Oncofusion

start / graph / localization-psip1-ledgf-chromatin-tether-subnuclear

Mechanismmoderate confidence 3 of 5: One strong study, or several smaller consistent ones.Q57-localization2

Where LEDGF/p75 actually is: bound to chromatin through mitosis, in the nuclear interior with H3K36me3 - and never once imaged in a KMT2A-rearranged cell

also called PSIP1 localization · LEDGF/p75 subnuclear · LEDGF chromatin tethering · p75 mitotic chromosome coating

LEDGF is the protein that helps hold the leukemia fusion's partner complex onto DNA, and unlike most chromatin proteins it stays stuck to the chromosomes even while the cell is dividing. The best pictures put it in the open interior of the nucleus next to a mark called H3K36me3 and away from the dense edge - but every one of those pictures was taken in HeLa cervical-cancer cells, never in a leukemia cell carrying a KMT2A fusion.

The same thing, for a scientist

LEDGF/p75 (PSIP1) is a constitutive chromatin-tethering factor rather than a compartment resident. In living human HeLa cells, EGFP-LEDGF/p75 coats condensed mitotic chromosomes and its knockdown abolishes the nuclear and chromosomal localisation of its cargo, HIV-1 integrase [E1]. Chromatin association is delivered by a tripartite element - the NLS plus two AT-hooks at residues 146-197 - with the PWWP domain contributing a protein/nucleosome contact rather than free-DNA binding; PWWP deletion subtly alters interphase nucleoplasmic distribution without abolishing mitotic chromosome binding [E2]. Quantitative live-cell FRAP/FCS shows the protein is not statically parked: it moves in a chromatin hopping/scanning mode typical of transcription factors, and binding a cargo through the IBD raises apparent chromatin affinity ~75-fold - a scan-and-lock model [E3]. The only sub-nuclear POSITIONAL measurement is expansion microscopy (ExEpi), which places LEDGF co-localised with H3K36me3/me2 deeper in the nuclear interior while H3K9me3 occupies the nuclear rim [E4] - in HeLaP4 cells, with an antibody that cannot separate LEDGF/p75 from LEDGF/p52. No published image places LEDGF/p75 anywhere in a KMT2A-rearranged cell [E5].

Go deeper
The one thing about LEDGF localisation that is not in doubt

LEDGF/p75 is chromatin-bound through mitosis. In living HeLa cells expressing EGFP- and HcRed-tagged constructs, LEDGF/p75 decorates condensed mitotic chromosomes, and RNAi knockdown of endogenous LEDGF/p75 abolishes the nuclear and chromosomal localisation of HIV-1 integrase 1. This is the behaviour that makes it a tether: a protein that stays on the template while the nuclear envelope is gone is available to re-deliver cargo to the same addresses in the daughter cell.

UniProt records this in one sentence - "Remains chromatin-associated throughout the cell cycle" - with no evidence code attached to that note (the Nucleus line itself carries ECO:0000269 for PMID 15642333 and PMID 9885563). The measurements behind the mitotic statement are 1 and 2, both live-cell imaging of overexpressed fluorescent fusions in HeLa, not endogenous protein and not a blood cell.

What holds it there, and what the PWWP domain does and does not do

Turlure et al. dissected this with complementary in-vitro and in-cell assays 2. Recombinant LEDGF/p75 shows no sequence-specific DNA binding by surface plasmon resonance or gel shift. Non-specific DNA binding maps to residues 146-197, spanning the NLS and two AT-hook motifs. EGFP fusions were then scored in interphase and in mitosis:

  • the PWWP domain was not required for binding condensed mitotic chromosomes;
  • deleting PWWP nonetheless subtly altered the nucleoplasmic distribution during interphase;
  • a dual AT-hook mutant associated normally with chromatin until the mutations were combined with NLS changes or PWWP deletion, at which point chromatin binding was lost.

