Oncofusion

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Mechanismstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q58-set-nup214

Where SET::NUP214 actually is: mobile intranuclear bodies that trap CRM1, dissolve in mitosis and under CRM1 inhibitor, and reassemble on washout

also called SET-Nup214 nuclear bodies · SET-Nup214 nuclear dots · nucleoporin fusion condensate

The fusion protein does not spread evenly through the nucleus. It gathers into bright spots that also hold the cell's main export carrier, and those spots vanish when the cell divides or when the export carrier is drugged - then come straight back when the drug is removed.

The same thing, for a scientist

**In the two fusion-positive leukaemia lines, LOUCY and MEGAL, SET-Nup214 forms discrete nuclear bodies containing CRM1** [E1]. The same structures are seen with the endogenous protein by anti-Nup214 and anti-CRM1 immunostaining in LOUCY and are absent from K562 and HL60 [E2]. **Their properties, measured:** - **Highly mobile and in equilibrium with the nucleoplasm** in interphase; they **disassemble during mitosis** [E1]. - They **dissolve on CRM1 inhibition** - leptomycin B [E1], KPT-330 [E2], and a targeted CRM1 antagonist that also re-localises the fusion throughout the nucleoplasm [E3] - and **reestablish shortly after the antagonist is cleared** [E3]. - They **recruit CRM1, CRM1 export cargoes and certain nucleoporins**, and correspondingly impair nuclear protein and polyA+ RNA export [E1]. The CRM1 interaction is **RanGTP-dependent** [E1]. - **Nucleoporins can be released from the bodies and reintegrated into existing nuclear pore complexes**, which is why the authors read the bodies as a storage compartment preventing insoluble aggregation rather than as a pure gain-of-function structure [E1]. - The tethering is functional beyond HOX: SET-Nup214 and DEK-Nup214 **tether XPO1 onto the nuclear dots**, reduce nuclear export of NES cargoes including cyclin B, and **inhibit NF-kB-mediated transcription by trapping a p65/IkB complex in the nucleus** [E4]. - A 2023 report describes these as **phase-separated** and as condensing MLL1 with CRM1 [see `mechanism-set-nup214-recruits-wild-type-mll1`]. **Also: a nuclear-rim component.** A BirA-tagged SET-NUP214 in HCT-116 formed intranuclear foci **and localised to the nuclear rim** [E5], so the fusion is not exclusively in bodies. **Every observation here is in a human cell line - LOUCY, MEGAL, HeLa or HCT-116. None is in a patient sample and none is in infant B-lineage KMT2A::AFF1.**

Go deeper
The condensate claim, held to this graph's standard

This graph's standing rule on liquid-liquid phase separation is that 1,6-hexanediol sensitivity and classical FRAP recovery both fail to distinguish LLPS from binding to spatially clustered sites, that hexanediol itself condenses chromatin in living cells, and that low-complexity-domain interactions at physiological expression can form dynamic hubs with no detectable phase separation.

Applied here:

  • The strongest observation is not a phase-separation assay at all. It is that the bodies dissolve when CRM1 is inhibited and reform when the inhibitor clears 123. That is a specific, ligand-dependent assembly, and it points at CRM1 binding as the organising interaction rather than at bulk demixing of FG repeats.
  • 'Highly mobile, in equilibrium with the nucleoplasm' is a dynamics statement of the kind FRAP produces, and under the standing caveat it does not discriminate the two models.
  • The rival model is substantive here, not a technicality. 'Binding to spatially clustered sites' predicts that the fusion is held wherever CRM1 is clustered - which is exactly what the ChIP-seq shows at HOXA and HOXB. So the clustered-binding reading and the chromatin-targeting mechanism are the same story, and the phase-separation reading is an extra claim on top.

Recorded position: the bodies exist and are CRM1-dependent; whether they are a condensate in the LLPS sense is not settled by anything read in this beat.

Why a storage-compartment reading is not a deflation

The JBC authors explicitly propose the bodies as a means of preventing potentially insoluble and harmful protein aggregates, and as storage compartments for nuclear transport factors 1. That reads like a benign interpretation and it is not, because the same structure is where CRM1 accumulates and where the fusion sits on chromatin. A sink and a platform can be the same object: sequestering CRM1 away from its export job and holding it on HOX chromatin are two descriptions of one event.

The NF-kB result 4 is the clearest demonstration that the sink half has consequences of its own - trapping p65 with IkB in the nucleus is a transcriptional effect produced purely by mislocalisation, with no chromatin recruitment needed.

