SON (P18583) - a nuclear speckle scaffold that BINDS MENIN and inhibits MLL complex assembly, and the one protein in this tranche the Skucha authors name in their own discussion

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 SON the MLL-AF4 total (8 spectra over two replicates) is rank 7 of the seven baits, against a maximum of 74 under another bait. All seven per-bait values, p (replicate spectral counts): MLL-AF1p 0.0063 (8|4); MLL-AF4 0.0257 (3|5); MLL-AF9 0.0001 (26|28); MLL-CBP 0.0001 (11|27); MLL-EEN 0.0002 (32|34); MLL-ENL 0.0000 (38|36); MLL-GAS7 0.0001 (32|30). SPECIFIC TO THIS PROTEIN: SON is among the most deeply recovered proteins in the pan-fusion set - six of seven baits at or below 1e-3, up to 38|36 spectra under MLL-ENL - and MLL-AF4 is by far its shallowest column at 8 total spectra against 74. SON is also a very large (2,426 aa) abundant nuclear protein, which raises its prior probability of recovery in any nuclear AP-MS independent of the bait. 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

This concerns WILD-TYPE MLL complexes, not any KMT2A fusion, and there is no t(4;11) or infant B-lineage material in the abstract. The leukaemia arm is AML. 'Interacts with menin' is a co-purification/interaction claim from 2016 read here from the abstract only - the binding interface, stoichiometry and whether the contact is direct were not checked, and this project has an explicit rule that a co-IP is not a direct contact. Nothing in the paper tests whether SON can bind a KMT2A FUSION, which retains the menin-binding motifs but has lost the SET domain, so the H3K4me3 arm of the mechanism cannot operate the same way on the fusion. Read from the abstract. Whether the short-isoform upregulation extends to KMT2A-rearranged AML specifically is not stated in the abstract.

• The direction is REPRESSIVE: SON inhibits MLL complex assembly and lowers H3K4me3. So SON's presence in every MLL-fusion purification is as consistent with the fusion being restrained by SON as with SON being a component of a functional fusion complex - and if the former, removing SON would increase fusion-target transcription. The Skucha AP-MS cannot distinguish a substrate, a regulator and a compartment neighbour. Skucha A et al. 2018
• SON is one of the two proteins required to build nuclear speckles at all, so a 2,426-residue chromatin- and speckle-resident protein is a high-prior prey in any nuclear-lysate purification. The menin interaction and the co-purification may have no causal relationship to each other. Ilik IA et al. 2020

Human cell lines, 2020; not haematopoietic and not a fusion system. The reagent correction is load-bearing for reading older literature: any claim that a protein 'co-localises with SC35' is a claim about SRRM2 colocalisation, and UniProt's own note on SON still says 'Colocalizes with the pre-mRNA splicing factor SRSF2'. This project's standing condensate rule applies to any phase-separation language here: a punctate appearance is compatible with binding to spatially clustered sites, and neither 1,6-hexanediol nor classical FRAP can distinguish the two. Read from the abstract.

• SRRM2, the necessary partner in this model, is ABSENT from the Skucha 960-protein network at any n (checked by this beat from the xlsx, 2026-09-21). If the fusion were sampling bulk speckle material one would expect the other scaffold; its absence weakens the 'speckle carry-over' explanation but equally weakens any claim that a speckle came along as a unit. Skucha A et al. 2018

MOUSE haematopoietic stem cells for the genetics, with a human engraftment arm; normal haematopoiesis, not leukaemia, and no KMT2A fusion anywhere. Cited here for two things only: that SON has a documented, non-redundant role in the cell compartment this disease arises from, and that manipulating it changes stem-cell quiescence - which is the bite-back. Read from the abstract.

• If SON supports normal HSC self-renewal and quiescence, then depleting it is expected to damage normal blood stem cells at least as much as leukaemic ones - the essential-function shape that the paper's own RFC1/SF3A3/CCT3 controls exemplify. That is an argument against SON as a target, independent of any interactome evidence. Skucha A et al. 2018