LNP1 (leukemia NUP98 fusion partner 1) is a small, highly charged and partly disordered human protein whose normal physiological role is not established. Interaction studies associate LNP1 with the LYN tyrosine kinase and repeatedly recover it with multiple 14-3-3 paralogs, consistent with a possible phosphoregulated interaction module, but the direct mechanism and cellular consequences remain unknown. Limited antibody imaging reports mainly vesicular staining with cell-line-dependent cytosolic and nuclear-speck signal. Chromosomal rearrangements can fuse LNP1 to NUP98 in rare leukemias; puncta formation and transforming activity demonstrated for NUP98::LNP1 are properties of the chimeric oncoprotein and do not establish a function for wild-type LNP1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0071889 14-3-3 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | NEW | Summary: LNP1 reproducibly co-associates with six human 14-3-3 paralogs in BioPlex AP-MS networks from both 293T and HCT116 cells; hu.MAP3.0 integrates this and other proteomic evidence into a family-level interaction model. Reason: The repeated family-specific pattern supports the informative 14-3-3 protein binding term rather than generic protein binding. The source evidence is anti-tag AP-MS/co-immunoprecipitation association, not purified direct binding; stable complex membership and physiological consequences remain unestablished. The duplicate raw protein-group rows for P62258-2 and E7ESK7 are retained in the provenance artifact but not counted as additional gene-level partners. The proposed phosphosite mechanism is also unresolved because PMID:40425816 names Ser114 but prints a motif that places the phosphate on current Ser112. Supporting Evidence: file:human/LNP1/LNP1-bioinformatics/RESULTS.md IntAct classifies the BioPlex LNP1-14-3-3 records as MI:0007 anti tag coimmunoprecipitation, MI:0914 association, and MI:1060 spoke expansion rather than direct binary binding. PMID:33961781 In contrast, affinity-purification mass spectrometry (AP-MS) enables enrichment and detection of even low-abundance proteins, though exogenous expression of tagged baits is required, and extensive sample preparation has limited scalability while precluding recovery of transient interactions ( Gingras et al., 2007 ). PMID:40425816 We also identify LNP1, an uncharacterized protein, as associated with members of the 14-3-3 complex (huMAP3_06971.1). |
| GO:1990782 protein tyrosine kinase binding | IPI PMID:23503679 Protein interaction discovery using parallel analysis of tra... | NEW | Summary: GST-LYN affinity precipitation followed by anti-tag Western blotting validated tagged human LNP1 as a LYN-binding candidate in HEK293T lysate. Reason: Figure 2c labels LNP1 and shows a GST-LYN pulldown band without a GST-Pep control band, supporting the specific kinase-binding term. The assay used overexpressed tagged LNP1 and bacterially produced GST-LYN; it does not establish endogenous interaction, LNP1 phosphorylation, or downstream signaling. Supporting Evidence: file:human/LNP1/LNP1-bioinformatics/RESULTS.md BioGRID maps the validated PLATO pair to LYN/P07948 and LNP1/A1A4G5 and classifies interaction 868526 as Affinity Capture-Western. PMID:23503679 GSTLYN precipitation and western blot analysis confirmed binding for five of seven novel candidates tested (Figure 2c). |
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Download this section (compressed HTML)Q: Does endogenous LNP1 bind multiple 14-3-3 paralogs directly, and is the interaction phosphoserine-dependent?
Q: Is Ser112 or Ser114 the relevant LNP1 phosphosite, and which kinase installs it?
Q: Is the LNP1-LYN interaction reproducible at endogenous abundance, and does LYN phosphorylate or regulate LNP1?
Q: Where does endogenous LNP1 localize, and is its vesicular distribution conserved across cell types?
Q: What normal cellular phenotype follows LNP1 loss, independently of NUP98::LNP1 fusion biology?
Experiment: Endogenously tag LNP1, compare reciprocal 14-3-3 co-immunoprecipitation before and after phosphatase treatment, map the site by targeted mass spectrometry, and test S112A, S114A, and double-mutant rescue constructs in purified and cellular binding assays.
Hypothesis: LNP1 is a phosphoserine-dependent 14-3-3 ligand whose association is controlled by one of the adjacent Ser112/Ser114 residues.
Type: interaction biochemistry and phosphoproteomics
Experiment: Re-test the interaction by reciprocal endogenous co-immunoprecipitation and purified-protein binding, then compare wild-type and kinase-dead LYN in kinase assays and quantitative LNP1 phosphoproteomics.
