Proteome analysis of nuclear Lipid‐Associated Promyelocytic Leukemia (PML) Structures (LAPS) Using Biotin Proximity Labelling
Bibliographic record
Abstract
Lipid droplets (LD) are organelles composed of a phospholipid monolayer surrounding a core of and triacylglycerol and cholesterol ester. LD have a primary role in energy homeostasis and lipotoxic stress through the regulated storage and release of fatty acids. While LD are cytoplasmic, lipoprotein secreting cells harbor nuclear LD (nLD) that associate with PML, the structural protein of PML nuclear bodies (PML‐NB) that regulate DNA repair and stress responses. Knockout studies in U2OS cells indicated that the 50% of nLDs contain PML isoform II (PML‐II) and have a unique lipid and protein composition marked by the lack of canonical PML‐NB‐associated proteins, such as DAXX, SP100 and SUMO. Owing to their unique composition, we term these subnuclear lipid:protein domains, lipid‐associated PML structures (LAPS). To gain insight into LAPS function, we conducted proximity labeling and mass spectrometry (MS) studies using PML‐I and PML‐II modified by fusion to the ascorbate peroxidase APEX2 that uses biotin‐phenol to biotinylate proteins. U2OS and Huh7 cells expressing PML‐APEX2 fusion proteins were treated with and without oleate, and biotinylated proteins were isolated and analyzed by LC‐MS/MS. Using standard filtering techniques (CRAPome, SAINT, Bayesian false discovery rate) we identified several high confidence interacting proteins associated with the COPII coatomer complex, including Sec24A, Sec23IP, Sec24B, and Sec23B. These Sec23/24 proteins were associated with PML‐I and, to a lesser extent, PML‐II under oleate‐treated conditions. Sec23B was observed to associate with both PML‐NBs as well as LAPS by immunofluorescence microscopy in U2OS cells expressing PML‐II‐APEX2. The COPII pathway has previously been implicated in protein delivery to cytoplasmic LD setting a precedence for the interaction we observed with LAPS. Thus, given our preliminary data showing interaction between Sec 23/24 heterodimer, PML‐NBs and LAPS we are now pursuing the hypothesis that lipid membrane deformation and/or cargo transport activity in the nucleus by COPII proteins could play a role in lipid homeostasis.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".