukemia, and it is mostly subclonal

  the most refractory infant subgroup is RAS-mutated, a signalling rather than chromatin addiction

• ← related toThe near-silent genome of infant KMT2A-r ALL — 1.3 non-silent mutations, and why that is bad news as well as good

  one of the quietest genomes in cancer: few escape routes, but also few co-targets

• ← causesTopoisomerase II cleavage and TOP2 poisons as a source of KMT2A breaks

  one candidate source of the initiating break

• ← causesWhich repair pathway glues the fusion together: classical NHEJ vs alternative end joining

  the repair pathway that joins the wrong ends

• ← refutesRAG off-target activity: the dominant mutator in ETV6::RUNX1 ALL, and probably not the cause of KMT2A fusions

  recorded as a mechanism that is almost certainly NOT responsible here

• ← analogous toWhy PML::RARA became curable — and what KMT2A::AFF1 does not share with it

  differentiation therapy as the closer precedent, since menin inhibitors also force maturation

• ← testsStep 4: the split-signal FISH nucleus - one fusion, one green, one red

  how the broken gene is actually seen in the diagnostic lab

• ← testsStep 3: the G-banded karyotype and t(4;11)(q21;q23)
• ← related toWhat is a fusion gene?

  the plain-English entry point

• ← part ofThe fusion junction itself as a small-molecule target: a candid verdict

  the only surface unique to the fusion, and a hard one

• ← related toIGF2BP3 — an RNA-binding protein required for MLL-Af4 leukaemogenesis in mice that CRISPR barely touches in human lines
• ← regulatesIGF2BP3 — an RNA-binding protein required for MLL-Af4 leukaemogenesis in mice that CRISPR barely touches in human lines
• ← refutesOpen ground: the questions in this graph that nobody in the landscape appears to be working on

  Counter-evidence (Prieto 2017, PMID 29137234): open-ground area 2 is uncontested because it failed -- AF4-MLL in human cord-blood CD34+ HSPCs enhanced engraftment but did not initiate leukaemia in 36 weeks; the live question is co-factor, not initiator

• ← related toScott Armstrong & Andrei Krivtsov (Dana-Farber / Boston Children's) — the group that turned menin dependency into a drug

  defined KMT2A-translocated ALL as a transcriptionally distinct entity (2001) and cured KMT2A-r ALL PDX models with menin inhibition

• ← related toThomas Milne (MRC WIMM, Oxford) — MLL-AF4 target biology, enhancer architecture and PROM1/CD133

  maps MLL-AF4 direct target genes and the enhancer-promoter architecture they sit in

• ← related toPablo Menendez & Clara Bueno (Josep Carreras Leukemia Research Institute, Barcelona) — cellular origin, fetal models and infant-specific drug resistance

  NG2 as a direct MLL-AF4 target driving glucocorticoid resistance via NR3C1

• ← related toThe LEDGF hole, measured: every published LEDGF-removal experiment removes it BEFORE or AT transformation, and none treats an established leukaemia in an animal

  the LEDGF literature intersects this fusion in 2 PubMed records

• ← related toThe nuclear pore and NUP98 fusions — a fusion that takes a pore protein's disordered repeats off the pore and builds nuclear droplets with them

  Counter-evidence limits the export: an unrelated FUS IDR substitutes for the NUP98 FG repeats, so 'FG repeats are essential' means 'an IDR is essential' — a generic property with no FG-specific interface to drug and no implication for KMT2A::AFF1

• ← related toThe nucleolus — the one compartment with direct published images of a KMT2A fusion inside it

  MLL-AF4 reported predominantly nucleolar in overexpression systems

• ← analogous toPML nuclear bodies and PML::RARA — the best-worked case of a fusion destroying a nuclear compartment, and what it actually predicts for KMT2A

  the benchmark for fusion-driven mislocalisation; KMT2A has no evidence of comparable grade

• ← related toThe endogenous MLL-AF4 localisation experiment was unattributable, not negative: an anti-AF4 polyclonal in a t(4;11) cell images mostly wild-type AF4

  240 kDa fusion detected in all t(4;11) lines, punctate, indistinguishable from wild-type AF4

• ← related toFLT3-ITD signals from inside the cell, not from the surface - and whether it is the ER or the Golgi decides which pathway fires

  the one compartment experiment in a KMT2A::AFF1-positive line (MV4-11) studies FLT3-ITD, not the fusion

• ← related toPAF1 is annotated as punctate everywhere in the nucleus EXCEPT the nucleolus - and a 2024 proximity map puts it in the nucleolus

  MLL-AF4 cooperates with PAF1 and FACT at high-density enhancer interactions, so PAF1's compartment is load-bearing here

• ← related toIGF2BP3 works in cytoplasmic RNA granules - the only compartment in this beat where a drug is already pointed, and nobody has looked at it in a leukaemia cell

  IGF2BP3 binds both reciprocal t(4;11) transcripts and sets their protein ratio, in a compartment nobody has imaged

• regulates →H3K27ac - named in 40 entries with no entry of its own, and the strongest KMT2A::AFF1 measurement of it is invisible to every abstract search

  MLL-AF4 knockdown reduces H3K27ac at the BCL-2 3' enhancer in SEM cells

• related to →H3K4me2 - the LSD1 substrate, and the only histone mark ever compared head-to-head between two KMT2A fusion partners in human cells

  KOCL-48 and MV4-11 (both KMT2A::AFF1) are the only index-fusion systems with any H3K4me2 data

• ← depends onITGA4 (VLA-4) and NG2 — the niche-adhesion axis of KMT2A-rearranged B-ALL, and the one approved drug that hits it

  NG2 is a direct epigenetically regulated target gene of the MLL-AF4 (KMT2A::AFF1) fusion

• ← testsExperiment: build the missing KMT2A::AFF1 degron and titrate it — what fractional occupancy does the program actually need?

  Design counter-evidence: the comparator degron dataset is MLL::AF9/AML (PMID 35245435) and KMT2A-r ALL responds qualitatively differently to loss of the menin-fusion axis (PMID 38892207), so the time window and terminal readout must be re-derived for ALL.

• ← related toDataset: cBioPortal - open, easy, and containing exactly two KMT2A::AFF1 fusion records

  Counter-evidence: only two KMT2A::AFF1 structural-variant records exist across cBioPortal's 546 studies, but fusion-caller benchmarking (PMID 31639029) shows recall varies widely between methods, so this is a pipeline artefact as much as a cohort fact.

• ← related toAFF1 / AF4 — the 3' half of the fusion, and a target with almost no structural footing

  Counter-evidence (Bursen 2010, PMID 20194896; Prieto 2017, PMID 29137234): AF4.MLL alone induced pro-B ALL in mice while MLL.AF4 alone induced none over 13 months, but AF4-MLL was insufficient to initiate leukaemia in human cord-blood CD34+ cells over 36 weeks. Which derivative product drives t(4;11) is an unresolved, species-split dispute.

• ← supportsRELA (p65) — menin binds it and represses it, and it is required to keep MLL oncoproteins on chromatin

  IKK/NF-kB required for MLL fusion retention on chromatin; RELA occupies MLL target promoters

• ← depends onELOVL1 - the fatty-acid elongase that infant MLL-AF4 ALL retains from its fetal origin, and the lipid enzyme on the opposite side of the divide from ACSL4

  critical for survival of MLL-AF4-positive ALL cells within the retained fetal signature

• ← part ofAK_7_3, a KMT2A::AFF1-derived fusion circRNA that holds down mitochondrial respiration and ROS in t(4;11) B-ALL - the only mitochondrial mechanism in this beat measured in the index fusion

  a fusion-derived circular RNA product of the t(4;11) rearrangement

• ← related toDOT1L and H3K79 in KMT2A::MLLT1: a direct partner contact, mutually exclusive with the elongation complex, and the only fusion with a DOT1L-inhibitor complete remission

  contrast case: AF4-family proteins do not bind DOT1L directly and carry lower H3K79me2 at their target loci

• ← related toThe transfer rule: which MLL-AF9 results can be carried into t(11;19) and t(4;11), and which are statements about a protein missing a reading module

  which MLL-AF9 results cannot be read into t(4;11)

• ← related toMRD by genomic breakpoint: the only assay in this disease that is fusion-specific by construction

  patient-specific der(11) junction is the tracked marker

• ← related toMRD by fusion transcript: fast, standardised, partner-limited - and structurally blind to KMT2A*

  t(4;11)/MLL-AF4 was one of the nine BIOMED-1 standardised targets

• ← related toMRD by Ig/TCR rearrangement: the standard in ALL, and the assay infant KMT2A-rearranged disease strains hardest

  MLL-AF4-positive infants showed the most immature Ig/TCR rearrangement patterns

• ← related toProximally biased V(D)J and IGHV6-1 in KMT2A::AFF1: the Ig MRD target is a moving target, and the clinic had already moved

  proximal IGHV bias and de novo DJH recombination across 121 KMT2A::AFF1 cases

• ← related toIs reciprocal status or breakpoint position used in MRD design or risk stratification? Once, by necessity, in 16 of 3,401 patients - and nowhere in any risk model

  reciprocal AF4-MLL expression in 45% of t(4;11) infants and its prognostic effect

• ← related toTNF — the only NF-kB-activating ligand with real KMT2A::AFF1 B-ALL evidence, and the evidence says the blasts are RESISTANT to it

  TNF resistance is specific to MLL-AFF1-positive lines and transgenic mice

• ← related toBortezomib is called an NF-kB inhibitor, and in MLL leukaemia it does two different things in two lineages — neither of which is reliably NF-kB in the lymphoid one

  in pro-B MLL leukaemia the mechanism is MLL-AF4 accumulation, not NF-kB

• ← testsCombine an IKK inhibitor with a clinical menin inhibitor in a KMT2A::AFF1 B-ALL line, and read out fusion OCCUPANCY rather than viability

  SEM and RS4;11 KMT2A::AFF1 B-ALL lines as the primary system

• ← co-occurs withKMT2A::SEPTIN11 (MLL-SEPT11) — the fusion that cytogenetically impersonates t(4;11)

  cytogenetically indistinguishable; SEPTIN11 lies within 250 kb proximal to AFF1

• ← related toWhat is actually conserved across KMT2A partner classes — forced self-association, with two documented exceptions that break the rule

  the elongation hijack as a special case of the general requirement

• ← related toI-BFM childhood KMT2A-r AML (n=1,130): the 3-prime partner defines two risk groups that differ by 24 EFS points

  AFF1 (4q21) assigned to the high-risk partner group in AML

• ← related toPonte-di-Legno non-infant KMT2A-r ALL (n=629): 5-year EFS spans 41.7% to 91.2% across partner-by-lineage cells

  t(4;11) B-ALL 5-year EFS 64.8% (n=266), the largest arm

• ← related toInfant BCP-ALL (n=175): KMT2A::AFF1 2-year EFS 36% versus 37% for every other partner (P=0.9)

  AFF1 indistinguishable from pooled other partners in infants

• ← related to465 KMT2A-r B-ALL cases from 1 month to 89 years: partner predicts MRD clearance independently of age

  AFF1 associated with slower MRD clearance (P=7.0E-04 univariate)

• ← related toThe age confound: a partner arm and an age arm are nearly the same arm

  AFF1 is 71% of adult versus 48% of infant/paediatric B-ALL, not an infant-only partner

• ← related toAUGMENT-101: the partner composition of the trial that approved a menin inhibitor, with KMT2A::AFF1 at n=2 evaluable

  KMT2A::AFF1 is 3.5% of the efficacy population and 7.4% of the safety population

• ← refutesThe CRISPR-ChIP H3K79 partition is a mouse MLL-AF9 result: resolved from GEO after the full text proved unreachable

  no sample in the study carries the index fusion; the partition is untested in KMT2A::AFF1

• ← supportsHow much of this graph's mechanism is somebody else's fusion? A counted answer: 54% of fusion-bearing evidence, and 0% from a dedicated human KMT2A::AFF1 experiment

  quantifies how little of the asserted mechanism was measured in the index fusion

• ← part ofKMT2A::AFF1 has no mapped interface to DOT1L: it lacks both structurally defined recruitment modules, and the one complex-level route claimed for it is contested by reconstitution

  the index fusion's interface ledger for DOT1L recruitment

• ← part ofPartner import: when a mechanism measured in one fusion is asserted about another

  the index fusion imports are measured against

• ← supportsThe imports that were never necessary: H3K79 methylation in KMT2A::AFF1 has its own literature, and this graph barely cites it

  the index-fusion H3K79 evidence that did not need importing

• ← part ofAFF1 AF4_int motif to AF9/ENL AHD: the index fusion's only documented elongation interface, and it competes with DOT1L

  the index fusion's only documented elongation interface

• ← part ofIn KMT2A::AFF1 there is no oncogenic DOT1L unit: all H3K79 methylation is the endogenous MLLT10-directed activity, working on genes the fusion has opened

  a hypothesis about the index fusion's H3K79 biology

• ← part ofRepeat the H3K79 partition in a human KMT2A::AFF1 line: menin inhibition and MLLT10 knockout, side by side with a KMT2A::MLLT3 line

  the index fusion arm

• ← part ofWhat could refute the menin-interface bet, restated after the provenance audit: three tests, none of which is about menin binding

  the index fusion the chain must hold for

• ← part ofBite-back: a target nominated from an imported mechanism inherits a fusion the index disease does not have

  the fusion whose interfaces bound the risk

• ← related toKMT2A::USP2, inv(11)(q23.3q23.3) - the minor-BCR fusion that keeps the PHD fingers

  contrast case: AFF1 breaks in the major BCR and loses the PHD fingers; USP2 breaks in the minor BCR and keeps them

