LYAR (Q9NX58) - a zinc-finger nucleolar growth regulator cloned from a T-cell leukaemia line, in six of seven MLL-fusion interactomes, and the one member of this block whose discovery system is the same lineage as the AP-MS host

LYAR IS in the MLL-AF4 column, at combined p = 0.141, recovered by 6 of the seven baits (MLL-AF1p, MLL-AF4, MLL-AF9, MLL-CBP, MLL-EEN, MLL-ENL). Negative control: ZERO spectra. AND THIS ROW IS ABOVE p = 0.05 IN THE INDEX COLUMN. It is listed only because the paper's inclusion rule is a rank cutoff - the top 300 preys per bait - and 63.9% of the MLL-AF4 column exceeds 0.05, with a maximum of 0.175. So membership of that column is a statement about rank, and for this protein the index-fusion p-value does not support an association on its own. Say so in the claim, not only here. SPECIFIC TO THIS PROTEIN AND MORE SERIOUS THAN THE P-VALUE: LYAR was CLONED FROM A MOUSE T-CELL LEUKAEMIA LINE and is reported expressed at very high levels in leukaemia cells. The AP-MS host is Jurkat, a human T-ALL line. Its recovery by six of seven baits is therefore fully consistent with high abundance in this particular host and requires no fusion contact. 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
• The abundance objection is documented rather than hypothetical for this protein. LYAR's founding paper defines it by very high expression in T-cell leukaemia, and the human follow-up repeats that it is expressed at very high levels in many tumour, leukaemia and embryonic stem cells. A protein selected by the literature for being abundant in T-cell leukaemia, recovered from a T-cell leukaemia lysate by six of seven unrelated baits, is the single weakest case in this block for a specific interaction. Su L et al. 1993

HUMAN cultured cells, 2014 Genes to Cells. Not leukaemia, not a fusion, not haematopoietic. Read from the abstract only. The actinomycin D result is a drug-induced relocalisation, which establishes transcription-dependence of the address but not the normal steady-state sub-compartment. Cited for two things: LYAR's molecular function, and the fact that its nucleolar position is conditional rather than constitutive - which matters because the AP-MS lysate came from cells in an undefined transcriptional state.

• If LYAR's nucleolar residency depends on active rRNA transcription, and the index fusion is itself reported to INTERFERE with Pol I transcription and ribosome biogenesis, then the two facts predict that LYAR should be LESS nucleolar in a cell expressing the fusion - which would make a fusion-driven nucleolar co-purification less likely, not more. Nobody has measured LYAR's distribution in a fusion-expressing cell, so this is a prediction and not a result, but it is a prediction that runs against the convergence. Siemund AL et al. 2022

MOUSE, 1993 Genes & Development, an expression-cloning and immunolocalisation paper. Not human, not a fusion. Read from the abstract only. Note the 388 aa is the MOUSE protein; the human protein is 379 aa (Q9NX58), so the length in this claim must not be used to check the human accession - a nine-residue difference between species is exactly the size of error that rule 66's length check is supposed to catch, and quoting the mouse number against a human accession would manufacture a false alarm. Cited for the provenance, which is the point: this protein entered the literature as a T-cell-leukaemia gene.

• A 1993 expression-cloning paper's 'predominantly nucleolar' is a polyclonal-antiserum immunolocalisation in mouse cells and is not a sub-compartment measurement. The modern record does not contradict it - UniProt carries nucleus and nucleolus with experimental codes - but the founding observation should not be quoted as though it resolved where in the nucleolus LYAR sits. It did not, and neither has anything since, in human cells. UniProt Knowledgebase 2026

Database record fetched live 2026-09-21; the comment text is quoted from the fetched record. Per rule 91 the distinction being recorded here is the point: nucleus (ECO:0000269 PubMed 25092918, 31413131), nucleolus (ECO:0000269 PubMed 12429849, 24495227), cytoplasm (ECO:0000269 PubMed 24990247) are experimental; the DFC line and the photoreceptor-outer-segment line are ECO:0000250 propagated from mouse Q08288. None of the cited papers was opened by this beat except 24495227, so the codes establish that a curator read an experiment, not that any of these is the founding or best observation.

• UniProt also records a cytoplasmic pool associated with 60S ribosomes but not polysomes (ECO:0000269 PubMed 24990247). A protein with a real cytoplasmic pool cannot have its nuclear-lysate co-purification interpreted as necessarily nucleolar, and no fractionation in the AP-MS experiment distinguishes which pool the recovered LYAR came from. Skucha A et al. 2018

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. Note the asymmetry worth stating: LYAR is a leukaemia-discovered gene with 73 records, and NONE of them intersects the KMT2A/MLL literature - so the absence is not for want of a leukaemia literature on this protein.

• An absence of publication is not an absence of measurement. LYAR 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, not never-measured. Skucha A et al. 2018