So chromatin retention is redundant and multipartite. This matters for the therapeutic proposal held elsewhere in this graph: a PWWP-directed ligand (see target-ledgf-pwwp-fragment-chemistry-and-its-ceiling) attacks the arm that this experiment shows is dispensable for gross chromatin retention. It may still be the arm that sets the address - occupancy and position are different quantities - but a compound cannot be assumed to evict LEDGF.

It is not parked - it scans, and cargo locks it

Hendrix et al. measured LEDGF/p75 in living HeLa nuclei with spot-FRAP, half-nucleus FRAP, continuous photobleaching, FCS and tunable-focus FCS 3. The protein moves in a chromatin hopping/scanning mode typical of transcription factors. The PWWP domain is necessary but not sufficient for chromatin binding in vivo. Once a cargo engages the IBD (measured with HIV-1 integrase), the kinetics shift to a ~75-fold larger apparent affinity for chromatin, and the PWWP is what locks the complex down.

Read across to leukaemia this predicts something testable and unmeasured: the menin/KMT2A-fusion cargo should itself increase LEDGF residence time on chromatin, and menin inhibition should shorten it. The graph already holds mechanism-ledgf-occupancy-falls-under-menin-inhibition from occupancy data; the kinetic version of that experiment has never been done, and occupancy and residence time can move in opposite directions.

The only sub-nuclear position measurement, and the antibody problem inside it

ExEpi (expansion microscopy for epigenetics) is the one method that has asked where in the nucleus LEDGF sits rather than what it binds 4. In HeLaP4 cells it found LEDGF co-localising preferentially with H3K36me3 and H3K36me2, increasing from heterochromatin (H3K27me3) toward open chromatin, and it reports the positional result directly: H3K9me3 occupies the nuclear rim, while LEDGF/H3K36me3 co-localisation occurs further inside the nucleus.

Rule 74 applies and the paper says so itself. The imaging primary antibody "targets both LEDGF/p75 and LEDGF/p52". The authors attempted a LEDGF/p75 knock-out control and state it was confounded because p52 is still detected in the knock-out; they fell back on a 180-degree image-rotation negative control, which left a residual co-localisation floor of 5.6 +/- 1.1. LEDGF/p52 is the splice variant that lacks the integrase-binding domain - the very domain that carries menin and KMT2A - and this graph already holds concept-psip1-p52-is-not-p75 for exactly this reason. So the only sub-nuclear position we have for "LEDGF" is a position for p75 and p52 together.

Reagents named in that paper's methods: LEDGF/p75 A300-848A (Bethyl, rabbit) and LEDGF 611715 (BD Biosciences, mouse) for western blot; H3K36me2 ab176921 and H3K36me3 ab9050 (Abcam). The imaging antibody identities sit in its Supplementary Table 11, which this entry did not retrieve - so the clone behind the positional claim is, strictly, still unread.

Bounded absence: nobody has imaged LEDGF in a KMT2A-rearranged cell

PubMed, 2026-09-20; exact strings, counts and controls in 5. The literature that places LEDGF anywhere in a nucleus is an HIV integration-site literature in HeLa and HEK293T. The literature that connects LEDGF to this disease is a ChIP / co-IP / dependency literature that never takes a picture. These are two non-overlapping bodies of work and the join has never been made.

What would settle it, cheaply: immunofluorescence of endogenous LEDGF/p75 in SEM or RS4;11 (KMT2A::AFF1, human B-lineage) co-stained with menin and with H3K36me3, before and after 48 h of revumenib - with an isoform-discriminating readout, i.e. an antibody raised against the p75-specific C-terminus or an endogenous tag, because the published imaging reagent cannot make that distinction.

