CK2 phosphorylates KMT2A at T2724/S2726 to license taspase1 cleavage - and that site is in the half the fusion throws away
also called CKII taspase1 licensing · MLL CS2 phosphorylation · T2724 S2726 · MLL-AA peptide
Healthy KMT2A gets cut in two by an enzyme called taspase1, and being cut makes it less stable. CK2 has to add phosphate right next to the cut site first. Blocking CK2 leaves KMT2A uncut and abundant, and the extra healthy protein pushes the leukaemia fusion off the DNA.
The same thing, for a scientist
Taspase1 cleavage of MLL1 **destabilises** it, reversing the older reading that cleavage is maturation. **Casein kinase II phosphorylates MLL1 proximal to the taspase1 site and facilitates cleavage.** The in vitro assay compares peptide `GVDD/GTESDTSVTAT` with `GVDD/GAEADTSVTAT`; only the wild-type is phosphorylated by recombinant CKII. Mapping the peptide onto Q03164 places GVDD at 2719-2722 and the two substituted acceptors at **T2724 and S2726**, both of which are independently observed phosphosites in the PRIDE re-analysis. **Both lie ~1,300 residues C-terminal to the breakpoint cluster region, so the fusion does not carry them.** The therapeutic consequence runs entirely through the wild-type allele: CX-4945 raised full-length MLL1 **without altering MLL-AF4 levels** in SEM cells, reduced genome-wide MLL-AFF1, AFF4 and ELL2 occupancy, and extended survival in an MLL-AF9 mouse. **This is the best-characterised phospho-switch on KMT2A, and it is on the lost fragment.**
Residue mapping, shown so it can be checked
The paper states its substrate as a peptide. Locating that peptide in the canonical Q03164 sequence:
2719 G V D D G T E S D T S V T A T
2719 2722 | 2724 2726
cleavage after D2722
So GVDD = 2719-2722, cleavage site CS2 is D2722, and GTESD -> GAEAD substitutes T2724 and S2726. Both appear in the PRIDE/PTMeXchange phosphosite set for Q03164, which is an independent confirmation that these residues really carry phosphate in cells and not only in a peptide assay 2.
This mapping is ours, done by string search; the paper does not give residue numbers. Different isoform numbering will shift them.
Why a lost-fragment switch is still a therapeutic lead
The fusion has no T2724. The mechanism nonetheless acts on the fusion, indirectly and at one remove:
- CK2 inhibition blocks cleavage of wild-type MLL1.
- Uncleaved MLL1 is more stable and its chromatin occupancy rises genome-wide.
- Stabilised wild-type MLL1 competes the chimera off chromatin: MLL-AFF1, AFF4 and ELL2 occupancy all fall, with matching falls in JUP and SLC43A2 transcription.
- CX-4945 delays leukaemic progression and extends survival in an MLL-AF9 syngeneic mouse, by oral gavage and by intraperitoneal injection.
The critical dependency, and it is not hypothetical: this requires a functional wild-type KMT2A allele. The published result explicitly shows fusion protein levels unchanged. A patient whose second allele is deleted, silenced or itself rearranged has nothing for the mechanism to work through, and no reported experiment tests that case.
| kinase | CK2 (CSNK2A1/CSNK2A2) |
|---|---|
| substrate | gene-kmt2a |
| uniprot | Q03164 |
| fate in fusion | lost |
| split residue | 1400 |
| cleavage site | taspase1 CS2, D2722 in Q03164 numbering (GVDD at 2719-2722) |
| tested on fusion | Indirectly - fusion protein levels unchanged; fusion chromatin occupancy decreased through competition by stabilised wild-type MLL1 |
| requires wild type allele | true |
sites
[ "T2724", "S2726" ]
peptides used
{
"wild_type": "GVDD/GTESDTSVTAT",
"mutant": "GVDD/GAEADTSVTAT"
}inhibitor ic50 uM
{
"CX-4945": 0.011,
"TTP22": 0.38
}- The intervention works only through the wild-type allele. Loss or silencing of that allele is a one-step resistance mechanism that requires no new signalling and would be invisible to any assay reading fusion levels.
- Raising wild-type MLL1 globally raises H3K4 methylation genome-wide; in normal haematopoiesis MLL1 dosage is not neutral, and the paediatric marrow is the tissue being exposed.