• ← related toThe partner's deubiquitinase domain is what lets a PHD-retaining KMT2A fusion survive and transform

  counterexample: two KMT2A::AFF1 minor-BCR patients retain the PHD fingers with no deubiquitinase partner, so UCH rescue cannot be necessary

• ← related toA six-month-old with a week of coughing: KMT2A::AFF1 pro-B ALL presenting with extreme hyperleukocytosis

  KMT2A::AFF1 confirmed by fusion panel and whole-transcriptome sequencing; 46,XY,t(4;11)(q21;q23)

• ← related toTwo clones, two antibodies: a four-month-old with refractory KMT2A::AFF1 mixed-phenotype leukaemia treated with blinatumomab and gemtuzumab together

  KMT2A::AFF1 (MLL-AF4) confirmed by RT-PCR; KMT2A rearranged in 93% of nuclei by FISH

• ← related toMixed phenotype acute leukaemia (MPAL) and acute leukaemia of ambiguous lineage

  15 of 233 children in the iBFM-AMBI2012 ambiguous-lineage cohort carried KMT2A::AFF1, with 11 more carrying another KMT2A rearrangement

• ← depends onPhase-2 dossier: the LEDGF/PSIP1 IBD - the best therapeutic index in the interactome, a solved structure, two hotspot residues, and three compounds in the world

  the dependency this programme would exploit

• ← related toPhase-2 dossier: the fusion junction - a negative feasibility finding, with the one surviving modality named

  the junction whose structural record was checked and found empty

• ← related toDataset: cBioPortal - open, easy, and containing exactly two KMT2A::AFF1 fusion records

  the public instance holds two KMT2A::AFF1 structural-variant records in total

• ← regulatesCSNK2A1 (casein kinase 2 alpha) - the one kinase that turns up three separate times in KMT2A biology

  CX-4945 reduces MLL-AFF1, AFF4 and ELL2 chromatin occupancy in SEM cells

• ← binds14-3-3 theta binds AF4 at Ser588 and rides into the MLL-AF4 complex - the phospho-gated contact the fusion really does carry

  14-3-3 theta forms a complex with MLL-AF4; S588 is retained in the fusion

• ← testsOne immunoprecipitation that decides whether 14-3-3 touches KMT2A at all

  run in SEM or RS4;11

• ← related toIs BENC even on in the disease this project is about? A module-resolved accessibility and deletion map in KMT2A::AFF1 B-lineage cells

  the index fusion, for which no BENC data of any kind exist

• regulates →HDAC7 - the eraser the index fusion silences, where the proposed therapy is to INDUCE the HDAC, and two 2024-2025 papers point in opposite directions

  fusion co-silences HDAC7 with EZH2; relieved by menin inhibition

• ← treated byValemetostat - an approved dual EZH1/EZH2 inhibitor that has already worked in an MLL-AF4 xenograft, in a disease nobody has enrolled it in

  significantly inhibited growth of a B-ALL PDX harbouring MLL-AF4 - the only index-fusion result for any PRC2 drug

• ← related toAFF1's modern proximity neighbourhood is four RNA-binding proteins - NPM1, RBM15, SBDS, ZRANB2 - and it barely overlaps AFF4's

  wild-type AFF1 only; no positional information and no fusion in the dataset

• ← related toKMT2A sits in the 14-3-3 proximity neighbourhood, and the YWHAG link reproduces across two independent studies

  retention by the fusion undetermined - no 14-3-3 motif mapped on KMT2A

• ← related toThe fusion-oncoprotein TurboID experiment this graph proposes has already been published - for PML::RARA, RUNX1::RUNX1T1, CBFB::MYH11, NUP98::HOXA9 and SET::NUP214, and not for any KMT2A fusion

  no KMT2A fusion has ever been proximity-labelled, while five other leukaemia fusions have

• ← related toThe fusion begins at AFF1 residue 347 and the cyclin T1-binding sequence ends at 308, so KMT2A::AFF1 is the one AFF-family protein that cannot enter the reservoir

  the fusion starts at AFF1 347; the cyclin T1-binding sequence ends at 308

• ← related toKMT2A::AFF1 cells run with more free P-TEFb than other leukaemias - and if they do not, this graph's CDK9 story is about recruitment only

  predicts a measurable difference in these blasts

• ← related toThe two t(4;11) products split AFF1 exactly at the P-TEFb-binding module, and the elongation half goes to the reciprocal

  the translocation splits AFF1's elongation-binding half from its scaffold-binding half

• ← analogous toBRD9::NUTM1, t(5;15)(p15.33;q14) - one fusion is enough to make infant B-ALL in a mouse, and it is the one that behaves best in a child

  CONTRAST CASE, NOT AN ANALOGY. Same disease, same age band, drawn from the same Interfant cohorts, and the opposite outcome: 4-year EFS 100% (n=35, NUTM1-r arm) against 36-37% 2-year EFS for KMT2A partners. Different mark (H3K27ac/p300 versus H3K79me2/DOT1L), no menin interface, no CXXC - and the SAME posterior-HOXA output, which is the part that constrains the menin-interface argument

• ← analogous toACIN1::NUTM1 - the commonest NUTM1 fusion in infants, cryptic to cytogenetics, and the only one with a human cell line

  CONTRAST PLUS ONE REAL STRUCTURAL ANALOGY. Contrast: p300/H3K27ac and DNA hypomethylation against DOT1L/H3K79me2-3, no menin interface, opposite prognosis in the same trials. Analogy: both are ADDRESS MODULE PLUS EFFECTOR, with the 5' partner deciding where (SAP here, AT-hooks and CXXC there) and the 3' partner deciding what - running in opposite directions, since here the 5' partner is the variable

• ← related toPRMT5 - the type II arginine methyltransferase this graph has reached for sixteen times, whose mark on H3R2 RECRUITS WDR5 to chromatin

  PRMT5 + DOT1L inhibitor synergy in a CRISPR MLL-AF4 cord-blood model; the only MLL-AF4 record

• ← related toPRMT6 - the enzyme whose mark is MUTUALLY EXCLUSIVE with the MLL complex on the H3 tail, and which shuts HOX genes down by evicting WDR5

  NO experiment in any KMT2A fusion; the relationship is inferred from wild-type KMT2A

• ← depends onJMJD1C / KDM3C - named in three entries of this graph as one of the only loci that loses fusion occupancy under a menin inhibitor, ranked 23rd of 17,728 for KMT2A-selective dependency in this project's own scan, with the strongest published shRNA effect in SEM - and no entry until now

  strongest shRNA effect of the human panel in SEM (KMT2A::AFF1) via apoptosis; 23rd most KMT2A-selective dependency of 17,728 genes in this project's DepMap scan

• regulates →JMJD1C / KDM3C - named in three entries of this graph as one of the only loci that loses fusion occupancy under a menin inhibitor, ranked 23rd of 17,728 for KMT2A-selective dependency in this project's own scan, with the strongest published shRNA effect in SEM - and no entry until now

  the JMJD1C locus is one of only three losing >2-fold fusion occupancy under VTP-50469 or MEN1 deletion, with MEIS1 and MEF2C

• ← inhibitsJDI-12 - published as a JMJD1C inhibitor that preferentially kills KMT2A-rearranged leukaemia and spares cord blood, then used as 'KDM3i' to CREATE KMT2A rearrangements in cord-blood progenitors, by two papers that do not cite each other

  the compound class kills MLL-rearranged acute leukaemia cells and the paralogue it targets has its strongest published shRNA dependency in SEM - the opposite therapeutic reading from the same molecule

• ← related toOne demethylase family sits at both ends of this disease - KDM3B gates whether KMT2A rearranges, JMJD1C is what the resulting fusion needs to survive - and a single compound hits both, so its therapeutic index runs in opposite directions in the two cell populations it reaches

  brackets the index fusion at both ends: the locus that becomes it, and the dependency it acquires - with SEM the one index-fusion datum

• ← testsMeasure H3R2 and H4R3 methylation states at KMT2A-fusion targets by isomer-resolving mass spectrometry, and test the gate by writer perturbation read out on the enzyme's product - the experiment that has never been done in any fusion

  the index fusion, in SEM and RS4;11 - and the allele-asymmetry arm turns on the fusion having lost PHD1-3, the bromodomain, the WIN motif and SET

• ← related toATF4 / CREB2 (P18848) - the hub this graph inferred from its targets and never wrote, and its own transcript does not move under either menin inhibitor

  ATF4 output collapses in both KMT2A::AFF1 lines under menin inhibition while ATF4's own transcript is flat (max -0.86) and the KMT2A wild-type line REH is unaffected

• ← related toCHAC1 / BOTCH (Q9BUX1) - the largest single effect in the whole menin-inhibitor response (-5.11 log2) and a glutathione-degrading pro-apoptotic enzyme, named nowhere in this graph until now

  largest single effect in the two-compound menin-inhibitor intersection: -5.11 log2 in RS4;11, +0.49 in KMT2A-wild-type REH

• ← related toTRIB3 / TRB3 (Q96RU7) - a pseudokinase that is the ISR's own brake, falls 3.1 log2 under either inhibitor, and has a published physical link to the MLL complex in the wrong tissue

  -1.23/-1.18 on two array probes in RS4;11 and -1.22 in SEM under MI-2-2, -3.10 under VTP-50469; but REH also moves -0.68, the weakest wild-type control of the 24

• ← related toDDIT3 / CHOP (P35638) - the cascade's middle node, and the symbol whose two reviewed human records and 16,893-record alias are the worst identifier trap in this beat

  -0.82 log2 under MI-2-2 and -1.50 under VTP-50469 in RS4;11; REH also moves -0.30, so fusion-selectivity is modest

• ← related toATF5 / ATFX (Q9Y2D1) - the most reproducible repression in the earlier dataset, and the three probe values the graph quotes are SEM, not RS4;11

  four independent array probes agree in direction in both t(4;11) lines and are flat-to-positive in KMT2A-wild-type REH; but the -3.02/-2.89/-2.77 values the graph quotes are SEM, not RS4;11 (RS4;11 gives -1.09/-1.12/-0.74)

• ← related toATF3 (P18847) - the one cascade member the DOT1L inhibitor hits HARDER than the menin inhibitor, and a transcriptional REPRESSOR being counted as a stress output

  -1.16 log2 under MI-2-2 in RS4;11 with a clean KMT2A-wild-type REH control (+0.06); SEM only -0.36

• ← related toSESN2 / sestrin-2 (P58004) - the ISR's exit into mTORC1: a leucine sensor that falls 1.4 log2 under either inhibitor, and the one panel member with a real structural record

  two agreeing array probes in RS4;11 (-1.32, -1.21) with a clean KMT2A-wild-type REH control (-0.04, +0.15); the most numerically reliable fold changes in the panel

• ← related toSTC2 / stanniocalcin-2 (O76061) - the second largest effect in the signature (-4.40 log2), a SECRETED glycoprotein, and its localisation rests on curator inference alone

  expressed 7 log2 higher in both t(4;11) lines (SEM 11.94, RS4;11 8.62) than in KMT2A-wild-type REH (4.89, at background) and falls 4.40 log2 under VTP-50469

• ← related toSOCS2 (O14508) - a MENIN-INHIBITOR-SELECTIVE member of the signature, a cullin-5 E3 substrate receptor, and its likeliest upstream regulator is MEF2C rather than ATF4

  largest MI-2-2 effect in the panel (-2.10 on three agreeing probes) in RS4;11 with a clean REH control - but SEM does not express SOCS2 at all, so this is an RS4;11 property, not a general KMT2A::AFF1 one

• ← related toIKZF3 / Aiolos (Q9UKT9) - the B-lymphoid transcription factor that goes UP under both inhibitors, regulates BCL2, and is a degradable drug target

  rises in BOTH t(4;11) lines under both compounds (SEM +2.73, RS4;11 +1.08 array / +1.34 RNA-seq) and FALLS in myeloid MOLM13 (-0.41) - lineage-coupled, from a low baseline

• ← related toSGK1 / SGK (O00141) - a MENIN-SELECTIVE upregulated kinase, a druggable AGC family member, and the panel's worst platform disagreement

  +1.00 log2 on one array probe in RS4;11 and +1.99 under VTP-50469 versus +0.07 under EPZ5676 - menin-selective in direction, but SEM is flat at a higher baseline and the two platforms disagree about whether the gene is expressed