Facts and figures
genegene-psip1
uniprotO75475
length AA530
compartment subcellularnucleus; chromatin-bound, retained on condensed chromosomes through mitosis
compartment subnuclearnuclear interior, co-distributed with H3K36me2/me3; explicitly NOT the H3K9me3 nuclear rim (ExEpi, HeLaP4)
antibody caveat rule74The ExEpi imaging antibody detects LEDGF/p75 AND LEDGF/p52; the paper states the p75 knock-out control was confounded by residual p52 signal. No published subnuclear position for this protein is isoform-resolved.
shown for fusionNO - no KMT2A fusion system anywhere in the localisation literature for this protein
endogenous protein imagedpartly - ExEpi images endogenous protein; the mitotic and kinetic work uses overexpressed fluorescent fusions
patient material datafalse
bounded absence date2026-09-20
methods
[
  "live-cell EGFP/HcRed fusion imaging",
  "RNAi plus immunofluorescence",
  "surface plasmon resonance",
  "electrophoretic mobility shift",
  "spot-FRAP / half-nucleus FRAP / continuous photobleaching / FCS / tunable-focus FCS",
  "expansion microscopy (ExEpi)"
]
antibody reagents named in sources
[
  {
    "target": "LEDGF/p75",
    "reagent": "A300-848A (Bethyl, rabbit polyclonal)",
    "use": "western blot",
    "source_pmid": "35716125"
  },
  {
    "target": "LEDGF (pan-isoform)",
    "reagent": "611715 (BD Biosciences, mouse monoclonal)",
    "use": "western blot",
    "source_pmid": "35716125"
  },
  {
    "target": "H3K36me2",
    "reagent": "ab176921 (Abcam)",
    "use": "western blot",
    "source_pmid": "35716125"
  },
  {
    "target": "H3K36me3",
    "reagent": "ab9050 (Abcam)",
    "use": "western blot",
    "source_pmid": "35716125"
  }
]
uniprot evidence codes
{
  "Nucleus": "ECO:0000269|PubMed:15642333, ECO:0000269|PubMed:9885563",
  "note_remains_chromatin_associated_throughout_cell_cycle": "no ECO code attached in the UniProt record"
}
species and systems
[
  "human HeLa",
  "human HeLaP4",
  "human HEK293T (knock-out control)"
]
How this could bite us back
  • A PWWP-site ligand may engage LEDGF fully and not move it: Turlure et al. show the PWWP is dispensable for gross chromatin retention, which the AT-hook/NLS element can supply. A trial-ready 'LEDGF displaced' biomarker may therefore be unobtainable with a PWWP compound.
  • LEDGF coats mitotic chromosomes in every cell type examined, so a chromatin-eviction strategy is not obviously selective for leukaemia; the therapeutic window argued for elsewhere in this graph rests on dependency data, not on any localisation difference.
  • Every reagent used to look at LEDGF in cells so far sees p52 as well as p75. A pharmacodynamic assay built on such an antibody would report an isoform the drug is not aimed at, and could read as no-effect while p75 is fully engaged.
  • If residence time rather than occupancy is the functional variable, ChIP-based pharmacodynamics could show a clean occupancy drop while the tether is unchanged - or the reverse - and the trial would be reading the wrong number.
Still open
  1. Where is endogenous LEDGF/p75 in a SEM or RS4;11 nucleus, and does it move when revumenib displaces the fusion? No image of LEDGF in any KMT2A-rearranged cell exists.
  2. Does the KMT2A-fusion/menin cargo lock LEDGF onto chromatin the way HIV-1 integrase does (75-fold in HeLa)? One FRAP experiment with and without menin inhibition would answer it.
  3. Can any published subnuclear statement about 'LEDGF' be attributed to p75 rather than p52? The only positional dataset used a pan-isoform antibody, so at present the answer is no.
  4. Does LEDGF stay on mitotic chromosomes at the SAME loci - does it bookmark fusion target genes through division? Whole-chromosome fluorescence cannot tell, and this is the mechanism by which a tether would matter across cell cycles.
Every source behind this entry (5)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In living human HeLa cells expressing EGFP- and HcRed-tagged constructs, LEDGF/p75 is associated with condensed chromosomes during mitosis, and RNA-interference knockdown of endogenous LEDGF/p75 abolishes the nuclear and chromosomal localisation of HIV-1 integrase; the alternative splice variant p52 does not interact with integrase in vitro or in living cells.