- CX-4945 is being proposed here and in a separate 2026 study for opposite-looking reasons in the same disease. If both are right the drug is good for two reasons; if one is wrong, a trial that succeeds will attribute its success to the wrong mechanism and the next compound will be optimised against the wrong target.
- Taspase1 also cleaves TFIIA and MLL2; the specificity claimed for the CK2 step rests on the observation that CX-4945 did not affect MLL2 or TFIIA cleavage in one cell line.
- Does the CX-4945 effect survive in a KMT2A-rearranged line engineered to lose its wild-type allele? That single experiment decides whether this is a general strategy or one restricted to wild-type-retaining disease.
- Is the chromatin displacement of the chimera genuinely competitive, or does stabilised wild-type MLL1 act by reassembling COMPASS components the fusion needs?
- Does CK2 inhibition simultaneously loosen the fusion's own LEDGF grip through S136/S142? The two CK2 routes have never been measured in the same experiment.
- What fraction of KMT2A-rearranged patients retain an expressed wild-type allele at diagnosis and at relapse?
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Taspase1-dependent cleavage of MLL1 destabilises it; casein kinase II phosphorylates MLL1 proximal to the taspase1 cleavage site and facilitates cleavage, and pharmacological CKII inhibition blocks cleavage, increases MLL1 stability and displaces MLL chimeras from chromatin, with CX-4945 delaying leukaemic progression in an MLL-AF9 mouse model.
Regulation of MLL/COMPASS stability through its proteolytic cleavage by taspase1 as a possible approach for clinical therapy of leukemia. · Zhao Z, et al. · Genes Dev 2019What this evidence cannot show
Full text read via Europe PMC fullTextXML (PMC6317322) on 2026-09-19. Mechanistic work is largely in 293T cells with CRISPR TASP1 knockout; leukaemia work is in SEM, MV4-11 and RS4;11 and in a mouse MLL-AF9 model. The in vitro CKII assay uses a synthetic peptide, so it establishes that CK2 can phosphorylate those residues, not the stoichiometry on full-length MLL1 in a cell. CX-4945 has reported off-target activity, and the survival effect is a delay.
Evidence that argues against this (2)
- The paper itself reports that CX-4945 increased full-length MLL1 without altering MLL-AF4 protein levels, so the intervention does not touch the oncoprotein. Its entire benefit is mediated by the wild-type allele, which makes it a therapy whose mechanism can be removed by a single further genomic event and which would be invisible in any model lacking a wild-type KMT2A copy. Zhao Z et al. 2019
- Taspase1's role in MLL biology has been read in the opposite direction for most of its history - as the maturation step that produces the functional MLL N/C heterodimer - and this project already carries a separate entry on the cleavage sites built on that framing. A reversal of the field's reading of an enzyme's purpose deserves replication before therapy is designed on it. Liu H et al. 2007
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
T2724 and S2726 of KMT2A are independently observed as phosphorylation sites in the PRIDE/PTMeXchange re-analysis of public proteomics served by the EMBL-EBI Proteins API, and both lie C-terminal to residue 1400, so neither is retained in KMT2A fusion proteins.
Proteins API proteomics-PTM, Q03164, sites T2724 and S2726 · EMBL-EBI 2026What this evidence cannot show
Fetched 2026-09-19. The proteomics observation says these residues carry phosphate in some cell type; it does not attribute them to CK2 and cannot distinguish them from neighbouring acceptors beyond the reported localisation probability. The residue numbers depend on our peptide mapping and on the canonical isoform.
Evidence that argues against this (1)
- Observing a phosphosite in pooled shotgun data says nothing about occupancy. If the fraction of MLL1 molecules carrying phospho-T2724 at any moment is small, the cleavage-licensing step could be rate-limited elsewhere and CK2 inhibition would then act through a different substrate entirely - CK2 has several hundred. Lei Y et al. 2026
the phospho-licensing step for the same cleavage
- depends on →CSNK2A1 (casein kinase 2 alpha) - the one kinase that turns up three separate times in KMT2A biology
CK2 is the kinase that licenses the cleavage
the phospho-step upstream of the cleavage this entry catalogues
- treated by →KMT2A::MLLT3 (MLL-AF9), t(9;11)(p21.3;q23.3)
CX-4945 delays progression in the MLL-AF9 mouse model
a lost-fragment phosphosite pair in the atlas
- ← testsSeparating CK2's two routes into KMT2A leukaemia, which every published experiment has confounded
route B of the separation
blocks the CK2 phosphorylation that licenses taspase1 cleavage