TBL3 / UTP13 (Q12788) - a UTP-B ribosome-biogenesis subunit in the pan-MLL-fusion core, whose loss in zebrafish severely reduces T cells and haematopoietic stem/progenitors

SYSTEM: the AP-MS host is JURKAT, a human T-ALL line, while KMT2A::AFF1 disease is B-lineage infant leukaemia; a partner requiring a B-cell or infant proteome cannot appear here and a T-lineage partner can appear spuriously. The bait is a Strep-HA-tagged, SINGLE-COPY, doxycycline-induced transgene at an FRT/Flp cassette, not the endogenous fusion. Prey came from bulk nuclear lysate (buffer C420, 420 mM NaCl) after a single STREP-Tactin step, so co-purification is NOT evidence of a direct contact. INCLUSION RULE: the paper kept the top 300 interactions per bait by combined p-value rather than applying a p threshold (Methods, verbatim: "All the identified bait-prey pairs were ranked by the combined p-value. The 300 most significant interactions per bait were retained."). Measured by this beat from the cached MOESM4 xlsx on 2026-09-21: 545 of the 2,049 per-bait p-values in the table (26.6%) exceed 0.05; within the MLL-AF4 column alone it is 186 of 291 (63.9%), and that column's maximum p is 0.175. MEASURED BY THIS BEAT, 2026-09-21, from the cached MOESM4 xlsx: across all 42 pan-fusion proteins the MLL-AF4 column carries the LOWEST total spectral counts of the seven baits for 34 of 42, and is sixth or seventh for 40 of 42. That is a bait-level property (transgene expression, purification depth or the DDX5/DDX17 GLM normalisation), not a statement about any one prey, so a low MLL-AF4 count must not be read as a weaker association than the same protein's count under another bait. For TBL3 the MLL-AF4 total (7 spectra over two replicates) is rank 7 of the seven baits, against a maximum of 53 under another bait. All seven per-bait values, p (replicate spectral counts): MLL-AF1p 0.0457 (5|2); MLL-AF4 0.0369 (4|3); MLL-AF9 0.0103 (11|7); MLL-CBP 0.0249 (3|50); MLL-EEN 0.0031 (13|14); MLL-ENL 0.0094 (10|9); MLL-GAS7 0.0440 (6|7). SPECIFIC TO THIS PROTEIN, AND THIS IS THE WEAKEST ROW IN THE TRANCHE: four of the seven baits are above p = 0.02 (MLL-AF1p 0.0457, MLL-GAS7 0.0440, MLL-AF4 0.0369, MLL-CBP 0.0249), and MLL-CBP's spectral counts are 3|50 - a seventeen-fold discrepancy between two replicates of the same bait, which makes that column uninterpretable. Nucleolar proteins are abundant in nuclear extract, and the index fusion has itself been reported predominantly nucleolar, so shared-compartment abundance is the leading alternative explanation and nobody has run the control that would exclude it. SELECTIVITY: the paper's named non-selectivity controls are RFC1, SF3A3 and CCT3 - knockdown inhibited MLL-wild-type K562 and HL-60 as much as MOLM-13 - against MEN1 as the selective positive. Only 40 of the 128 ('the 40 candidate genes with the highest confidence') entered that MLL-r versus MLL-wild-type re-screen, and the paper does not list which 40. This protein is not named among the controls, but that is NOT evidence of selectivity: it is equally consistent with the protein never having reached the second screen. Recorded as unknown, and this entry must not be read as nominating a target. Values re-read from the cached xlsx on 2026-09-21 and cross-checked against analyses/skucha-mll-fusion-interactome/results.json, whose two controls (128 proteins shared by >=5 baits and 42 by all seven, both matching the paper; MEN1 present with all seven) both PASS on today's re-run.

• IntAct has never curated this dataset, so no independent curator has re-examined these calls and no interactome-coverage metric built on IntAct can see them; the raw spectra at ProteomeXchange PXD009338 have not been reanalysed here. The authors themselves removed seven proteins from the shared set by hand as 'either frequently observed contaminants or ... not detected in human hematopoietic cell lines', which concedes that the rank cutoff lets contaminants through - and ACTB survived that filter, sitting in the pan-fusion 42 with a NON-ZERO negative control (3|3). Ten of the 42 carry a non-zero negative control: PSIP1 0|5, MCM2 0|2, ACTB 3|3, CSNK2A1 2|0, RUNX1 0|2, SF3A3 0|3, TCEB3 0|1, CHD4 2|2, SMARCC1 1|0, ZNF512 0|2 - counted by this beat from the xlsx neg_ctrl column, 2026-09-21. ProteomeXchange/PRIDE 2018
• The paper states that 'more than one third of proteins in the network of conserved MLL-fusion protein interaction partners were identified as essential in recent genome-wide screens'. Abundance and essentiality both raise the odds of recovery in an AP-MS experiment, so membership in the conserved core is partly a statement about how much of a protein is present in a nucleus, not only about what it binds. Skucha A et al. 2018

2014, Biochemistry and Cell Biology; GFP fusions and photobleaching in living HeLa-type cells, with the protein set originally defined from a nuclear-matrix fraction. A GFP fusion of a structural nucleolar protein can itself perturb the assembly it reports on, and 'very low mobility' from photobleaching is a measurement about exchange, not about stoichiometry. Not haematopoietic, not a fusion system. Read from the abstract. This is the only source this beat found for TBL3's sub-nucleolar distribution.

• If TBL3 is a structurally immobilised nucleolar component with very low exchange, then its recovery in a 420 mM nuclear extract means it was solubilised out of a dense structure, and what co-purifies with a bait after that treatment is harder to interpret than a soluble interaction would be. No other SSU processome UTP-B subunit - PWP2, WDR3, WDR36, UTP15, UTP20 - is in the network, though UTP18, UTP14A and RRP9 are. Skucha A et al. 2018

ZEBRAFISH developmental genetics, 2012, Developmental Biology. Not human, not leukaemia, not a fusion. Cited for one thing: TBL3 loss has a documented, strikingly haematopoietic and T-lineage phenotype, which is unusual for a ribosome-biogenesis factor and which makes this protein's presence in the pan-fusion core worth more than a generic nucleolar recovery. Read from the abstract. The p53-independence is the paper's own framing from morpholino experiments in p53 mutants, and morpholino phenotypes carry their own well-known caveats.

• A lineage-restricted phenotype from a housekeeping ribosome-biogenesis gene is the ribosomopathy pattern, in which the restriction reflects differential sensitivity to reduced translational capacity rather than a lineage-specific function. So the T-cell and HSPC phenotype is not evidence that TBL3 does something particular in blood, and it is a direct preview of the toxicity any TBL3-directed intervention would carry. Wada K et al. 2014

Mammalian cells with ectopically expressed MLL-AF4, 2022, Cell & Bioscience - an OVEREXPRESSION system, not the endogenous t(4;11) fusion in a patient blast, and this project's standing rule is that compartment enrichment in an overexpression system is weak evidence about the endogenous protein. Cited for context only. Read from the abstract.

• This observation is simultaneously the reason the nucleolar block is interesting and the reason it may be meaningless: if the bait is predominantly nucleolar, every abundant nucleolar protein becomes a high-probability co-purification partner on compartment grounds alone. The same paper that motivates the row supplies its null hypothesis. Skucha A et al. 2018