WDR18 (Q9BV38) - the Rix1/PELP1-TEX10-WDR18 60S maturation subunit, in five MLL-fusion interactomes but NOT the index fusion's, and the block's only member whose nucleolar partitioning is SUMO-controlled

THE INDEX FUSION DID NOT RECOVER THIS PROTEIN. WDR18 is absent from the MLL-AF4 column of Supplementary Table 5 entirely -- there is no p-value and no spectral count for it under the index bait. It is an MLL-FUSION interactor, not a demonstrated KMT2A::AFF1 interactor, and nothing in this entry should be read as a KMT2A::AFF1 contact. The 5 baits that did recover it are MLL-AF9, MLL-CBP, MLL-EEN, MLL-ENL, MLL-GAS7. Negative control: ZERO spectra. THE HEADLINE OF THIS ENTRY, AND IT BELONGS IN EVERY QUOTATION OF IT: this protein is NOT in the MLL-AF4 column. It is an MLL-FUSION interactor and NOT a demonstrated KMT2A::AFF1 interactor. Five of the eleven nucleolar-block proteins written by this beat are in that position - RRP12, WDR18, UTP14A, RRP9 and FTSJ3 - plus UTP18, six in total. The 'thirteen-protein nucleolar block' is a POOLED statement over seven baits; in the index fusion's own column there are seven members and four below p = 0.05. SPECIFIC TO THIS PROTEIN: WDR18 is a constitutive subunit of the PELP1-TEX10-WDR18 Rix1 module, and NEITHER PELP1 NOR TEX10 IS IN THIS 960-PROTEIN NETWORK. Recovering one subunit of a tight three-protein module without the other two is weak evidence that the module was captured, and is more consistent with an individual protein being recovered for another reason. 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

MAMMALIAN cultured cells, 2011 EMBO Journal, biochemical purification plus SUMO manipulation. Not leukaemia, not a fusion, not haematopoietic. Read from the abstract only. This is also the paper behind UniProt's single experimental (ECO:0000269) nucleolar localisation call for human WDR18, so the localisation and the function rest on the same source - a single-source dependency worth knowing about.

• If SUMO controls whether this complex sits in the nucleolus, then WDR18's compartment at the moment of lysis is a function of the cell's SUMO state, which is undefined in a doxycycline-induced Jurkat transgene line. A co-purification cannot then be attributed to the nucleolar pool. And UniProt's own record, extrapolating from the zebrafish orthologue, says WDR18 is MAINLY NUCLEOPLASMIC - which if true of the human protein would remove WDR18's principal claim to membership of a nucleolar block. UniProt Knowledgebase 2026

MAMMALIAN cultured cells, 2012 Molecular Biology of the Cell. Not leukaemia, not a fusion, not haematopoietic. Read from the abstract only. Cited to establish that WDR18 is a constitutive module subunit rather than an independent protein, which is the basis of this entry's main reservation about the AP-MS row - so it is load-bearing for a NEGATIVE argument here, and the reader should weigh it as such.

• The module argument has a limit. A protein can be a stable subunit of one complex and still have an independent pool or a second complex, and neither of these papers rules that out for WDR18; UniProt separately gives it a dynein axonemal particle assignment by similarity. So the absence of PELP1 and TEX10 from the network weakens the module reading without establishing that WDR18's recovery is spurious. Finkbeiner E et al. 2011

Database record fetched live 2026-09-21; both comment lines are quoted from the fetched record. Per rule 91 the distinction is the content of this item: 'Nucleus, nucleolus' carries ECO:0000269 PubMed 21326211; 'Nucleus, nucleoplasm', 'Cytoplasm' and the 'mainly found in the nucleoplasm' note all carry ECO:0000250 from zebrafish Q4VBE8; the dynein axonemal particle line is ECO:0000250 from A0A1L8HX76. This beat did not open PubMed 21326211's figures, so even the experimental line establishes only that a curator read an experiment. NO sub-nucleolar assignment of any kind exists. This entry does NOT resolve the nucleolar-versus-nucleoplasmic conflict and states it as unresolved.

• Recorded as a live tension rather than a settled fact: if the by-similarity nucleoplasmic assignment turns out to hold for the human protein, WDR18's inclusion in a NUCLEOLAR block is partly a classification artefact. The 26-subunit set used by this repo's complex analysis was assembled from canonical ribosome-biogenesis membership, not from measured human localisation, so a member whose own record says 'mainly nucleoplasm' is a warning about how that set was built. Skucha A et al. 2018

The record was FETCHED AND TITLE-CHECKED rather than counted: PMID 40677927, Human Mutation 2025, 195 individuals from 105 families with suspected Cornelia de Lange syndrome. WDR18 and KMT2A co-occur only as separate entries in the paper's own gene lists; there is no WDR18-KMT2A relationship in it and no leukaemia. Recorded as a BOUNDED REJECTION so a future beat does not re-find it and mistake it for a hit. It is worth one line on its own account: it is the only human WDR18 variant report this beat found, it is a single de novo variant in one proband, and the authors classify WDR18 among genes not previously associated with any developmental disorder - so it is a candidate, not an established disease gene. The bounded query for WDR18 is otherwise zero; bare operand 18 records, positive control 85.

• An absence of publication is not an absence of measurement. WDR18 is one of the 128 conserved interactors shRNA-screened in MLL-AF9 MOLM-13 with six shRNAs in the source paper itself: measured-not-reported. As with RRP12, note the asymmetry - WDR18 was functionally screened against MLL-AF9 while never having been recovered by the index fusion at all. Skucha A et al. 2018