• ← related toEIF2AK4 / GCN2 (Q9P2K8) - the amino-acid-sensing eIF2alpha kinase: transcript flat, and NOTHING has ever been published about it in any KMT2A-rearranged system under either name

  BOUNDED ABSENCE: four independent PubMed zeros (EIF2AK4 and GCN2, each against an eight-operand fusion list and a thirteen-name menin-drug list), all with valid querytranslations and 'No items found.'; the only fusion-context data are this beat's flat transcripts

• ← related toOne blot: phospho-eIF2alpha and ATF4 protein in RS4;11 under VTP-50469, with a dose-response and a DOT1L comparator arm

  designed in two independent t(4;11) KMT2A::AFF1 lines plus a KMT2A-wild-type control, which would make it the first protein-level ISR measurement in the index fusion

• ← related toPremise (iii) was not falsified at this locus - Gothe 2019 measures MLL breakage and MLL-AF4 fusion in the same cells and they move TOGETHER under TDP2 loss; what TDP2 actually falsifies is a premise about break FORMATION that the triad never stated

  MLL-AF4 fusion formation measured directly by 4-color C-Fusion 3D in TK6, K562, HCT116, HT1080, Cal51 and primary CD34-positive cells at 6e-4 to 2e-3

• ← related toPHGDH (O43175) - the largest menin-SELECTIVE fall in the whole serine panel, and the least essential gene in it

  transcript collapse measured in three KMT2A::AFF1 lines (RS4;11, SEM, MV4;11); no dependency ever measured in this fusion

• ← related toALDH1L2 (Q3SY69) - the second-largest fall in the serine/one-carbon panel (-3.40), named nowhere in this graph, zero of 1,258 DepMap lines require it, and a tumour SUPPRESSOR where it has been studied

  falls 3.40 log2 in RS4;11 and 2.06 in MV4;11, both KMT2A::AFF1; flat in KMT2A::MLLT3

• ← related toSHMT2 (P34897) - the mitochondrial one-carbon step, and the paralogue that rises while it falls is why its loss may not matter

  all three array probes fall in RS4;11 and SEM and rise in KMT2A-wild-type REH from detected baselines - the best-controlled readout in the panel

• ← related toThe junction-peptide absence was a claim about mass-spectrometry datasets bounded by a PubMed abstract search: PRIDE holds three human MLL-AF4 proteomics projects, so measured-not-searched is now named rather than asserted

  PXD009338 is an interaction proteome of seven MLL fusion proteins and is the deposit most likely to contain a junction-spanning peptide if one is recoverable at all

• ← testsThe one experiment that would close the SUV39H1 arm of this graph's H3K9 argument: CST #8729S CUT&RUN in a CD34+ progenitor and in SEM or RS4;11, with an IgG arm and a SUV39H1-degron arm that neither existing deposit has - because after this cycle the enzyme has been measured in exactly two human cell types and neither is a blood cell

  SEM and RS4;11 against a KMT2A-germline comparator

• ← related toA junction-specific monoclonal antibody against a paediatric leukaemia fusion oncoprotein exists: clone TEL 6F2, raised against a 12-mer spanning the ETV6::RUNX1 fusion site and used for genome-wide ChIP

  the feasibility precedent for the six computed KMT2A::AFF1 junction epitopes; no equivalent reagent exists for this fusion

• ← testsRaise a KMT2A::AFF1 junction-specific monoclonal by the published TEL 6F2 protocol - rat immunisation with a junction peptide, ELISA and western screen, then a ChIP test against the wild-type-parent controls that the ETV6::RUNX1 campaign never ran

  a reagent that detects this fusion and neither parent, which would make fusion-versus-wild-type attribution decidable in occupancy experiments

• ← related toThe experiment this beat could not do: an epitope-tagged KMT2A::AFF1 ChIP with a Drosophila spike-in, in a human infant-derived B-lineage line, at three replicates and two menin-inhibitor exposures - the design that would turn a within-sample ranking into an absolute occupancy measurement

  the proposed system is a human KMT2A::AFF1 line with an endogenously tagged fusion allele

• ← related toIn human RS4;11 (KMT2A::AFF1), menin occupancy at its own top 0.1% of 2 kb bins falls 14.9x to 2.0x over the track median and its share of total coverage falls to 0.200 - reproducing Q117's murine FLAG-MLLAF9 figures (15.9x to 3.0x, ratio 0.179) to within 1.3-fold on all five statistics

  the line carries the index fusion, but the antibody is anti-menin and the measurement is not attributed to the fusion

• ← related toIn the human index fusion the menin inhibitor subtracts MENIN and leaves MLL1-N-reactive material in place at the same sites - so the drug's chromatin action is decoupling rather than eviction, and what this literature calls fusion eviction is a menin measurement

  the hypothesis is about the index fusion in RS4;11, although no measurement supporting it distinguishes the fusion from wild-type MLL1

• ← testsTag the endogenous KMT2A::AFF1 allele in RS4;11 and ChIP the tag with and without VTP-50469 alongside MENIN and MLL1-N in the same chromatin - the one experiment that converts every occupancy claim in this literature from a reagent statement into a fusion statement

  tag the endogenous der(11) KMT2A::AFF1 allele in RS4;11 and ChIP the tag with and without VTP-50469

• ← related toAt the 692 RS4;11 bins where an MLL1 N-terminus and menin co-occupy, VTP-50469 takes menin to 0.20 and DOT1L to 0.20, drops H3K79me2 to 0.66, and leaves MLL1-N-reactive material at 0.83 - four factors, one drug, one chromatin, and a clean ordering

  measured in RS4;11, the index-fusion line, at 330 nM VTP-50469 for 3 days

• ← related toBAHCC1 - a BAH-domain H3K27me3 reader that an MLL fusion binds and upregulates in mouse, and the locus carrying the two largest MLL1-N-reactive rises under a menin inhibitor in human RS4;11

  locus carrying the two largest per-bin MLL1-N-reactive rises under VTP-50469 in RS4;11 - NOT a fusion-specific measurement

• regulates →RUNX2 - a direct KMT2A-chimera target and dependency in T-ALL, a patient-specific enhancer target in KMT2A::AFF1 B-ALL, and the gene a menin inhibitor represses to restore steroid sensitivity in t(4;11) infants

  patient-specific enhancer activity at RUNX2 in KMT2A::AFF1 ALL (Micro Capture-C, primary patients); RUNX2 repressed under MI-538 + chidamide in t(4;11) infant PDX

• ← analogous toZMYND11 (BS69) - an H3.3K36me3 reader that restrains elongation, is itself the 5' partner of a chromatin-hijacking AML fusion driving HOXA/MEIS1/MYB, and whose promoter is the third-strongest MLL1-N bin in RS4;11

  ZMYND11::MBTD1 is a chromatin-reader 5' module welded to a chromatin-opening 3' module producing HOXA/MEIS1/MYB/MYC - the KMT2A-fusion architecture with different parts

• ← related toFOXP1 - the forkhead repressor that licenses the pro-B to pre-B transition and blocks apoptosis with NF-kB, sitting at a 105x MLL1-N bin in a leukaemia whose defining lesion is a pro-B arrest

  105.2x MLL1-N-reactive bin at its promoter in RS4;11, share ratio 0.509 under VTP-50469 - NOT a fusion-specific measurement and mid-range among the top thirty

• ← analogous toZMYND11::MBTD1, t(10;17)(p15;q21) - a chromatin reader welded to the NuA4/TIP60 acetyltransferase, maintaining Hoxa/Meis1/Myb/Myc/Sox4 in AML: the KMT2A-fusion architecture built from different parts

  same two-module plan and same HOXA/MEIS1/MYB/MYC output, no shared molecule; the index fusion retains CXXC and both MBMs in cis where this one has neither

• ← analogous toMBTD1::EZHIP (MBTD1-CXorf67), t(X;17)(p11.2;q21.33) - MBTD1's other fusion, in which a NuA4 subunit delivers an H3K27M-mimicking PRC2 poison to low-grade endometrial stromal sarcoma

  a 5' module supplying the address fused to a 3' module supplying the effector - and the negative image of it, because this fusion's effector REMOVES a repressive mark where the KMT2A fusion's ADDS an activating one

• ← related toRS4;11 - the human KMT2A::AFF1 index-fusion line - has a deposited H3K79me2 pair, a MENIN pair, an MLL1-N pair, a DOT1L pair and an input under the same menin inhibitor in GSE127507. Every track needed to run this beat's test on the index fusion exists. The download is 1.99 GB measured by HEAD request, and nobody has run it.

  the index fusion whose eviction gradient is undetermined

• ← related toDownload and bin GSE127507's nine RS4;11 tracks (1.99 GB), rebuild a human binner, and score the eviction gradient in the index fusion KMT2A::AFF1 - the one measurement that would move this finding from KMT2A::MLLT3 to the disease this graph is about

  the index fusion the experiment would measure

• ← depends onLIN28B - a one-row BioID prey of KMT2A that a 2026 Blood paper shows is REQUIRED for KMT2A::AFF1 to transform human fetal cells

  human fetal liver CD34+ cells fail to transform on induction of KMT2A::AFF1 in the absence of LIN28B (Blood 2026); the dependency runs fusion-on-LIN28B

• ← testsPUBLISHED, DONE: human fetal liver CD34+ cells fail to transform on KMT2A::AFF1 induction without LIN28B (Ling et al., Blood 2026) - a dedicated human index-fusion experiment, read from the abstract only

  endogenous CRISPR-engineered KMT2A::AFF1 in human fetal liver CD34+

• ← related tolet-7 microRNA family (12 HGNC loci) - the effector LIN28B blocks. CORRECTED IN-SESSION: the headline 'zero papers in KMT2A leukaemia' was a NAME-LIST ARTEFACT; searching MLL instead of KMT2A returns three, one of them directly on point

  BOUNDED ABSENCE: zero title/abstract co-mentions with KMT2A, MLL-AF4 or t(4;11) as of 2026-09-23

• ← testsPROPOSED: swap the partner, hold everything else - KMT2A::MLLT3 versus KMT2A::AFF1 in LIN28B-null human fetal liver CD34+ cells

  KMT2A::AFF1 reference arm

• ← related toFetal-restricted permissive factors across fusion families - the class has exactly ONE fully worked member, and for ETV6::RUNX1 the fetal advantage is real but no factor is named

  the index case of the class

• ← related toLIN28B and IGF2BP3 are co-regulated members of ONE onco-fetal module in infant leukaemia - which strengthens the graph's existing scepticism about IGF2BP3 rather than weakening it

  IGF2BP3 binds both reciprocal t(4;11) transcripts and REDUCES KMT2A::AFF1 protein abundance

• ← related toTwo groups invoke LIN28B to explain the SAME epidemiological fact in OPPOSITE directions - and neither claim is the one this graph has been repeating

  the index fusion whose age restriction is the explanandum

• ← related toCORRECTS A DISPATCH PREMISE: GSE149183's menin-versus-DOT1L-inhibitor head-to-head exists in MOLM13 (KMT2A::MLLT3) ONLY. RS4;11 - the index fusion - is in the series but carries H3K79me2 alone, with no VTP-50469 arm, no MEN1 ChIP and no DOT1L ChIP, and the two arms are on different genome builds

  RS4;11 is in this series and carries H3K79me2 only - no MEN1 ChIP, no VTP-50469 arm

• ← testsThe one experiment that would close this beat: MEN1 and DOT1L ChIP in RS4;11 (KMT2A::AFF1) under DMSO, a menin inhibitor and a target-engaging DOT1L inhibitor, with Drosophila spike-in and two replicates per arm - about 24 libraries, and the depositing lab already runs every component of it

  the whole point of the design: run the menin-versus-DOT1L head-to-head in the index fusion

• ← related toDifferentiation syndrome is the one human pharmacodynamic readout KMT2A-rearranged leukaemia already shares with APL - and in APL it is a complication of a cure, while here it is a complication of a 30% response rate

  the index fusion the analogy is aimed at

• ← analogous toPML::RARA, t(15;17)(q24;q21)

  same clinical differentiation syndrome on target engagement; APL adds oncoprotein degradation and gets cure, the menin axis does not

• ← related toA pocketless fusion already had its protein-protein-interface drug taken to phase I/II - and TK216 turned out to be a microtubule destabiliser, not an EWS::FLI1 antagonist. This is the closest thing the field has to a controlled failure of the interface hypothesis.

  the index fusion whose interface programme the analogy bears on

• ← analogous toEWSR1::FLI1 (EWS-FLI1), t(11;22)(q24;q12)

  both pocketless neomorphs treated by disrupting an obligate wild-type partner interaction; only the menin axis has genetic validation of the drug-target link

• ← related toAn H3K4me3-reading PHD finger fused to NUP98 makes a potent leukaemia oncoprotein; the H3K4me3-reading PHD finger of KMT2A is deleted from every KMT2A fusion and reinstating it abolishes transformation. Same module class, opposite sign - and the one NUP98 fusion that carries KMT2A's PHD cassette is the weakest member of its family.

