GNL2 / Ngp-1 (Q13823) - a nucleostemin-family nucleolar GTPase in the MLL-fusion nucleolar block, in the index fusion's column at p = 0.0492, and the one member with a published granular-component assignment

GNL2 IS in the MLL-AF4 column, at combined p = 0.0492, recovered by 5 of the seven baits (MLL-AF4, MLL-AF9, MLL-CBP, MLL-EEN, MLL-GAS7). Negative control: ZERO spectra. THIS P-VALUE IS 0.0008 INSIDE AN ARBITRARY LINE. The table's inclusion rule is a rank cutoff, not a threshold, and 63.9% of the MLL-AF4 column exceeds 0.05 with a maximum of 0.175 - so 0.0492 is a rank position, not a categorical result, and it should not be treated as qualitatively different from LYAR at 0.141. FUNCTIONAL SCREEN. Supplementary Data 2 (MOESM5) is the shRNA library for the negative-selection screen: 768 data rows, 128 unique gene symbols, EXACTLY six shRNAs each -- counted with openpyxl by this beat on 2026-09-21, and this protein's symbol IS in it with six shRNAs. So it was functionally tested against an MLL fusion (MLL-AF9 in MOLM-13), which is more than a co-purification. But per-gene scores are published only as the heatmaps in Fig. 2c/2d with no table anywhere in the paper or its five supplementary files, so the outcome for this protein is not recoverable: measured-not-reported. THE BLOCK, re-measured by this beat on 2026-09-21 by re-running analyses/mll-fusion-interactome-complexes/run.py. A 26-subunit nucleolar / ribosome-biogenesis set returns 15 of 26 present in the 960-protein network against 1.25 expected by chance, hypergeometric p = 6.99e-14, q(BH) = 8.39e-13 across the twelve complexes tested -- the TOP-RANKED complex in the whole interactome, ahead of the CCT/TRiC negative control (q = 1.4e-09) and the SEC positive control (q = 1.5e-09). The fifteen are FBL, FTSJ3, GNL2, LYAR, NOLC1, NOP2, NOP58, PA2G4, RRP12, RRP9, TBL3, TCOF1, UTP14A, UTP18, WDR18. BUT THE BACKGROUND IS THE ~20,000-PROTEIN PROTEOME, not the ~4,600 proteins the study actually recovered before filtering, so every q here is an UPPER BOUND on significance and it is loosest for a complex of abundant nuclear proteins -- which this one is, more than any other row in that table. AND THE POOLED NUMBER IS NOT THE PER-BAIT NUMBER. Subunits of the block recovered per bait, out of 26: MLL-AF1p 8, MLL-AF4 7, MLL-AF9 12, MLL-CBP 10, MLL-EEN 12, MLL-ENL 11, MLL-GAS7 7. The index fusion is TIED LAST. In its column there are seven members and only four at p<0.05 -- GNL2, NOP2, PA2G4 and TBL3; LYAR (0.141), NOLC1 (0.134) and TCOF1 (0.163) are above it. So the strongest complex-level signal in this entire interactome is weakest in the fusion this project studies. 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 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."). In the MLL-AF4 column 186 of 291 listed p-values (63.9%) exceed 0.05; the pooled rate over all baits is 26.6%, and the pooled rate must NOT be quoted for a per-bait claim. BAIT DEPTH: MLL-AF4 is the shallowest of the seven baits by spectral counts, so a low or absent MLL-AF4 count is a property of the bait (transgene expression, purification depth, normalisation) and must not be read as a weaker association. ABUNDANCE IS THE LEADING ALTERNATIVE EXPLANATION. The nucleolus is the densest compartment in the nucleus, every bait here is a tagged nuclear protein, and the complex-level analysis in this repo exists to make exactly that point: its strongest per-bait signature in the index fusion's own column is CCT/TRiC, a canonical AP-MS contaminant, at 8 of 9 subunits with 6 at p<0.05 -- BETTER represented in MLL-AF4's column than the nucleolar block is. Complex-wide enrichment is not by itself evidence of specific binding. THE ARGUMENT ON THE OTHER SIDE: all thirteen members of the nucleolar block, this protein included, have a negative control of ZERO spectra. A non-specific sticky abundant protein would be expected to appear in the control purification too, and none of them does. That is the strongest single fact about this block and it is not explained by abundance alone. SELECTIVITY: the paper's own 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. This protein is not among them. That is NOT evidence of selectivity: only 40 of the 128 entered the MLL-r versus MLL-wild-type re-screen and the paper does not say which 40, so absence from the control list is equally consistent with never having reached the second screen. Recorded as UNKNOWN. This entry does not nominate a target. Per-bait membership re-derived by this beat on 2026-09-21 by re-running analyses/skucha-mll-fusion-interactome/run.py (both controls PASS: 128 shared by >=5 baits, 42 by all seven, MEN1 present with all seven) and analyses/mll-fusion-interactome-complexes/run.py. n_fusions and the MLL-AF4 p-value were supplied pre-verified by the coordinator from the cached MOESM4 xlsx and were independently reproduced by this beat's re-run of the complex analysis.