    LEDGF/p75 is essential for nuclear and chromosomal targeting of HIV-1 integrase in human cells. · Maertens G, Cherepanov P, Pluymers W, Busschots K, De Clercq E, Debyser Z, Engelborghs Y · J Biol Chem 2003
    PMID 12796494DOI
    What this evidence cannot show

    HeLa cells (human cervical carcinoma), not a haematopoietic or KMT2A-rearranged system; the imaged species are overexpressed EGFP/HcRed fusion proteins, not endogenous LEDGF. The experiment is framed around HIV-1 integrase as cargo; nothing about menin or a KMT2A fusion is measured. A fluorescent-protein fusion can itself alter chromatin residence. Read: abstract only (PubMed efetch, 2026-09-20).

    Evidence that argues against this (1)
    • Mitotic chromosome coating establishes that LEDGF is retained on the template; it does not establish that it is retained at the SAME addresses. No source read for this entry follows a specific locus through mitosis. A protein can be bookmarking the genome or merely adhering to condensed chromatin non-specifically, and whole-chromosome fluorescence cannot separate those two readings.
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In human cells scored by EGFP-fusion imaging in interphase and mitosis, LEDGF/p75 chromatin association is mediated by a tripartite element spanning the NLS and two AT-hook motifs at residues 146-197; the PWWP domain is not required for binding condensed mitotic chromosomes but its deletion subtly alters the nucleoplasmic distribution during interphase, and purified LEDGF/p75 shows no sequence-specific DNA binding by surface plasmon resonance or gel shift.

    PMID 16549878DOI
    What this evidence cannot show

    EGFP-fusion overexpression in cultured human cells; 'subtly affected the nucleoplasmic distribution' is a qualitative description of confocal images with no quantitative positional metric. Deletion mutants report sufficiency/necessity of domains in an artificial construct, not the behaviour of endogenous protein. No leukaemia system, no haematopoietic cell. Read: abstract only (PubMed efetch, 2026-09-20).

    Evidence that argues against this (1)
    • This result is in tension with the therapeutic reading of the PWWP domain. If PWWP is dispensable for gross chromatin retention, a PWWP-site ligand may displace the reader function while leaving LEDGF on chromatin via the AT-hook/NLS element - a compound could be fully engaged and produce no visible relocalisation. Any pharmacodynamic biomarker of 'LEDGF displaced' built on imaging would then read as failure while the drug works, or as success while it does not.
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Quantitative live-cell fluorescence (spot-FRAP, half-nucleus FRAP, continuous photobleaching, FCS and tunable-focus FCS) in HeLa nuclei shows LEDGF/p75 moves in a chromatin hopping/scanning mode typical of transcription factors, that the PWWP domain is necessary but not sufficient for in vivo chromatin binding, and that engagement of a cargo through the integrase-binding domain shifts the kinetics to a 75-fold larger apparent affinity for chromatin.

    The transcriptional co-activator LEDGF/p75 displays a dynamic scan-and-lock mechanism for chromatin tethering. · Hendrix J, Gijsbers R, De Rijck J, Voet A, Hotta J, McNeely M, Hofkens J, Debyser Z, Engelborghs Y · Nucleic Acids Res 2011
    PMID 20974633DOI
    What this evidence cannot show

    HeLa cells and fluorescent-protein fusions again; the cargo is HIV-1 integrase, not menin or a KMT2A fusion, so the 75-fold figure is a property of that pair and not transferable. FRAP-derived affinities are model-dependent. The brief's standing condensate caveat applies in general form: recovery kinetics alone do not distinguish binding to spatially clustered sites from other retention modes. Read: abstract only (PubMed efetch, 2026-09-20).