Facts and figures
mechanism classsubnuclear localisation
fusionfusion-set-nup214
structurediscrete intranuclear bodies / nuclear dots, plus a nuclear-rim pool in at least one expression system
obligate componentCRM1/XPO1 - the bodies dissolve when CRM1 is inhibited and reform when the inhibitor clears
ran dependencethe fusion-CRM1 interaction is RanGTP-dependent
cell cyclebodies disassemble during mitosis
phase separation claimasserted in one 2023 report (PMID 37516964); NOT independently verified in this beat, and the standing caveat applies that hexanediol and classical FRAP cannot distinguish LLPS from binding to spatially clustered sites
never observed ina patient sample
assemblies trapped
[
  "CRM1/XPO1",
  "NXF1/TAP",
  "NES cargoes including cyclin B",
  "a p65/IkB complex",
  "certain nucleoporins (reversibly - they can reintegrate into real NPCs)",
  "wild-type MLL1 (reported 2023, abstract-level)"
]
functional consequences
[
  "impaired nuclear protein export",
  "impaired polyA+ RNA export",
  "inhibited NF-kB-mediated transcription",
  "HOXA and HOXB activation on chromatin"
]
systems
[
  "LOUCY (endogenous)",
  "MEGAL (endogenous)",
  "HeLa (overexpression)",
  "HCT-116 (tagged transfection)"
]
How this could bite us back
  • The bodies reform within a short time of CRM1 inhibitor washout, so any therapeutic strategy aimed at dissolving them needs continuous exposure to a common-essential target's inhibitor.
  • Because the bodies also act as a sink that releases nucleoporins back into real nuclear pores, dissolving them could in principle release trapped CRM1 and cargo in a bolus, with consequences nobody has measured.
  • If the structure is genuinely a condensate, the standard assays used to argue so are the two this graph records as non-discriminating, so a therapeutic rationale built on 'disrupt the condensate' rests on evidence that cannot support it.
Still open
  1. Are these bodies present in primary SET-NUP214 patient blasts? Every image in this literature is a cell line, and the two available lines have been in culture for decades.
  2. Is the body the site of HOXA transcription, or a separate compartment? The ChIP-seq says the fusion is on HOXA and the imaging says it is in dots; nothing shown in this beat puts the HOXA locus inside a dot.
  3. Does the mitotic disassembly matter? A structure that dissolves every division is a poor candidate for heritable transcriptional memory, which is a problem for any model where the body maintains the HOXA state.
  4. Does the NF-kB tethering contribute to the corticosteroid resistance seen in SET-NUP214 adults? The two are separately documented and nobody has connected them.
Every source behind this entry (5)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    SET-Nup214 nuclear bodies containing the nuclear export receptor CRM1 were observed in the leukaemia cell lines LOUCY and MEGAL; overexpression in HeLa forms similar bodies that recruit CRM1, export cargo proteins and certain nucleoporins and impair nuclear protein and polyA+ RNA export; the CRM1 interaction is RanGTP-dependent by co-immunoprecipitation and binding assay; the bodies are highly mobile, in equilibrium with the nucleoplasm in interphase, and disassemble during mitosis or on treatment with the CRM1 inhibitor leptomycin B; and nucleoporins can be released from the bodies and reintegrated into existing nuclear pore complexes.

    PMID 27613868DOI
    What this evidence cannot show

    Abstract-level for this beat. The endogenous observation is in two leukaemia lines; the mechanistic dissection (cargo recruitment, export assays, mobility) is in HeLa cells OVEREXPRESSING the fusion, and an overexpressed low-complexity protein forms foci readily - this graph's standing caveat is that punctate appearance under overexpression is weak evidence about the endogenous protein. The comparison that carries the specificity is internal: SQSTM1-Nup214, with a shorter FG fragment, is mostly cytoplasmic and blocks protein but not polyA+ RNA export.

    Evidence that argues against this (1)
    • The authors' own interpretation is deflationary about gain-of-function: they read the bodies as a means of preventing insoluble and harmful protein aggregates and as storage compartments for nuclear transport factors, and they show nucleoporins leaving the bodies and reintegrating into real nuclear pores - so the structure is at least partly a sink rather than purely a platform. Port SA et al. 2016
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Immunostaining with anti-Nup214 and anti-CRM1 shows distinct nuclear dots of SET-Nup214 in LOUCY that co-localise with CRM1 and are not observed in K562 or HL60; these dots disappear in the presence of KPT-330.

    PMID 31755865DOI
    What this evidence cannot show

    A supplementary-figure observation confirming a previous report, in cell lines only. KPT-330 also degrades SET-Nup214 in this system, so the loss of dots under KPT-330 is not purely a disassembly readout - some of it is loss of the protein. Full text read via Europe PMC (PMC6874418).