  the index fusion, which like every KMT2A fusion lacks PHD1-3

• ← analogous toNUP98::KDM5A (NUP98-JARID1A), t(11;12)(p15;p13)

  same H3K4me3-reading PHD module class, required in one family and incompatible with transformation in the other

• ← related toA genuine small-molecule disruptor of an oncogenic oligomer DOES exist - 7.44 against the RUNX1::RUNX1T1 NHR2 tetramer - which corrects this graph's record; and its eighteen-year potency curve says the class is a chemistry problem, which is what this graph concluded for the wrong reason

  the index fusion whose hypothesised self-association interface this roadmap prices

• ← analogous toRUNX1::RUNX1T1 (AML1-ETO), t(8;21)(q22;q22)

  partner-contributed self-association module as the obligate, mutation-resistant target - established in one family, hypothesised in the other

• ← related toChildren with NPM1::ALK lymphoma immunise themselves against their own fusion protein, and the antibody titre predicts relapse - while no autoantibody against any KMT2A fusion has ever been reported. The difference is not the junction; it is that ALK is an ectopic self-antigen and KMT2A and AFF1 are not.

  the index fusion, for which no patient autoantibody has been reported under either gene symbol

• ← analogous toNPM1::ALK (NPM-ALK), t(2;5)(p23;q35)

  fusion as spontaneous tumour antigen - present in one family because the 3-prime partner is ectopic, absent in the other because both partners are ubiquitous

• ← related toCBFA2T3::GLIS2 supplies its own CAR-T antigen - FOLR1 came out of a list of fusion-specific genes in an isogenic human model. KMT2A-rearranged leukaemia is treated with a LINEAGE antigen it can abandon, or with one a drug has to create; nobody has built the fusion-specific surface list for KMT2A::AFF1.

  the index fusion, for which no fusion-specific surface-gene library has been built

• ← analogous toCBFA2T3::GLIS2, inv(16)(p13.3q24.3)

  infant leukaemia with dismal prognosis; one supplies an escape-proof fusion-driven CAR antigen, the other is treated with an abandonable lineage antigen

• ← related toEWS::FLI1 builds its own enhancers at GGAA microsatellites, and a single inherited base change that lengthens one repeat raises the fusion's binding and the patient's risk. KMT2A fusions occupy pre-existing, invariant CpG islands - which is why this disease has no germline modifier of its target set, and why its mouse models work at all.

  the index fusion, whose target set is invariant between patients and conserved in mouse

• ← related toThe deposited RS4;11 H3K79me2 table in GSE149183 is two-thirds MOLM13: 38,580 of its 57,794 rows are byte-for-byte identical to the MOLM13 file, so the index fusion is measurable at only 19,214 TSS entries

  the deposit's index-fusion arm is measurable at only 19,214 of 57,794 TSS entries

• ← related toOn an absolute scale, H3K79me2 in the index fusion falls 52-fold (EPZ5676) to 91-fold (compound 10) by day 9 and NOT ONE of 17,341 measurable genes holds its signal - the first absolute-scale chromatin statement this project has been able to make about KMT2A::AFF1

  the first absolute-scale chromatin measurement this project holds for the index fusion

• ← related toRS4;11 retains 2.5x more H3K79me2 than MOLM13 under EPZ5676 at every one of ten baseline deciles - and 0.71x under compound 10, with the sign reversing in deciles 5-10: the between-line difference survives the baseline confound and fails the drug replication, so it cannot be attributed to the fusion partner

  the index fusion's line, compared with the MLLT3 line on an absolute scale for the first time

• ← testsSix to twenty-four libraries in RS4;11: two DOT1L inhibitors titrated to equal spike-in-measured global H3K79me2 loss, three replicates per arm, plus the no-primary control that no public deposit contains - the smallest experiment that would convert four moderate entries in this beat into testable ones

  run in RS4;11 because magnitude does not transfer from the MLLT3 line

• ← testsA surfaceome-first screen for KMT2A::AFF1: 2,404 surface proteins, 169 expressed in the fusion's own cell lines, 15 fusion-enriched, 3 clean in normal tissue - and the two sets do not intersect

  surfaceome-first target screen against the index fusion's three cell lines

• regulates →NG2/CSPG4 is the one antigen in the whole surfaceome that KMT2A::AFF1 itself drives - and it is a pericyte and vascular protein, at 124.5 nTPM in normal blood vessel and 246 TPM in tibial artery

  MLL-AF4 is the direct, epigenetically acting transcriptional driver of NG2/CSPG4

• regulates →LAMP5 (BAD-LAMP) - a direct MLL-fusion target gene, a proposed immunotherapy antigen, and a brain protein

  LAMP5 is a direct target of the oncogenic MLL fusion protein (partner-agnostic MLL-r signature)

• ← related toOf every antigen this project names, only NG2, LAMP5 and CD123 are present on all three KMT2A::AFF1 cell lines - CD19 is at 0.2 nTPM in MV4-11 and CD33 at 2.3 in RS4;11

  antigen-by-lineage matrix across the fusion's three cell lines

• ← related toREFUTED IN THE CYCLE IT WAS WRITTEN - the proposal that fusion-driven and normal-tissue-clean surface antigens are disjoint in KMT2A::AFF1 because of what the fusion's output programme is; an expression-matched permutation says it is the base rate

  the disjointness is proposed to follow from the fusion's developmental output programme

• ← testsCell-surface capture proteomics on an isogenic human KMT2A::AFF1 model against its matched normal progenitor - the experiment an mRNA screen cannot replace

  surface proteome of the index fusion against its matched normal progenitor

• ← expressed inSIT1 - one of only three surface proteins in the screen that is both expressed in KMT2A::AFF1 lines and absent from normal parenchyma, and it is clean because it is leukocyte-restricted, not because it is leukaemic

  49.6 nTPM in SEM and 65.4 in RS4;11, but 1.18x other KMT2A partners - not fusion-specific

• ← expressed inS1PR4 - the third parenchymally clean surface protein in the screen, a leukocyte-restricted GPCR, and not fusion-specific either

  44.8 nTPM in SEM and 236.1 in RS4;11, 1.75x a B-precursor comparator - not fusion-specific

• ← related toGSE159608 — 419 automated CUT&Tag libraries across 7 KMT2A-rearranged primary patient samples, 5 lines and a normal CD34+ donor, including KMT2A fusion occupancy, a menin-inhibitor arm in SEM, and three single-cell CUT&Tag libraries

  two KMT2A::AFF1 primary patient samples (ALL-1, MPAL-2) plus SEM and RS4;11

• ← analogous toETO2::GLIS2 rewires chromatin in stages and hijacks the osteogenic homeobox factor DLX3 as its first required step — a genome-edited human iPSC model that resolves leukaemia initiation into an ordered sequence

  the transferable lesson: the first REQUIRED chromatin step need not be the canonical output, and four of the five reagents for the same experiment already exist for the index fusion

• ← related toIn SEM, the infant-derived KMT2A::AFF1 line, VTP-50469 lowers H3K4me3 at menin-bound sites by 23% relative to H3K4me3-matched menin-free sites (95% CI 13-33%), while the DOT1L inhibitor EPZ-5676 changes it by 1% (CI -4 to +6%)

  Measured in SEM, a t(4;11) KMT2A::AFF1 line

• ← supportsIn an unsupervised 5 kb correlation of 41 SEM libraries, both KMT2A N-terminal AutoCUT&RUN libraries have menin as their single nearest neighbour - the menin-interface hypothesis appearing as the top-level structure of an analysis that was not looking for it

  Menin co-distribution with the retained N-terminus, shown unsupervised in the index fusion's own line

• ← related toSpike-in-normalised menin CUT&RUN in a KMT2A::AFF1 degron line, with replicates and a PSIP1 arm

  moves the measurement into the index fusion, where no equivalent degron dataset exists

• ← related toGSE252378 holds the only AFF1 CUT&RUN in primary KMT2A::AFF1 patient material - four libraries across two patients, three disease states and the SEM cell line, all hg38

  AFF1, KMT2A-N/C, DOT1L, ENL, H3K4me3 CUT&RUN in primary KMT2A::AFF1 infants

• ← related toAFF1 occupancy does not distinguish fusion-occupied promoters from wild-type KMT2A promoters in primary infant KMT2A::AFF1 - reproduced at promoter resolution, and the corpus should stop reading a partner ChIP as a fusion readout

  fusion-site calls rest on KMT2A N/C, not on the partner

• ← related toThe taspase-1 N/C antibody control separates fusion-occupied from wild-type KMT2A promoters in every primary infant sample, and it is the C-terminal arm that does the work while being the less reproducible arm

  defines fusion-occupied promoters in primary infant material

• ← related toThe B-ALL and the AML of one infant share no more fusion-occupied promoters than two unrelated infants do - lineage, not patient identity, sets where KMT2A::AFF1 sits

  fusion target set is lineage-contingent

• ← related toRun a fusion-specific and a total-AFF1 readout side by side in the same KMT2A::AFF1 nuclei, and report the two target sets rather than one

  fusion-specific occupancy readout

• ← related toThe menin interface cannot be what decides where KMT2A::AFF1 sits: within one patient the fusion's target promoters were almost entirely replaced while the menin-binding motif was unchanged

  fusion address is state-dependent, interface is not

• ← related toThe menin that matters in an infant KMT2A-rearranged leukaemia is the menin on the fusion, and the N-minus-C antibody difference can measure it in any patient sample without a tag

  the index fusion in which the hypothesis is untested and testable on public files

• ← related toSpike-in-normalised menin CUT&RUN with paired N- and C-terminal KMT2A antibodies in an infant KMT2A::AFF1 sample, on and off drug, in the same disease state

  the index fusion this experiment would use

• ← related toGSE252378 fragment BEDs: a complete KMT2A N-terminal / C-terminal antibody set in 27 patient samples across six fusion partners, deposited and until now unopened by this corpus

  8 of the 27 complete N/C sample sets are KMT2A::AFF1

• ← related toGSM8006584 names its antibody KMT2A-C1 in its title, its characteristics field and its own filename, and KMT2A-C2 in its description - so keying the antibody off the free-text description gives patient TB-92-0488 two C2 libraries and no C1

  the affected patient TB-92-0488 is one of eight KMT2A::AFF1 samples in the N/C arm

• ← related toThe menin interface is identical in all 27 of these patients and the amount of chromatin their oncoproteins occupy differs by up to two orders of magnitude - so the interface can be a permission for binding but cannot be what sets how much binding happens

  eight of the 27 samples

• ← related toIRX1 — Iroquois homeobox 1, the gene that names the HOXA-negative half of infant t(4;11) ALL

  defines the HOXA-negative subgroup of t(4;11) infant ALL (expression)

• ← testsIRX1 carries the KMT2A::AFF1 oncoprotein in exactly the patients where HOXA does not — seven patients, GSE252378

  where the KMT2A::AFF1 oncoprotein sits in primary infant material

• ← arises iniALL-IRX1 — the HOXA-negative, IRX1-high state of infant KMT2A::AFF1 ALL

  a state of t(4;11) blasts

• ← arises iniALL-HOXA9 — the HOXA-high state of infant KMT2A::AFF1 ALL, and the one everything is modelled on

  a state of t(4;11) blasts

• ← related toSEM, the standard t(4;11) model line, has zero signal at IRX1 — every model of this disease is a model of one subgroup

  the standard t(4;11) cell line for this fusion

• ← bindsIRX1 binds the MLL-AF4 complex non-competitively — menin, LEDGF and DOT1L are all unchanged

  IRX1 binds the MLL-AF4 complex at target promoters

• ← refutesHOXB4, the one direct IRX1 target with ChIP evidence, carries no oncoprotein in any of seven infant patients

  HOXB4 is not an oncoprotein target, concordant with Kuhn

• ← related toGSE252378 holds eight KMT2A::AFF1 oncoprotein panels from two centres, not the three this corpus had used

  eight KMT2A::AFF1 sample records with full oncoprotein panels

• ← depends onIRX1 is a second address for the KMT2A::AFF1 oncoprotein, not merely the gene that turns HOXA off

  a second address for the KMT2A::AFF1 oncoprotein

• ← related toOn one universe with one rule and a structure-respecting null, the two lineages of one infant overlap no more than two unrelated KMT2A::AFF1 infants do

  all 8 samples in the comparison arm carry KMT2A::AFF1

• ← related toThe KMT2A::AFF1 oncoprotein-target promoter set is a fusion-level property, and patient identity adds nothing measurable on top of it

  the fusion whose target set is proposed to be the organising level

• ← related top279 and p318: one infant, two diseases, and an oncoprotein target map that does not carry over

  both states carry KMT2A::AFF1

• ← related toIRX1 fusion occupancy is confined to KMT2A::AFF1: 0 of 18 samples across five other partners
• ← related toTB920488, the other HOXA-negative IRX1-negative blast, has the highest GMP-over-B-lineage ratio of any B-lineage sample in the deposit - and it fails both the matched null and the N-over-C test