• 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 frequently observed contaminants, which concedes that a rank cutoff lets contaminants through. ProteomeXchange/PRIDE 2018
• The same paper that motivates the nucleolar reading supplies its null hypothesis: MLL-AF4 is reported predominantly nucleolar, so every abundant nucleolar protein becomes a high-probability co-purification partner on compartment grounds alone. And the prediction that reading makes fails -- if nucleolar residency of the bait drove recovery, the index fusion should pull MORE of the block than the other six baits, and it pulls the FEWEST (7 of 26, tied last with MLL-GAS7). The report is also an ectopic-overexpression system, which this project treats as weak evidence about an endogenous protein. Siemund AL et al. 2022

ZEBRAFISH developmental genetics, 2014 Developmental Biology. Not human, not leukaemia, not a fusion, and no haematopoietic readout is claimed here for gnl2 specifically - unlike TBL3, whose zebrafish mutant has a documented T-cell and HSPC phenotype, this beat found no comparable blood phenotype for gnl2 and does not assert one. Read from the abstract only. Cited for one thing: GNL2 has a specific, non-redundant 60S function, established in a vertebrate, independent of anything in this graph.

• A comparative family study is designed to find differences between paralogues, so 'distinct sites' is the result the design was powered to produce; the same data are consistent with substantially overlapping function plus a difference at the margins. And a vertebrate developmental phenotype says nothing about whether the protein is required in a transformed human blast, where ribosome demand and p53 status are both abnormal. Wang Y et al. 2017

DROSOPHILA, 2017 Chromosoma. Two layers of indirectness that must travel with this claim wherever it is quoted: it is an INVERTEBRATE homologue, and the localisation is from an EXOGENOUS GFP FUSION, which this project treats as weak evidence about an endogenous protein. Read from the abstract only. It is recorded because it is the most specific sub-nucleolar assignment available for GNL2 anywhere, and a homology-based GC assignment stated as such is more useful than 'nucleolus' - but it must not be promoted to a human fact. No human imaging of GNL2 at sub-nucleolar resolution was found by this beat.

• The human record does not corroborate the sub-compartment. UniProt Q13823 gives only 'Nucleus, nucleolus' with two experimental citations and no GC or DFC assignment, and the human work this beat read on GNL2 localisation is about nucleolar RETENTION signals rather than sub-compartment - it identifies two nucleolar localisation signals sufficient to move a heterologous protein into the nucleolus, which is a targeting result, not a sub-compartment result. Chennupati V et al. 2011

A counted negative with a date, the exact query, the querytranslation and the tool. Bounded by TITLES AND ABSTRACTS ONLY - supporting figures not searched (rule 80). Bounded also by the name list in data.bounded_literature.names_tried; 'nucleostemin 2' was included because the Drosophila and comparative literature calls this protein NS2, and NS2 alone is far too short and collision-prone to search. The bare operand returns 32, so the instrument can return a one for this symbol (rule 67).

• An absence of publication is not an absence of measurement. GNL2 is one of the 128 conserved interactors shRNA-screened in MLL-AF9 MOLM-13 with six shRNAs in the source paper itself, so a functional measurement against an MLL fusion exists and was never tabulated: measured-not-reported, not never-measured. Skucha A et al. 2018