    Evidence that argues against this (1)
    • AUTHORS' OWN CONFOUND PLUS A PUBLISHED CONFLICTING RESULT. KPT-330 degrades SET-Nup214 in this system, so 'the dots disappear' conflates disassembly of a structure with loss of the protein that marks it - a fixed-cell immunostain at one timepoint cannot separate those. And an independent study of the same phenomenon reports the bodies REESTABLISH shortly after the CRM1 inhibitor is cleared, which a degradation-only account does not predict and which a disassembly account does. The two readings make different predictions for washout kinetics, and no published experiment measures fusion protein level and body number in the same cells at the same timepoints. Mendes A et al. 2020
  3. E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    Endogenous and exogenous SET-NUP214 and DEK-NUP214 form nuclear bodies that disperse on targeted CRM1 inhibition, with the fusion proteins re-localising throughout the nucleoplasm, and the bodies reestablish shortly after clearance of the CRM1 inhibitors; viability, metabolism and proliferation of leukaemia lines harbouring these fusions are compromised by CRM1 inhibition.

    PMID 32934780DOI
    What this evidence cannot show

    Abstract-level for this beat. Cell lines only, no in vivo work. The viability effect cannot be attributed to the fusion without a lineage-matched fusion-negative control, because CRM1 is common-essential. The abstract reports both a sustained anti-cancer effect after inhibitor clearance and rapid reassembly of the bodies after clearance; those two statements are in tension and are recorded here as published.

    Evidence that argues against this (1)
    • PUBLISHED CONFLICTING RESULT FROM THE SAME GROUP on what the distribution actually is. 'Nuclear bodies' is not the whole picture: the same laboratory's BioID study found a tagged SET-NUP214 in intranuclear foci AND at the NUCLEAR RIM, matching the distribution of the corresponding GFP fusion, and used that as the localisation control for the proximity labelling. A rim pool at the nuclear envelope is exactly what a nucleoporin-derived fusion might be expected to have and it is absent from every leukaemia-cell description in this entry. Either the rim is an artefact of the tag or the colon-carcinoma host, or the leukaemia imaging has not looked for it; nobody has run the comparison. Mendes A et al. 2020
  4. E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    SET-Nup214 and DEK-Nup214 interact with XPO1/CRM1 and with NXF1/TAP, decrease XPO1-mediated nuclear export of NES-containing proteins such as cyclin B by tethering XPO1 onto the nuclear dots where the fusions are localised, and inhibit NF-kB-mediated transcription by abnormally tethering a complex containing p65 and its inhibitor IkB in the nucleus.

    PMID 27114368DOI
    What this evidence cannot show

    Abstract-level for this beat. The system is not stated in the abstract and the phrase 'SET-Nup214 and DEK-Nup214 expression' suggests an expression system rather than the endogenous fusion in LOUCY. An NF-kB reporter result under fusion overexpression is a long way from NF-kB signalling in a patient's blast, and this graph separately records that menin represses NF-kB transactivation - so the two lesions would push NF-kB in the same direction by unrelated routes, which is interesting and is not evidence that either does so in vivo.

    Evidence that argues against this (1)
    • PUBLISHED CONFLICTING RESULT on the direction of the tethering. This item's model is that the fusion sequesters XPO1 onto its own nuclear dots. The in-cell chromatin work in the fusion-positive line reports the reverse causal order: CRM1 is selectively bound at the HOXA and especially the HOXB clusters in LOUCY, absent from K562 and HL60, and knockdown of SET-Nup214 lowers HOX gene expression WITHOUT significantly reducing the amount of CRM1 at those regions - so CRM1 is the recruiter, not the cargo being trapped. The tethering result comes from an expression system in which the fusion is present at non-physiological levels, which is the condition under which a sequestration phenotype is easiest to produce. Oka M et al. 2019
  5. E5moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    A BirA(R118G)-tagged SET-NUP214 expressed in HCT-116 cells formed intranuclear foci AND localised to the nuclear rim, matching the distribution of the corresponding GFP fusion, while the BirA control was distributed throughout the cell.

    PMID 32664447DOI
    What this evidence cannot show

    HCT-116 COLORECTAL CARCINOMA cells, transient transfection, exogenous tagged construct - three removes from the endogenous fusion in a T-lymphoblast. Cited here as the localisation control for that study's BioID rather than as an independent localisation finding. The nuclear-rim component is worth recording because the body-only picture from the leukaemia lines may be incomplete. Full text read via Europe PMC (PMC7407662).

    Evidence that argues against this (1)
    • PUBLISHED CONFLICTING RESULT in the system that matters. The nuclear-rim component is not reproduced anywhere the ENDOGENOUS fusion has been imaged: in LOUCY, anti-Nup214 and anti-CRM1 staining shows distinct nuclear dots co-localising with CRM1 and no rim pool is described, and the same is true of the founding paper's description. That leaves three candidate explanations for the rim - the BirA tag, the HCT-116 colorectal host, or transient overexpression saturating a nuclear-pore-associated pool - and the study's own localisation control cannot distinguish them, because it compares the BirA fusion with a GFP fusion in the same non-haematopoietic cell rather than with the endogenous protein in a T-lymphoblast. Oka M et al. 2019
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