  TB920488 is a HOXA-negative, IRX1-negative KMT2A::AFF1 infant Pre-B-ALL

• ← related toIn infant ALL, IRX1 transcript is enriched in KMT2A::AFF1 (21 of 48) and present but rare outside it (3 of 26) - so the occupancy zero outside AFF1 is not an expression zero

  IRX1 ON in 21 of 48 KMT2A::AFF1 infant ALL cases, 43.8%

• ← related toNo KMT2A-rearranged haematopoietic cell line in CCLE expresses IRX1 - including all four KMT2A::AFF1 lines MV4-11, NALM-19, RS4;11 and SEM at 0.0000-0.0053 RPKM

  MV4-11, NALM-19, RS4;11 and SEM are all IRX1-negative

• ← related toIRX2 - the IRX-cluster neighbour that is this disease's own prognostic gene, activated only in KMT2A::AFF1, and never written here until now

  IRX2 is ON in 9 of 48 KMT2A::AFF1 infant ALL cases and 0 of 49 other infants in the same cohort

• ← related toThe 'raw library promoter mean' that two cycles treated as library coverage tracks the in-promoter fragment FRACTION at Spearman +0.993 and true sequencing depth at only +0.292, and the oncoprotein share correlates with true depth at -0.255

  the index fusion is 10 of the 27 GSE252378 samples

• ← related toIRX2 is not fusion-occupied at promoter scale in GSE252378: 0 of 27 samples, against a null of 2.73

  0 of 8 KMT2A::AFF1 samples show IRX2 promoter occupancy

• ← related toThe 17-promoter AFF1-only recurrent core is not more recurrence than a label permutation of the same matrix gives

  the index arm whose promoter exclusivity is tested

• ← related toThe 332-promoter AFF1-only set is BELOW the count a random eight-sample arm produces (null 425)

  the arm the 332 is exclusive to

• ← regulatesEPHA7 - ephrin type-A receptor 7, a published direct promoter target of the ALL1/AF4 (KMT2A::AFF1) fusion protein

  ALL1/AF4 fusion protein occupies the EphA7 promoter by ChIP and its knockdown lowers EphA7

• ← related toAFF1's promoter window is 92.5% AFF1-AS1's - worse than IRX2's 89.2% - and the project's promoter table has no row for the neighbour at all

  the index fusion's 3' partner sits at a divergent promoter, so 'does the fusion occupy its own partner's promoter' cannot be answered at 2 kb scale

• ← related toThe deposit paper's own supplementary table calls IRX1 an oncoprotein target in exactly p279, p318 and p454 - the same three samples this project reached by a different instrument

  all three IRX1-positive samples carry KMT2A::AFF1; the authors bound their own negative to MLL::ENL only

• ← related toIn the deposit paper's own target-gene table, the AFF1-exclusive class is 64 genes against a permutation null of 2.3, and it survives call-rate matching, institution stratification, B-lineage restriction and patient collapse

  64 oncoprotein-target genes are exclusive to the KMT2A::AFF1 arm of GSE252378 at a rate 28 times the permutation null

• ← related toAt gene-body scale the AFF1-exclusive recurrent class is 6 against an exact institution-stratified null of 0.86 - but the singleton class is 63 against 74, so recurrence carries the signal and exclusivity alone does not

  six gene bodies are occupied in >=3 of 8 KMT2A::AFF1 samples and none of 18 comparators, against a null of 0.86

• ← related toAFF1-AS1 - the antisense RNA 151 bp from the index fusion partner's TSS, which Ensembl does not recognise and this project's promoter table cannot see

  shares 92.45% of its promoter window with the 3' partner of the index fusion, so no promoter-scale fusion measurement at AFF1 can exclude it

• ← related toAFF1's own promoter window is occupied in 20 of 27 samples - top 4% of the whole table - and the call cannot be attributed to AFF1

  the index fusion's own 3' partner's promoter, measured in 27 primary KMT2A-fusion samples

• ← refutesThe fusion-biased peak at the AFF1 locus fires in 23 of 27 samples across all six partners, so it is not the fusion visiting its own partner

  no partner-specific occupancy: 7/8 KMT2A::AFF1 against 16/19 other partners, so the fusion does not preferentially occupy its own partner's locus

• ← testsFour hours of MS67 in MV4;11, two KMT2A antibodies: the cheapest test of whether WRAD reaches the fusion or only wild-type KMT2A

  asks whether the index fusion's chromatin residence depends on WDR5

• ← treated bySGC-iMLLT - the MLLT1/MLLT3 YEATS chemical probe, and the 2026 paper that put it into KMT2A::AFF1 in vivo with a healthy-HSPC comparison

  2026 Exp Hematol: inhibits KMT2A::AFF1 leukaemia growth in vitro and in vivo while sparing human and mouse HSPC function - and KMT2A::AFF1 carries no YEATS domain

• ← related toThe prey-only interactome is 36.3% written, not 0% - the census, by identity, of all 212 human prey-only partners of the six core proteins

  no bait in the entire 879-record set is the fusion protein

• ← related toThe 2015 paper did not discover the KMT2A acetylation site - it inherited it from the 2009 Choudhary acetylome, which was run in a cell panel that includes MV4-11, a KMT2A::AFF1 line

  MV4-11 (CVCL_0064) is a t(4;11) KMT2A::AFF1 line in the founding acetylome panel

• ← related toEvery MS-evidenced KMT2A modification site, flagged retained or lost against the breakpoint - and the retained portion is NOT enriched for acetylation once you use the right null

  which KMT2A modification sites survive into the fusion protein

• ← related toRanked against four fusion families, the KMT2A acetylation site is the only candidate with no evidence on the fusion at all - and the strongest argument for it is one nobody has made

  the AML1-ETO mechanism transplanted: does the partner change which enzymes reach the retained N-terminus

• ← regulatesThe partner, not the site, is what could make a retained KMT2A modification fusion-specific - the AML1-ETO mechanism asked of KMT2A::AFF1

  proposes that the partner changes the enzyme environment at the retained N-terminus

• ← related toAKAP95 reaches this disease by two separate routes - through WRAD/DPY30 and through the retained KMT2A fragment - and only the second one survives the fusion

  the SET-domain loss is what decides which route can reach the index fusion

• ← related toThe lymphoid-restricted DAXX dependency survives three nulls and two comparator restrictions - and ATRX, MEN1 and DOT1L do not survive the same test in the same lines

  three of the four index lymphoid lines (SEM, SEM-K2, RS4;11) carry the index fusion; none is infant-derived

• ← related toNobody has ever looked at whether a KMT2A fusion is at PML nuclear bodies - a counted zero, with the one biochemical hint pointing yes

  the subnuclear address of the index fusion has never been measured against this compartment

• ← related toFLT3 in ZNF384-rearranged leukaemia - the fusion builds its own enhancer 25 kb upstream, and gilteritinib works in xenografts

  KMT2A-r and ZNF384-r are the two highest-FLT3 B-ALL subtypes, but the z-FLT3 enhancer is CLOSED in KMT2A-AF4 - same output, different cis element

• ← analogous toThe ZNF384 family is not the inverse of KMT2A::AFF1 - it is the SAME grammar written in the opposite gene order, and three of the four claims in the inverse framing are false

  not inverse architectures but the SAME grammar: both retain the index gene's DNA-targeting module and discard its machinery

• ← analogous toEP300::ZNF384 - the commonest ZNF384 fusion, and it throws away the acetyltransferase

  the grammar instantiated: EP300::ZNF384 discards the acetyltransferase exactly as KMT2A::AFF1 discards the SET methyltransferase - each family keeps the index gene's address module and throws away its catalytic machinery

• ← analogous toZNF384::TEX41 - the case that breaks the family's architecture: ZNF384 is the 5' partner, the 3' partner is a lncRNA, and the fusion is out of frame

  the boundary case that tests the rule: ZNF384 sits 5', the 3' partner is a lncRNA and the product is out of frame - the architecture KMT2A::AFF1 never violates

• ← related to"Seen in MLL-AF4 and no other bait" excludes AFF1, AFF4 and ELL — the three most AFF1-specific proteins in the experiment — and keeps ACADM and GLUD1

  MLL-AF4 in Skucha 2018 is the index fusion; this adjudicates what its 'specific' partner list can and cannot mean

• ← related toEvery partner this project imports from the only MLL-fusion AP-MS interactome was pulled from a Strep-HA transgene in Jurkat T-ALL cells — so the host's own lineage factors are in the prey pool, and one of them is LEF1

  bounds what the only MLL-fusion AP-MS interactome can say about the index fusion: T-ALL host, tagged single-copy transgene, nuclear extract, benzonase-treated

• ← related toLEF1 — the Wnt/β-catenin DNA-binding factor of the T-lineage, named as an MLL-AF4-specific interactor in a T-ALL cell line and with essentially no B-lineage or KMT2A literature

  named as an MLL-AF4-specific prey at p 0.0261 on 18 spectra in the only MLL-fusion AP-MS interactome; adjudicated and declined

• ← related toKMT2A::AFF1 has no measured fusion-specific interactome: the one dataset that appears to supply one is a rank-selected tail in the wrong lineage, and the question is open rather than answered badly

  the hypothesis is about the index fusion's specific interactome and asserts it has never been measured

• ← related toEvery WRAD subunit, DOT1L, ENL, AF9 and LEDGF carries a cited histone-mark finding and none carries an epigenetics field - 12 of the 32 index-fusion core proteins are pure notation gaps, 9 are covered, and the 11 with nothing are all on the negative-regulatory side of elongation

  audits the epigenetics record of the 32 proteins on the index fusion's own elongation and WRAD axis

• part of →SEC — the AFF1/AFF4-scaffolded super elongation complex, the particle KMT2A::AFF1 is a permanent subunit of

  SEC was purified from several commonly occurring MLL chimeras and found associated with all of them

• ← related toScored against the literature: the composition half of the YEATS-selectivity objection holds and the selectivity half is refuted — a scaffold-blind probe already has an in vivo window in the index fusion with no HSPC toxicity

  the index fusion is the system in which the window was measured

• ← related toWhat the paralogues' disease biology says about AFF1: the AFF family shares one SIAH degron — and the index fusion DISCARDS it, because the whole degron lies in the AFF1 leader that the junction at residue 347 throws away

  the degron at AFF1 268-290 is RETAINED in the direct fusion; the entry's own junction field contradicts its exon assignment

• ← related toNo fusion oncoprotein in any family has a published replication-protein-A measurement: 23 queries across five fusion families and four spelling variants each, every querytranslation read back, zero records - so the PI's analogy dimension for RPA has no comparator at all, and the index fusion's single locus-level result is the entire field

  the index fusion is the only fusion family with any RPA measurement at all, and it is a locus measurement in cells without a fusion

• ← related toThe MLL-fusion interactome recovers corepressor SCAFFOLDS and not their HDAC1/2 catalytic core: NuRD splits 5/7 remodelling arm versus 0/7 deacetylase arm (Fisher p = 0.021), and HDAC1, HDAC2, RBBP4 and RBBP7 are absent from all seven baits

  in the index fusion's own AP-MS column, NuRD is one protein and Sin3/HDAC is nothing

• ← depends onMBD3 (O95983) - the methyl-CpG-binding subunit that does NOT bind methylated DNA, and a validated KMT2A::AFF1-selective CRISPR vulnerability that is absent from every column of the pan-fusion interactome

  MBD3 knockout depletes the KMT2A::AFF1 line SEM and not the KMT2A-wildtype line 697 (GFP competition)

• ← related toThe NuRD complex - two separable modules, three paralogue choices that change what it does, and a graph that carried its ATPase and its shared core but never the scaffolds that make it NuRD

  NO complex-level demonstration exists; the index fusion's column contains CHD4 alone of 14 subunits

• ← depends onARID4B / SAP180 (Q4LE39) - the Sin3A-complex subunit that shares SIN3A's HDAC1-binding region, is in the MLL-fusion interactome, and is the second of only two epigenetic vulnerabilities a CRISPR screen found in KMT2A-rearranged ALL

  validated CRISPR vulnerability in a KMT2A-r ALL panel containing two KMT2A::AFF1 lines

• ← related toNo experiment has ever ASKED whether MTA2, MBD3, GATAD2A or SIN3A binds a KMT2A fusion - four of them were nonetheless in the lysate of a seven-fusion pulldown, and the class of that absence is measured-not-reported, not never-measured

  the bounded absence is about the index fusion's own column

• ← related toMLL fusions engage NuRD's remodelling arm without its deacetylase arm - and if so, every 'NuRD is repressive' inference in this graph is pointing the wrong way

  nearly unconstrained for the index fusion, whose column contains CHD4 alone

• ← related toCXCR4 function in KMT2A-rearranged blasts is an output of the fusion's own HOXA/MEIS1 program, so a menin inhibitor should switch off the niche axis without a CXCR4 antagonist

  index fusion; the only direct evidence is in RS4;11, a KMT2A::AFF1 line

• ← related toSPP1 (osteopontin) - the endosteal matrix protein whose knockdown prolongs survival in MLL-AF9 mice, and the one KMT2A::AFF1-specific paper about it cannot be read

  one title-only Letter asserts osteopontin-c overexpression in KMT2A-AFF1 versus ETV6-RUNX1 paediatric B-ALL