    Evidence that argues against this (1)
    • The scan-and-lock model predicts that removing the cargo returns LEDGF to fast scanning. If menin inhibition displaced the KMT2A fusion and LEDGF residence time did NOT change, the leukaemic cargo would not be acting through this mechanism at all. That experiment has not been done, so the model is imported into this disease untested.
  4. E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    Expansion microscopy (ExEpi) in human HeLaP4 cells places LEDGF co-localised preferentially with H3K36me3 and H3K36me2 over H3K27me3 and H3K9/14ac, and reports that H3K9me3 occupies the nuclear rim while LEDGF/H3K36me3 co-localisation occurs further inside the nucleus; the imaging primary antibody detects both LEDGF/p75 and LEDGF/p52, and the authors state the LEDGF/p75 knock-out control was confounded because p52 remains detected.

    Expansion microscopy allows high resolution single cell analysis of epigenetic readers. · Acke A, Van Belle S, Louis B, Vitale R, Rocha S, Voet T, Debyser Z, Hofkens J · Nucleic Acids Res 2022
    PMID 35716125DOI
    What this evidence cannot show

    RULE 74: the readout cannot distinguish LEDGF/p75 from LEDGF/p52, which is the distinction the whole leukaemia argument turns on, since p52 lacks the IBD that carries menin and KMT2A. HeLaP4 cells with engineered LEDGF/p75 knockdown and back-complementation - not endogenous-level, not haematopoietic, not KMT2A-rearranged. Co-localisation ratios are spot-overlap statistics after physical expansion; the negative control is a 180-degree image rotation rather than an isoform-null, because the isoform-null was unavailable, and it leaves a chance-overlap floor of 5.6 +/- 1.1. Read: full text via Europe PMC PMC9508849, 2026-09-20; the imaging antibody identities are in Supplementary Table 11, which was NOT retrieved.

    Evidence that argues against this (1)
    • The authors themselves report residual co-localisation of 5.6 +/- 1.1 after forcing a mismatch by image rotation, i.e. a non-zero floor from chance overlap at this spot density. Any positional claim from this method must be read against that floor, and 'not at the rim' is a stronger and safer statement than 'in the interior'.
  5. E5moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database

    Bounded absence, measured 2026-09-20: no published study images LEDGF/p75 subcellular or subnuclear localisation in a KMT2A-rearranged cell of any lineage or species.

    What this evidence cannot show

    QUERIES RUN (PubMed, 2026-09-20). (1) `(LEDGF[tiab] OR PSIP1[tiab] OR p75[tiab]) AND chromatin[tiab] AND (mitosis[tiab] OR mitotic[tiab] OR localization[tiab] OR tethering[tiab])` = 53 records; the top 20 were title-checked and every localisation paper among them is in HeLa, HEK293T or in vitro, none in a leukaemia line. (2) `(LEDGF[ti] OR p75[ti]) AND (chromatin[ti] OR chromosomal[ti] OR chromosome[ti] OR mitotic[ti] OR mitosis[ti])` = 19 records, same outcome. RULE 67 CONTROL: both queries return large non-zero counts through the identical shape, so the instrument demonstrably returns ones; this is not a non-composing zero. NAME LIST searched: LEDGF, LEDGF/p75, PSIP1, p75, and the protein name 'PC4 and SFRS1-interacting protein'. NOT searched: DFS70 (the autoantigen name), p52 alone (too generic), non-English literature. SCOPE: this absence is about IMAGING only - LEDGF genomic occupancy in KMT2A-rearranged cells by ChIP-type assays does exist and is recorded elsewhere in this graph. RULE 80 (added mid-beat): this count is bounded by TITLES AND ABSTRACTS, not by papers. Localisation panels are very often supporting figures whose abstracts never mention them, so a PubMed zero here means 'no paper ANNOUNCES this measurement', not 'no such figure exists'. Supporting figures and supplementary material were NOT searched.

    Evidence that argues against this (1)
    • An absence of imaging is not an absence of localisation knowledge. ChIP-seq occupancy in KMT2A-rearranged cells constrains where LEDGF is on the genome even though nobody has photographed where it is in the nucleus. The honest statement is that the GENOMIC address is measured in this disease and the NUCLEAR address is not. Rule 77 was also applied: the queries were run without any disease term, so the absence is not an artefact of scoping to leukaemia.
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