Hypothesis: LYN binds LNP1 directly and regulates it through phosphorylation.
Type: kinase and interaction assays
Experiment: Introduce a minimally disruptive endogenous tag in PC-3, U-2 OS, and additional LNP1-expressing models, and combine knockout-controlled microscopy, organelle-marker colocalization, live imaging, and biochemical fractionation.
Hypothesis: Wild-type LNP1 is a vesicle-associated protein in a restricted set of human cell types.
Type: endogenous localization and trafficking
Experiment: Perform CRISPR knockout with wild-type and interaction-defective rescue in retina- and testis-relevant human models, using unbiased transcriptomic, proteomic, trafficking, proliferation, and stress-response readouts to discover a causal process.
Hypothesis: LNP1 loss produces a measurable phenotype that depends on its reported interaction module.
Type: genome editing and multi-omics phenotyping
Experiment: Compare wild-type LNP1, full NUP98::LNP1, and matched fusion constructs lacking or mutating the LNP1 segment for puncta formation, chromatin occupancy, transcriptional effects, and hematopoietic transformation.
Hypothesis: The LNP1 segment contributes a fusion-specific property to NUP98::LNP1 that is not shared by wild-type LNP1.
Type: fusion-domain dissection
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The normal physiological process and cellular phenotype controlled by wild-type LNP1 are unknown.
OPEN BIOLOGY WHOLLY_DARK
What is known: LNP1 is a protein-level-supported 178-residue human gene product, but its reviewed UniProt record has no FUNCTION statement, no curated pathway, and no PAN-GO annotation; the defensible evidence currently stops at physical associations and provisional antibody localization.
Significance: Without a causal phenotype or process, even reproducible interaction partners cannot be interpreted as the gene product's biological role.
What would resolve it: Identify a reproducible loss-of-function phenotype in an endogenously expressing human model and rescue it with wild-type LNP1 while mapping the responsible molecular interaction.
Provenance (the field's own admissions):
Gap: It is unknown whether LNP1 binds 14-3-3 proteins directly, which phosphosite controls the association, and what the association does in cells.
NARROWING BIOLOGY MF_DARK
What is known: BioPlex repeatedly recovers LNP1 with six human 14-3-3 paralogs in two cell lines, and hu.MAP3.0 integrates overlapping proteomic evidence into a phosphoserine-dependent LNP1-YWHAE model. Current-sequence inspection exposes an unresolved Ser112-versus-Ser114 discrepancy in the published motif description.
Significance: Resolving this would distinguish a regulated interaction module from repeated co-complex recovery and could provide the first mechanistic handle on LNP1.
What would resolve it: Use site-resolved phosphoproteomics, S112A/S114A mutants, phosphatase treatment, reciprocal endogenous co-immunoprecipitation, and purified binding assays across representative 14-3-3 paralogs.
Provenance (the field's own admissions):
Gap: The physiological significance of the LNP1-LYN interaction and whether LYN phosphorylates LNP1 are unknown.
OPEN BIOLOGY BP_DARK
What is known: A LYN affinity-capture screen followed by targeted Western validation supports physical association, but no endogenous context, catalytic consequence, or downstream pathway has been established for LNP1.
Significance: LYN could connect LNP1 to a defined signaling context, but merely binding a kinase does not show that LNP1 is its substrate or pathway component.
What would resolve it: Reproduce the interaction at endogenous abundance, test direct binding and phosphorylation with purified proteins and kinase-dead LYN, and measure the consequence of disrupting the interaction in a relevant human cell type.
Provenance (the field's own admissions):
Gap: The endogenous subcellular localization and trafficking behavior of LNP1 are unresolved.
OPEN BIOLOGY CC_DARK
What is known: Human Protein Atlas imaging with one approved antibody reports vesicles in two cell lines and cytosolic plus nuclear-speck signal in only one, while UniProt has no curated SUBCELLULAR LOCATION statement.
Significance: A validated compartment is required to judge which reported partners can meet LNP1 physiologically and to choose an appropriate model for functional studies.
What would resolve it: Endogenously tag LNP1 in multiple expressing human cell types and combine knockout-controlled imaging with biochemical fractionation and organelle-marker colocalization.
Provenance (the field's own admissions):
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