• ← related toNiche biology HAS been measured in KMT2A-rearranged disease - but in the index fusion itself there is essentially one marrow-niche molecular experiment, from 2011

  one marrow-niche molecular measurement in 1,050 index-fusion papers

• ← regulatesHOXA7 - the one HOXA paralogue besides HOXA9 with a published loss-of-function requirement for MLL-fusion transformation, and the requirement was shown in vitro only

  HOXA7 transcription falls when MLL-AF4 is knocked down in RS4;11 (co-regulation, not requirement)

• ← related toFOXC1 - a mesenchymal forkhead factor derepressed in HOXA-high AML that blocks monocytic differentiation, with a real mechanism and zero published connection to KMT2A rearrangement

  COUNTED ABSENCE: FOXC1 and MLL/KMT2A title-check to zero joint records against operands of 977 and 9,228

• ← related toERG - a heptad stem-cell transcription factor whose 15 mentions in this graph are mostly about OTHER diseases, and whose best-established role in B-ALL is loss of function, not cooperation

  ANTI-SELECTIVE: ERG is less required in KMT2A-rearranged lines than in other leukaemia lines (genome-scan rank 15,074 of 17,728)

• ← related toLMO2 (rhombotin-2) - a bridging LIM-only protein, higher in pro-B and MLL-rearranged B-ALL, anti-selective in KMT2A-rearranged lines, and a physical partner of the KDM5A module that NUP98::KDM5A retains

  ANTI-SELECTIVE: positive gene effect in the B-lineage half of the KMT2A-rearranged arm

• ← refutesUBTF tandem duplications INVENT an export signal, and that invented signal is what puts the protein on chromatin - the cleanest proof the XPO1 address is real

  UBTF-ITD was found in 6 of 503 Japanese paediatric AML, 0 of 175 adults and 0 of 65 cell lines including 39 ACUTE LYMPHOBLASTIC LEUKAEMIA lines, with FLT3-ITD in 5 of 6 cases (PMID 36448876) - the cleanest proof of a created NES is myeloid-restricted and confounded, and cannot reach infant B-lineage KMT2A::AFF1

• ← refutesChromatin-bound XPO1 as a shared, druggable address for HOXA-driven leukaemia - and the objection that it may be a general chromatin cofactor rather than an address at all

  the hypothesis's single strongest support is a lesion absent from every one of 39 lymphoid cell lines tested and from 175 adults, in six children, five of whom also carried FLT3-ITD

• ← analogous toKMT2A::ELL (MLL-ELL), t(11;19)(q23;p13.1)

  AXIS: SHARED MECHANISM CLASS - AN AFF/AF4-FAMILY ACIDIC ACTIVATION DOMAIN DELIVERED TO KMT2A TARGETS - DIFFERING ONLY IN CIS VERSUS TRANS. AFF1 carries the activation domain inside the oncoprotein; ELL recruits an AF4/LAF4/AF5q31-homologous activation domain in trans on EAF1, and ELL's own elongation activity is dispensable while its EAF1-interaction domain is essential. TESTED PREDICTION: handing the module to KMT2A directly should work at least as well - MLL-EAF1 induces AML with a SHORTER latency than MLL-ELL. DISANALOGY: same mechanism class, opposite lineage - KMT2A::ELL is myeloid-restricted and its adult form is therapy-related, so an AFF-class activation domain does not specify infant B-lineage disease.

• ← analogous toBCR::ABL1 (Philadelphia chromosome), t(9;22)(q34;q11)

  AXIS: SHARED CLINICAL BEHAVIOUR UNDER A TARGETED DRUG - acquired resistance by missense mutation at the drug-binding interface that spares the pathogenic function. Imatinib resistance is substitution of the ABL1 threonine that hydrogen-bonds the drug; revumenib resistance is somatic MEN1 mutation at the revumenib-menin interface that attenuates drug binding but not the menin-MLL1 interaction. THREE DISANALOGIES: (1) T315I is in the ONCOPROTEIN while MEN1 mutations are in a wild-type, germline-essential host gene, so the drug target is a cofactor and the resistance allele is not a fusion-specific handle; (2) imatinib resistance is selected by imatinib, whereas menin-inhibitor resistance is observed in KMT2A::AFF1 samples never exposed to the class; (3) ATP-site resistance was rescued by an orthogonal allosteric site on the same oncoprotein, and KMT2A::AFF1 has no catalytic domain to host one.

• ← analogous toETV6::RUNX1 (TEL-AML1), t(12;21)(p13;q22)

  AXIS: SHARED PRENATAL ORIGIN IN A B-LINEAGE PROGENITOR, OPPOSITE PENETRANCE. Both fusions are generated before birth and both are recoverable from neonatal blood spots; monozygotic twin pairs then measure penetrance directly, because a monochorionic circulation delivers the clone to both fetuses. Roughly 5% concordance across childhood ALL, where ETV6::RUNX1 is the largest contributor, against a rate believed close to unity in infant KMT2A-rearranged disease. DISANALOGY: ETV6::RUNX1 needs cooperating lesions (commonly deletion of the untranslocated ETV6 allele), has years of latency and cord-blood clones at ~100x the disease incidence; infant KMT2A::AFF1 needs almost none. AND THE CONTRAST IS A GRADIENT, NOT CATEGORICAL - the infant rate is not unity, since a discordant pair with spontaneous clearance of the MLL-ENL clone is published.

• ← analogous toDUX4::IGH (IGH-DUX4), t(4;14)/ins(14;4) — D4Z4 repeat insertion into the IGH locus

  AXIS: CONTRAST CLASS ON COOPERATING-LESION REQUIREMENT AND OUTCOME. DUX4-rearranged B-ALL is enriched in adolescents and young adults, requires a co-occurring ERG lesion in most cases, and has 5-year EFS of 88.3% in the CD371-positive group despite slow early treatment response and a transient myelomonocytic switch; infant KMT2A::AFF1 needs almost no cooperating lesion, presents within months, and is among the worst-outcome subtypes. Both are B-lineage, so lineage is held constant and the difference is in what else the driver needs.

• ← analogous toKMT2A::MAML2, inv(11)(q21q23) - a therapy-related fusion that also causes a solid tumour

  AXIS: SHARED 5-PRIME PARTNER, OPPOSITE ANSWER ON SUFFICIENCY. Both retain KMT2A's AT-hooks, CXXC and menin-binding motif. KMT2A::AFF1 is de novo, in utero, B-lineage and close to sufficient in a fetal progenitor; KMT2A::MAML2 is mostly therapy-related, T-lineage biased in children, also causes an epithelial tumour (4% of type B thymomas), and in one child emerged during neuroblastoma therapy, was expressed at low level, became undetectable and produced no leukaemia over 12.8 years. That is the graph's most direct evidence that a KMT2A fusion is not by itself sufficient. DISANALOGY CAVEAT: partner, cell, expression level and therapy context all move together, so the case refutes a universal sufficiency claim without identifying the missing ingredient.

• ← related toMAPK7 (ERK5) - a DOT1L partner on one 1:365 spoke of one atlas pulldown, and a kinase with real leukaemia literature that has never been connected to DOT1L

  No connection demonstrated: zero PubMed records pair MLL or KMT2A with any MAPK7/ERK5 name, recorded as a bounded absence

• ← related toAFF1 reaches P-TEFb only through AFF4, and the index fusion's elongation phenotype is therefore a claim about AFF4 availability

  the fusion retains the AFF1 region proposed to heterodimerise with AFF4, so the topology question is a question about the fusion

• ← related toIntAct curates SEVEN MLL fusion proteins as first-class interactors - ENL, AFF4, AF9, GAS7, ELL, AF6 and CALM - and not the index one

  no IntAct interactor entity exists for the index fusion, so no curated interaction record is a record of it

• ← related toThe measurement everybody said was missing exists: in SEM cells KMT2A::AFF1 occupies 20% of unmethylated CpG sites, CXXC1 50% and KDM2B 89%, and only the fusion tracks menin (r2 = 0.96)

  Measured in SEM, a human t(4;11) KMT2A::AFF1 line - the index fusion in the index lineage, which is rare for an occupancy dataset in this graph.

• ← testsPut mutant IDH2 into SEM and ask three questions at once: does the unmethylated-CpG pool shrink, does the fusion move, and does its competitor move

  Run in SEM, the index fusion in the index lineage, in human cells, with the published Bio-CAP-seq baseline in the same line.

• ← related toThe CXXC-DNA affinity is a ten-point ladder from 44 uM to 33 nM, not two numbers 1,300-fold apart, and every step but the last is under 5.5-fold

  The affinity argument the ladder corrects is load-bearing for the index fusion's chromatin-targeting mechanism.

• ← part ofThe MT/BCB domain, Q03164 1147-1244: the CXXC fold plus a 41-residue basic tail nobody has measured on its own

  The whole 1147-1244 region lies about 200 residues N-terminal to the breakpoint cluster region and is retained in every leukaemogenic KMT2A fusion.

• ← regulatesRe-founding the address argument: the CXXC domain cannot specify a location at any affinity, and a tighter one would be worse

  States what the CXXC domain does for the index fusion - protect particular CpGs from methylation - and what it does not do, which is choose where the fusion goes.

• ← related toTen affinity measurements for this contact and not one uses a fusion protein, full-length KMT2A or a nucleosome

  No affinity measurement uses a fusion protein, so the whole affinity argument concerns a species that does not exist in a leukaemia cell.

• ← related toThe pivotal menin-inhibitor paper reports that the drug does NOT globally displace MLL1 or the fusion from chromatin - menin goes, the fusion largely stays

  profiled in RS4;11 and MV4;11 with a shared-epitope antibody; retention observed

• ← testsKerry 2017's 'sufficient but not necessary' is a figure title with no experiment behind the second half - and the paper's own knockdowns run the other way

  the sufficiency and necessity claims concern this fusion in SEM

• ← related toBounded absence: no published study has tested whether a KMT2A fusion GAINS chromatin sites under a menin inhibitor - and the same pipelines found gains for two other proteins when they looked

  the gain question has never been asked of the index fusion

• ← related toBounded absence: every chromatin measurement under a menin inhibitor is in an adult-derived line, and none is in an infant KMT2A::AFF1 model

  the index fusion is profiled only in adult-derived lines

• ← testsExperiment: spike-in-calibrated, fusion-attributable occupancy of KMT2A::AFF1 in the first 24 hours of menin inhibition, scored for gains as well as losses

  proposed in SEM and RS4;11, both KMT2A::AFF1

• ← related toHypothesis: the menin inhibitor's effect is inactivation in place, not eviction - the fusion keeps most of its sites and loses its output

  proposed for the index fusion; assembled from data in KMT2A::MLLT3, AFF1 and AFDN backgrounds

• ← bindsSETD2 (Q9BYW2) - the H3K36 trimethyltransferase that binds all seven MLL fusions, and the only one of them with a published KMT2A::AFF1 dependency test

  co-purified with MLL-AF4 in Jurkat AP-MS, p=0.0372, 3|4 spectra (tagged single-copy transgene, not endogenous)

• depends on →SETD2 (Q9BYW2) - the H3K36 trimethyltransferase that binds all seven MLL fusions, and the only one of them with a published KMT2A::AFF1 dependency test

  SETD2 knockdown is antiproliferative and pro-apoptotic in the t(4;11) lines MV4-11 and SEM; contested by SETD2 loss-of-function mutations in 22% of MLLr patients

• ← bindsCHD4 (Q14839) - the NuRD ATPase, a pan-MLL-fusion co-purifier, and the gene whose disruption drives lineage switching in KMT2A::AFF1 relapse

  co-purified with MLL-AF4 in Jurkat AP-MS, p=0.0116, 7|9 spectra against a 2|2 negative control

• ← bindsCSNK2B / CK2beta (P67870) - the regulatory subunit of casein kinase 2, in the pan-MLL-fusion core, with no CSNK2B-and-KMT2A literature at all

  co-purified with MLL-AF4 in Jurkat AP-MS, p=0.0119, 3|3 spectra - low abundance, no orthogonal validation

• ← bindsPML / TRIM19 (P29590) - the scaffold of PML nuclear bodies, co-purified with all seven MLL fusions, and never once studied as a KMT2A-fusion partner

  co-purified with MLL-AF4 in Jurkat AP-MS, p=0.0282, 4|4 spectra; compartment scaffold, so a shared condensate cannot be excluded

• ← bindsNOLC1 / Nopp140 (Q14978) - a nucleolar and Cajal-body phosphoprotein in the pan-MLL-fusion core, and the first physical bridge to this graph's nucleolar convergence

  co-purified with MLL-AF4 at p=0.134 with a 7|0 spectral split - not significant for the index bait; strong for five other MLL fusions in the same experiment

• ← bindsSMARCC1 / BAF155 (Q92922) - the SWI/SNF core scaffold, in the pan-MLL-fusion core, and the missing gene entry in this graph's SWI/SNF beat

  co-purified with MLL-AF4 at p=0.0707 (5|4 spectra, 1|0 control) - above conventional significance, retained by the rank rule

• ← bindsTRIM28 / KAP1 / TIF1beta (Q13263) - the KRAB-ZFP corepressor scaffold in the pan-MLL-fusion core, with the weakest index-fusion p-value but a leukaemic role in another fusion family

  co-purified with MLL-AF4 at p=0.129 (3|2 spectra) - not significant; three of seven baits are below 0.05

• ← bindsSPEN / SHARP / MINT (Q96T58) - the RNA-binding corepressor that silences the X chromosome, in the pan-MLL-fusion core

  co-purified with MLL-AF4 at p=0.0532 (3|5) - marginal; four other baits at 1e-6 with 12-46 spectra

• ← bindsJADE3 / PHF16 (Q92613) - the HBO1-complex scaffold with the strongest pan-fusion evidence in this beat, and an independent published contact with MLL

  co-purified with MLL-AF4 at p=0.00529 (5|5); every one of the seven per-bait p-values is below 0.01, four below 1e-8

• ← bindsSF3A3 / SF3a60 (Q12874) - a U2 snRNP splicing subunit in the pan-MLL-fusion core, and the paper's own named example of a NON-selective hit

  co-purified with MLL-AF4 at p=5.95e-4 (15|12 spectra, 0|3 control) - one of the stronger index-fusion calls in the Skucha table

• ← bindsMCM2 (P49736) - replicative helicase subunit and parental-histone chaperone in the pan-MLL-fusion core, and a live gene_exact collision with MCM7

  co-purified with MLL-AF4 at p=0.00708 (12|14 spectra) - the deepest index-fusion identification of the twelve

• ← bindsTPR / Megator (P12270) - the nuclear-basket nucleoporin that builds heterochromatin exclusion zones, in the pan-MLL-fusion core

  co-purified with MLL-AF4 at p=0.0258 (12|7 spectra, 0|0 control); a nuclear-envelope protein in a nuclear lysate, so carry-over is the leading alternative

• ← bindsNUDT21 / CFIm25 (O43809) - the CFIm subunit that picks poly(A) sites, in the pan-MLL-fusion core, and a paraspeckle protein

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0382 (3|4)

• ← bindsWDR33 (Q9C0J8) - the subunit that reads AAUAAA, in the pan-MLL-fusion core, and the plant homolog of which physically links 3' processing to H3K4 demethylation

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0214 (6|3)

• ← bindsSON (P18583) - a nuclear speckle scaffold that BINDS MENIN and inhibits MLL complex assembly, and the one protein in this tranche the Skucha authors name in their own discussion

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0257 (3|5)

• ← bindsNUP50 / Npap60 (Q9UKX7) - a MOBILE nuclear-basket nucleoporin in the pan-MLL-fusion core, and the evidence says basket, not nuclear envelope

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0121 (4|5)

• ← bindsELOA / TCEB3, Elongin A (Q14241) - a Pol II elongation factor in the pan-MLL-fusion core, ALONE, with none of its own complex and a non-zero negative control

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0059 (7|6) BUT negative control 0|1

• ← bindsSCAF11 / SRrp129 (Q99590) - an SR-related protein that binds the RNA Pol II CTD, in the pan-MLL-fusion core, and alone among the SCAF family

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.00125 (6|7) - strongest index-fusion p in this tranche

• ← bindsGPATCH4 (Q5T3I0) - a nucleolar and Cajal-body helicase cofactor in the pan-MLL-fusion core, with no DHX15 and no G-patch relative beside it

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.00238 (6|11)

• ← bindsWBP11 (Q9Y2W2) - a splicing activator in the pan-MLL-fusion core, isolated from its own partners, and a human haploinsufficiency gene

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0078 (5|5); tightest row in the tranche

• ← bindsZC3H18 (Q86VM9) - the CBC-to-exosome bridge in the pan-MLL-fusion core, and the ONLY member of this tranche whose own complex came with it

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0319 (5|4)

• ← bindsKPNA2 / importin-alpha-1 (P52292) - the classical NLS receptor in the pan-MLL-fusion core, and the ONLY karyopherin of any kind in the whole 960-protein network

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0167 (5|2)

• ← bindsUBAP2L (Q14157) - a BMI1-interacting protein essential for haematopoietic stem cell activity, in the pan-MLL-fusion core, and a stress-granule nucleator recovered from NUCLEAR lysate

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0225 (6|2)

• ← bindsTBL3 / UTP13 (Q12788) - a UTP-B ribosome-biogenesis subunit in the pan-MLL-fusion core, whose loss in zebrafish severely reduces T cells and haematopoietic stem/progenitors

  co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0369 (4|3) - weakest row in this tranche

• ← bindsPA2G4 / EBP1 (Q9UQ80) - the best-evidenced member of the MLL-fusion nucleolar block in the index fusion's own column (p = 0.014), and the only one with a published AML phenotype

  co-purifies with MLL-AF4 in Jurkat AP-MS, p = 0.014, neg ctrl 0 - not a demonstrated direct contact

• ← bindsNOP2 / NSUN1 / p120 (P46087) - the 28S rRNA m5C4447 methyltransferase in the MLL-fusion nucleolar block, present in the index fusion's column at p = 0.0223, and the gene whose PubMed token is two-thirds contaminated by its NSUN paralogues

  co-purifies with MLL-AF4 in Jurkat AP-MS, p = 0.0223, neg ctrl 0 - not a demonstrated direct contact

• ← bindsGNL2 / Ngp-1 (Q13823) - a nucleostemin-family nucleolar GTPase in the MLL-fusion nucleolar block, in the index fusion's column at p = 0.0492, and the one member with a published granular-component assignment

  co-purifies with MLL-AF4 in Jurkat AP-MS, p = 0.0492 - 0.0008 inside an arbitrary line in a rank-selected table

• ← related toLYAR (Q9NX58) - a zinc-finger nucleolar growth regulator cloned from a T-cell leukaemia line, in six of seven MLL-fusion interactomes, and the one member of this block whose discovery system is the same lineage as the AP-MS host

  in the MLL-AF4 column but at p = 0.141, above 0.05 - listed on rank, not a usable index-fusion association

• ← related toTCOF1 / treacle (Q13428) - the Treacher Collins nucleolar phosphoprotein in the MLL-fusion nucleolar block, the block's only link to rDNA damage signalling through NBS1, and the only member whose loss causes a named human developmental syndrome

  in the MLL-AF4 column at p = 0.163 against a column maximum of 0.175 - rank only, not evidence of association

• ← related toRRP12 (Q5JTH9) - a pre-40S export factor in six of seven MLL-fusion interactomes but NOT in the index fusion's, and the block's only member with a recessive human disease published in 2025

  NOT recovered by MLL-AF4 - an MLL-fusion interactor, not a demonstrated KMT2A::AFF1 interactor

• ← related toWDR18 (Q9BV38) - the Rix1/PELP1-TEX10-WDR18 60S maturation subunit, in five MLL-fusion interactomes but NOT the index fusion's, and the block's only member whose nucleolar partitioning is SUMO-controlled

  NOT recovered by MLL-AF4 - an MLL-fusion interactor, not a demonstrated KMT2A::AFF1 interactor

• ← related toUTP14A (Q9BVJ6) - an SSU processome component that binds and destabilises p53, in four MLL-fusion interactomes but NOT the index fusion's and below the screen threshold

  NOT recovered by MLL-AF4 and below the shRNA-library threshold - no binding row and no functional test

• ← related toRRP9 / U3-55K (O43818) - the U3 snoRNP-specific core protein in four MLL-fusion interactomes but NOT the index fusion's, and the block's only member with a published acetylation switch

  NOT recovered by MLL-AF4 and below the shRNA-library threshold - no binding row and no functional test

• ← related toUTP18 / WDR50 (Q9Y5J1) - the SSU processome subunit that recruits the exosome helicase MTREX to rRNA fragments; in three MLL-fusion interactomes but not the index fusion's, and separately the subject of a 21-year-old IntAct curation error in this graph

  NOT recovered by MLL-AF4 and below the shRNA-library threshold; recovered by MLL-AF9, EEN and ENL only

• ← related toFTSJ3 (Q8IY81) - the pre-rRNA 2'-O-methyltransferase at the weakest edge of the MLL-fusion nucleolar block: two baits of seven, not the index fusion, and never screened

  NOT recovered by MLL-AF4; two baits of seven, the fewest in the block, and never functionally screened

• ← bindsMAP7D1 (Q3KQU3) - the strongest index-fusion p-value of the nine deferred pan-MLL-fusion preys, on a protein UniProt places entirely outside the nucleus

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.00818 (8|3), neg 0|0 - co-purification only, not a demonstrated contact

• ← bindsVIM / vimentin (P08670) - a pan-MLL-fusion prey with a clean negative control, and separately a genuine KMT2A rearrangement partner in sarcoma, which are two different facts

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.0109 (4|3), neg 0|0 - probably contamination; co-purification only

• ← bindsACTB / beta-actin (P60709) as a SUBJECT, not a loading control - the dirtiest negative control in the pan-MLL-fusion 42, and the one the paper's authors kept

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.0145 (22|16), neg 3|3 - the dirtiest control of the 42; undecidable, co-purification only

• ← bindsMAPRE1 / EB1 (Q15691) - a microtubule plus-end tracking protein that is BOTH a pan-MLL-fusion prey and a genuine KMT2A fusion partner in pro-B ALL

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.0273 (3|3), neg 0|0 - lowest index-fusion depth in the tranche; probably contamination

• ← analogous toKMT2A::MAPRE1 (MLL-EB1) - a coiled-coil dimerisation fusion from pro-B ALL with a mouse model, low leukaemogenic potential, and Ets1 as its effector

  comparator for the menin-interface hypothesis: both retain the KMT2A N-terminus, but MAPRE1 supplies only dimerisation and is measurably less leukaemogenic than MLL/AF10, while AFF1 supplies the SEC

• ← bindsEIF4G1 (Q04637) - a translation-initiation scaffold in the pan-MLL-fusion core, alone, with no other eIF4F subunit anywhere in the 960

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.0448 (7|2), neg 0|0 - undecidable; co-purification only

• ← bindsZNF512 (Q96ME7) - the one protein of the nine deferred pan-MLL-fusion preys that is a sequence-specific chromatin factor, and it initiates pericentric heterochromatin

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.0463 (4|6), neg 0|2, six of seven baits below 0.01 - the strongest candidate of the nine

• ← bindsPRKAR1A (P10644) - a PKA regulatory subunit in the pan-MLL-fusion core with no catalytic subunit anywhere in the network, and a fusion oncogene in variant APL

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.048 (3|3), neg 0|0 - clears 0.05 by 4%; no PKA catalytic subunit anywhere in the network

• ← bindsDHX16 / hPRP2 (O60231) - the spliceosomal catalytic-activation helicase, pan-MLL-fusion, and one of only two in the 42 whose index-fusion p-value exceeds 0.05

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.0929 - ABOVE 0.05, rank 38 of 42; three of seven baits exceed 0.05

• ← bindsLUZP1 / fimbacin (Q86V48) - the weakest index-fusion call of the nine, and the strongest non-index call: p = 0.127 against MLL-AF4 and 2.6e-10 against MLL-ENL

  co-purified, all 7 MLL fusions, Jurkat nuclear-lysate AP-MS, MLL-AF4 p=0.127 - ABOVE 0.05, rank 39 of 42, the weakest index call of the nine; MLL-ENL gives 2.63e-10

• ← analogous toYAP1::KMT2A::YAP1 (YKY) - an insertional KMT2A rearrangement that keeps the CXXC zinc finger and throws the menin-binding exon away

  same gene, inverted polarity: KMT2A is the internal/3' contributor, the menin-binding exon is absent and the partner is a Hippo co-activator rather than an elongation factor

• ← analogous toVIM::KMT2A - the one KMT2A rearrangement that keeps the SET domain and still throws away the menin-binding exon

  inverted polarity and inverted domain retention: keeps SET, loses the menin-binding motif

• ← analogous toIn leukaemia KMT2A gives the front of the protein; in sarcoma it gives the back. Every consequence follows from that.

  the 5-prime-KMT2A polarity this concept contrasts against

• ← supportsThe menin interface is a requirement of 5'-KMT2A fusions in haematopoiesis, not of KMT2A rearrangement as such - and a solid tumour has been quietly proving it for six years

  strengthens the menin-interface hypothesis as a claim about leukaemogenesis specifically

• ← analogous toEvery published KMT2A partner in sarcoma, counted - plus the papers this beat read and did not use, so the next beat does not repeat the search without the decisions

  not one sarcoma partner is elongation machinery, which is the entire partner class of the index fusion

• ← related toSMARCA4 (BRG1) - a tumour suppressor by mutation and a maintenance requirement by knockdown, and in KMT2A-rearranged lines the dependency data say it is not selective at all

  NEGATIVE, AND MEASURED IN THIS REPOSITORY: in the MLL-fusion AP-MS complex analysis the MLL-AF4 bait's BAF hits are SMARCB1, SMARCC1 and SMARCC2 - SMARCA4 is absent, appearing in only one of seven baits (MLL-CBP) - and BAF as a complex reaches q = 0.076 at a nuclear background and 0.186 at the recovered background. BAF is not an established module of this fusion.

• ← analogous toLDB1::KMT2A - the clearest statement in this literature that a sarcoma fusion keeps KMT2A exons 4 to 36 and discards exons 1 to 3

  INVERTED ORIENTATION, AND THE PARTNER IS AN ARCHITECTURAL FACTOR RATHER THAN AN ELONGATION ONE: the index fusion joins KMT2A's targeting N-terminus (MBM, LEDGF IBMs, AT-hooks, CXXC) to an elongation partner. LDB1::KMT2A joins a self-associating enhancer-looping factor to KMT2A aa 1053-3969 -- CXXC through SET -- discarding the menin and LEDGF tethers and all three AT-hooks. Same gene, opposite halves, opposite partner class.

• ← related toMED19 - the Mediator subunit curated against an engineered MLL-AFF4 fusion protein, and the one REST uses to deliver G9a

  co-IP is with an engineered MLL-AFF4 chimera (IntAct EBI-2620048), not with KMT2A::AFF1 - candidate, not member

• ← related toBUD13 - a RES-complex splicing factor 1.66 Mb from KMT2A on 11q23.3, whose one chromatin paper puts it in the soluble fraction

  BUD13 is an 11q23.3 gene 1.66 Mb from KMT2A and has NEVER been reported as a fusion partner - recorded so the cytoband is not misread as a breakpoint claim

• ← co-occurs withAFF1::KMT2A (AF4-MLL), the der(4) product: what it is made of, residue by residue

  The two products of one balanced t(4;11); complementary halves of KMT2A with no overlapping module.

• ← related toThe infant breakpoint mutilates the reciprocal protein's first PHD finger - so 'the reciprocal product' is at least two different proteins

  The same break defines both products; more KMT2A in one means less in the other.

• ← related toCompeting model 3: reciprocal status is a proxy for where the break fell, and the thing that changed is the DIRECT product

  Proposes that the direct product's composition, set by the same break, is the causal variable.

• ← co-occurs withPut both fusion proteins in the same cell and you get something neither produces alone

  Cooperation between the two products of one translocation, reported in three systems.

• ← related toA tested negative: neither fusion product alters DNA double-strand break repair

  Tested for both products of t(4;11) in the same experiment.

• ← related toThe MLL3/4-UTX switch fails to throw — menin inhibition kills by turning something ON, and cells that cannot turn it on survive

  the patient material in which KMT2C-edited cells were selected under menin inhibitor was KMT2A::AFF1 ALL

• regulates →CCND3 (cyclin D3) — the scan's rank-4 hit, and the only one of the four with a drug class already in children

  indirect: the fusion transcriptionally drives CDK6, the kinase cyclin D3 activates; fusion knockdown lowers CDK6 in infant ALL

• ← related toThree addresses, one output: what SET::NUP214 actually does to the menin-interface hypothesis, and why it is a weaker test than CALM-AF10

  the index fusion against which both comparators are read; lineage and age both differ

• depends on →The KMT2A-fusion causal chain: six links, one measured ordering, and two arms that are parallel rather than sequential

  the index fusion the chain is written about; only one in-vivo AFF1-backbone link exists

• ← testsDoes the fusion's programme fall apart in the same order in KMT2A::AFF1 as in MLL::AF9? The chain's only ordering measurement, repeated on the index fusion

  the index fusion, for which no degron model exists

• ← related toThe soluble-nucleoplasm versus chromatin-bound axis - the one localisation readout that keeps a size dimension, and nobody has run it on a KMT2A fusion

  the soluble-versus-chromatin-bound ratio of KMT2A::AFF1 has never been measured

• ← related toThe clustered PHD fingers (KMT2A aa 1416-1640) are a chromatin-targeting module and the canonical t(4;11) junction removes them by ten residues

  the canonical junction at KMT2A 1406 removes the cluster beginning at 1416

• ← related toMLL was reported at regions attached to the nuclear envelope in 2000, which is indirect evidence at the lamina that this graph currently records as absent

  MLL-AF4 was among the conditionally expressed chimeras imaged

• ← testsExperiment: five-fraction subcellular blot of a t(4;11) line, with a menin-inhibitor arm - converting thirty years of unattributable images into attributable numbers using only existing antibodies

  measures the fusion's chromatin-bound fraction against wild-type AFF1 in the same lane

• ← related toHypothesis: what the KMT2A half loses is control of its own abundance, not control of its activity

  [describes] predicts the fusion is the longer-lived species in its own cell

• ← related toTASP1 (taspase1) - the protease that cuts KMT2A, and the timer the fusion escapes

  [does_not_act_on] both cleavage sites are ~1,300 residues C-terminal to the breakpoint; no der(11) fusion is a substrate

• ← inhibitsSilmitasertib (CX-4945) - a CKII inhibitor that works on KMT2A-rearranged leukemia by strengthening the allele the fusion does not have

  [displaces] decreases genome-wide MLL-AFF1, AFF4 and ELL2 chromatin occupancy in SEM cells without binding the fusion

• ← testsRedesign: the proximity-labelling map of KMT2A::AFF1 cannot be controlled with the wild-type allele - it has to be controlled with time

  [measures] fusion-dependent proximity by degron-timed labelling in one line

• ← testsExperiment: titrate wild-type KMT2A up and down in one leukemia cell and watch what happens to the fusion's grip on chromatin

  [measures] fusion chromatin occupancy as a function of wild-type KMT2A abundance

• ← part ofLost from the KMT2A half: the four-residue HCF-binding motif (DHNY, aa 1799-1802)

  module absent from this and every other KMT2A fusion protein

• ← part ofLost from the KMT2A half: the WIN motif and the whole WRAD interface (aa 3762-3767, Arg3765)

  module absent from the fusion, yet druggable on the wild-type allele in the same cell

• ← testsExperiment: put four residues back - the minimal add-back control the PHD3 result has never had

  run in the commonest infant fusion, which the 2008 study never tested

• ← related toAFF1 as the subtraction control: the refutation is WITHDRAWN - the degron is lost, not retained

  the degron refutation is about the forward fusion only; AF4-MLL alone induced ALL in mice where MLL-AF4 alone did not (Bursen 2010)

• ← part ofAFF1 as the subtraction control: the refutation is WITHDRAWN - the degron is lost, not retained

  mechanism class of this fusion: addition, confirmed by audit

• ← related toExperiment: CRISPR knockout of CLEC12A in KMT2A-rearranged models, with and without a cooperating RAS lesion

  arm 3 is the B-lineage index-fusion arm, expected negative and worth having

• ← related toFUT4 - the myeloid alpha-1,3-fucosyltransferase, a hub gene of the KMT2A-rearranged expression module, and the gene HGNC once officially called CD15

  hub gene of the co-expression module most correlated with MLL rearrangement in paediatric ALL

• ← related toSS18 - a SWI/SNF subunit that is itself a fusion partner in another cancer, and a lineage-independent dependency in KMT2A-rearranged lines

  no KMT2A fusion partner is a BAF subunit; SS18 marks the boundary of the analogy

• ← related toTwo published ways a fusion oncoprotein engages BAF - be a subunit, or recruit it with a disordered domain - and KMT2A has never been tested for either

  route 2 is untested for this fusion; recorded as a question, not a negative

• ← testsSeparate ncBAF from canonical BAF in KMT2A-rearranged cells: paired degron, paralogue-pair CRISPR, and complex-resolved CUT&RUN

  arm 3 maps complex-resolved occupancy against the fusion's own targets

• ← bindsKDM4C (JMJD2C/GASC1) — recruited by the retained KMT2A N-terminus, drugged in a KMT2A::AFF1 line, and invisible to CRISPR

  recruited via the MLL 5' moiety retained in every KMT2A fusion

• ← depends onBOD1L (BOD1L1) — the top SETD1A co-dependency, and the only candidate in this cycle tested by CRISPR tiling in a KMT2A::AFF1 line

  CRISPR tiling in iCas9-MV4-11 (KMT2A::AFF1) shows a strong Shg1-domain dependency; no physical interaction with the fusion is reported

• ← testsOne experiment that decides whether KDM4C is a target or the KDM4 family is: paralogue rescue of SD70 sensitivity in SEM

  run in SEM and RS4;11, KMT2A::AFF1 lines without the FLT3-ITD confounder

• ← related toIn human KMT2A::AFF1 MV4;11 (monocytic, not B-lineage), the vehicle-versus-vehicle noise floor is 9.4% at the top 0.1% of menin/MLL1 sites and 0.1-2.6% in every other stratum - so cycle 102's borrowed 4-10% band is about right AT THE PEAKS and four to five times too generous everywhere else, and it was applied everywhere
• ← related toThe missing reagent is a spike-in, not a better statistic: a spike-in-normalised H3K4me3, H3K79me2 and H3K27me3 ChIP-seq at 72 h of a clinical menin inhibitor in a KMT2A-rearranged human line, which is the only design that can tell a genuine genome-wide mark redistribution from the compositional shadow of a peak-localised change
• ← treated byBlinatumomab in infant KMT2A-rearranged ALL — the largest single outcome gain in thirty years

  CD19xCD3 engagement is orthogonal to the fusion transcriptional program

• ← treated byVenetoclax in KMT2A-rearranged leukemia — the apoptotic partner every other drug needs

  high BCL-2 expression in KMT2A-rearranged infant ALL; azacitidine+venetoclax prolongs xenograft survival

• ← inhibitsBET bromodomain inhibition in KMT2A-rearranged leukemia — spectacular preclinically, stalled clinically

  I-BET151 arrests growth, impairs PDX engraftment and resensitises to prednisolone in MLL-AF4 models

• ← treated byAUGMENT-101 (NCT04065399) — the registration trial, and what 22.8% actually means

  KMT2A-rearranged relapsed/refractory acute leukemia, eligibility from 30 days of age

• ← related toDoes menin inhibition have any MHC class II headroom to work with in B-precursor infant ALL? A flow cytometry experiment on samples that already exist

  primary KMT2A::AFF1 infant B-ALL blasts are the index samples

• ← related toA caveat that weakened the index fusion, wrongly: the MLL-AF4 spreading deposition is 30 SEM samples plus six other lines, all human

  this unstated system resolves to the index fusion rather than an import

• ← related toThe panobinostat H2Bub result is SEM and KOPN8 against a REH comparator: three human lines, two KMT2A partners, one non-KMT2A control

  the SEM arm is the index fusion

• ← related toThe unnamed KMT2A-rearranged B-ALL line is SEM, and the deposition says KMT2A::AFF1 in a genotype field

  the only deposition in this beat that states the index fusion in a structured genotype field

• ← related toHalf the KDM4C deposition is not a KMT2A fusion at all: MOZ-TIF2 8, MLL-GAS7 6, MLL-AF9 2, and the human xenograft deposited nothing

  zero deposited samples carry the index fusion

• ← related toBounded failure: the one unresolved source that is actually about the index fusion

  the only unresolved source in this beat whose subject is the index fusion

• ← related toAn unstated system is not a coin flip: four out of five resolve away from the index disease, so silence in this graph is systematically optimistic

  three of sixteen resolutions reach the index fusion, all through one cell line

• ← related toCord blood does transform — when the translocation is engineered rather than expressed
• ← related toWDR5: an established wild-type KMT2A contact, and no fusion contact ever measured

  No published experiment tests association between this subunit and the direct KMT2A::AFF1 fusion protein, in either direction.

• ← related toRBBP5: the thinnest fusion literature of the four subunits, and one chromatin datum

  No published experiment tests association between this subunit and the direct KMT2A::AFF1 fusion protein, in either direction.

• ← related toASH2L: the only WRAD subunit ever perturbed in a KMT2A::AFF1 cell, once, weakly

  No published experiment tests association between this subunit and the direct KMT2A::AFF1 fusion protein, in either direction.

• ← related toDPY30: the founding negative does not cover it, and it has no KMT2A contact to lose

  No published experiment tests association between this subunit and the direct KMT2A::AFF1 fusion protein, in either direction.

• ← related toForty-five percent of t(4;11) patients express a KMT2A fusion transcript that keeps the whole WRAD interface

  The der(4) counterpart of this fusion, expressed in about 45% of t(4;11) infant B-ALL, is menin-blind and WRAD-competent - the mirror image of the der(11) product.

• ← related toAn anti-MLL-C antibody in a t(4;11) cell is looking at two proteins at once

  Every published WRAD-adjacent observation in a KMT2A::AFF1 cell rests on anti-MLL-C or anti-MLL reagents that cannot assign the species they detect.

• ← testsSettle the WRAD question: tagged co-IP plus degron-timed proximity across three fusion classes

  Arm A tags the direct fusion in SEM or RS4;11 and blots for all four WRAD subunits with menin as the internal positive.