PES1 / pescadillo (O00541) - the missing PeBoW subunit of this graph's nucleolar block, pan-essential in 96.9% of DepMap lines, and the one myeloid experiment on it shows proliferation WITHOUT a differentiation block

This is a prediction, not a measurement. No one has seen this protein in this shape. The colours say how much the software trusts itself, and that is worth reading before anything else — the orange stretches are places the model is effectively saying this part has no fixed shape.

• PES1 is required by 96.9% of DepMap lines. Any intervention against PeBoW is an intervention against 60S ribosome maturation in every dividing cell, including normal haematopoietic progenitors - the textbook essential-function toxicity, and the leukaemia arm of DepMap gives no window at all (leukaemia mean -1.0214 versus panel mean -1.0246).
• The one myeloid experiment says PES1 supplies proliferation and NOT a differentiation block. So even if PES1 were drugged, the fusion-imposed differentiation block - the phenotype this project treats as central - would be untouched, and the effect would be a generic anti-proliferative one obtainable more cheaply.
• Nucleolar stress is itself a p53-activating and differentiation-modulating signal. Partial inhibition of ribosome biogenesis in a leukaemia with wild-type TP53 may select for TP53 loss, which is a resistance route this graph already tracks in other contexts.
• Because PES1 is abundant and present in every nucleus, it is exactly the class of protein for which a co-purification with a tagged nuclear bait carries least information. Anyone building an argument on the AFF4 rows should note that the same abundance that makes it a bad target also makes the rows a weak premise.

1. Does an AFF4-directed experiment recover PES1? Both IntAct rows have PES1 as the bait, so the reciprocal pulldown has never been done - and for a pan-essential nucleolar protein the reciprocal is the only version of the experiment worth believing.
2. Should BOP1 and WDR12 get entries? Rohrmoser 2007 shows BOP1, not PES1, is the integral PeBoW subunit, so this graph currently represents the complex by its least integral member and neither of the other two exists as a node.
3. Does the nucleolar pool of the KMT2A::AFF1 fusion overlap PES1 specifically, or only the compartment? This graph holds localization-nucleolus-kmt2a-fusion and eleven nucleolar-block genes, and the discriminating experiment - a sub-nucleolar co-localisation rather than a compartment-level co-purification - has not been done for any of them.
4. Is PES1's proliferation-without-differentiation-block result reproducible in a B-lineage system? The only haematopoietic experiment is murine, myeloid, and by overexpression; the knockdown version in a human B-ALL line has never been reported.
5. What is in the Nop7 literature about this protein's interactions? Two of its three name generations were queried here and the third was not.

1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   IntAct holds exactly two rows placing PES1 (O00541) against AFF4 (Q9UHB7): PMID 28514442 and PMID 33961781, both anti-tag co-immunoprecipitation (MI:0007), both in HEK293T, both at IntAct MI-score 0.53, and in both rows the experimental role of PES1 is bait and the experimental role of AFF4 is prey.

   IntAct PSICQUIC, MITAB2.7 rows for Q9UHB7 (AFF4), filtered on O00541 · EMBL-EBI IntAct 2026
   ▸What this evidence cannot show

   Queried live 2026-09-22; the experimental role, host organism, detection method and MI-score were read out of MITAB2.7 columns 19/20, 29, 7 and 15 rather than assumed. THE TWO PUBLICATIONS ARE ONE SCREENING PROGRAMME (BioPlex 2017 and BioPlex 2021, same group), so 'two publications' is not two laboratories. HOST HEK293T in both rows: embryonic kidney, not haematopoietic, not B-lineage, no fusion. MI-score 0.53 is the joint-highest in the read queue and is still BELOW IntAct's 0.6 conventional high-confidence cut. DIRECTION: PES1 is the bait in both rows, so no AFF4-directed experiment has ever recovered PES1. Rule 93 endpoint caveat: PSICQUIC returns 179 rows for AFF4 against 207 from IntAct REST, so this is a floor.

   ▸Evidence that argues against this (1)

   • PES1 is a nucleolar protein that is pan-essential in 96.9% of DepMap lines, i.e. abundant and present in every nucleus. A proteome-scale anti-tag coIP with PES1 as bait in HEK293T cannot distinguish a specific contact with AFF4 from co-purification of abundant nuclear material, and this project's own complex-level analysis exists to make exactly that point about nucleolar proteins in tagged-nuclear-bait experiments. Huttlin EL et al. 2021
2. E2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

   PES1 is ABSENT from the 960-protein seven-bait MLL-fusion AP-MS network of Skucha 2018, as are BOP1 and WDR12, the other two PeBoW subunits - so the PeBoW complex does not appear in the dataset that established this project's nucleolar block, and PES1's route into this graph is independent of it.

   MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. · Skucha A, Ebner J, Grebien F, et al. · Nat Commun 2018
   PMID 29777171DOI
   ▸What this evidence cannot show

   Checked directly by this beat on 2026-09-22 against the cached Supplementary Table 5 workbook (41467_2018_4329_MOESM4_ESM.xlsx) in analyses/skucha-mll-fusion-interactome/cache/, by matching the gene_name column: 960 distinct gene symbols, and PES1, BOP1 and WDR12 are none of them. AN ABSENCE FROM THIS DATASET IS WEAK EVIDENCE: the paper retained the top 300 interactions PER BAIT by combined p-value rather than applying a threshold, so a protein can be a real partner and fall outside the rank cutoff; the host is Jurkat T-ALL with Strep-HA-tagged single-copy fusion transgenes, not endogenous protein and not B-lineage; and MLL-AF4 is the shallowest of the seven baits. Cited for one narrow thing: the nucleolar block this graph already holds and the PeBoW complex are disjoint, so PES1 is not a rediscovery of an entry that already exists.

   ▸Evidence that argues against this (1)

   • The same check found that RSBN1 IS in that network, on one bait. So the dataset is capable of returning a read-queue member, which strengthens the PES1 absence slightly - but it returned only one of the sixteen queue and adjudicated-queue symbols tested, so the discriminating power of this control is low and it must not be read as a refutation of the BioPlex rows. Skucha A et al. 2018
3. E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

   In murine 32D IL-3-dependent myeloid cells and 32D IGF-IR derivatives, ectopic PES1 (and UBF1) increased cell size and/or altered cell-cycle distribution but failed to make the cells IL-3 independent and failed to inhibit the IGF-IR-initiated differentiation programme - the cells differentiated into granulocytes like their parents - while the same proteins did transform mouse embryo fibroblasts with high endogenous IRS-1.

   Role of pescadillo and upstream binding factor in the proliferation and differentiation of murine myeloid cells. · Prisco M, et al. · Mol Cell Biol 2004
   PMID 15169904DOI
   ▸What this evidence cannot show

   SYSTEM, AND THE CLAIM IS WRITTEN WITH IT IN THE FIRST CLAUSE per rule 73: MURINE 32D myeloid cells with ECTOPIC OVEREXPRESSION of PES1. Not human, not B-lineage, not infant, and no MLL or KMT2A fusion appears in the paper. Read from the abstract only; the cell-size, cell-cycle and differentiation readouts are the abstract's own. This is the ONLY published experiment placing PES1 in a haematopoietic cell, and it is cited here for a NEGATIVE result - that PES1 does not block myeloid differentiation - which is the half of the two-hit model a KMT2A fusion is argued to supply. An overexpression negative is weaker than a knockdown negative: failing to block differentiation when overexpressed does not establish that endogenous PES1 is uninvolved.

   ▸Evidence that argues against this (1)

   • The authors' own conclusion is framed positively - that their results provide a model for myeloid leukaemia in which both a proliferation stimulus and a differentiation block are required - so the paper is not a refutation of PES1's relevance to leukaemia, only of its sufficiency. And the transformation of mouse embryo fibroblasts in the same paper shows PES1 CAN be transforming in a cell type not prone to differentiation, which is the reading a target-focused beat would emphasise and which this entry deliberately does not. Prisco M et al. 2004
4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   PES1 is the pescadillo subunit of the PeBoW complex, required for maturation of the 28S and 5.8S rRNAs and formation of the 60S ribosome; by indirect immunofluorescence, cell fractionation and sucrose-gradient centrifugation, Pes1 migrates to the nucleolus and binds pre-ribosomal particles independently of Bop1 while transport of Bop1 to the nucleolus is Pes1-dependent; and UniProt O00541 (588 aa, BRCT 322-415) records nucleolar, nucleoplasmic and chromosomal localisation with NO evidence code on any location comment.

   Interdependence of Pes1, Bop1, and WDR12 controls nucleolar localization and assembly of the PeBoW complex required for maturation of the 60S ribosomal subunit. · Rohrmoser M, et al. · Mol Cell Biol 2007
   PMID 17353269DOI
   ▸What this evidence cannot show

   TWO SOURCES IN ONE ITEM, deliberately, because rule 91 is the point. The UniProt half was fetched live 2026-09-22 (gene_exact:PES1 AND organism_id:9606 AND reviewed:true returns exactly one reviewed row, O00541, 588 aa, primary gene name PES1, 26 PDB cross-references, Domain BRCT 322-415) and its subcellular-location comments carry NO evidence codes - not ECO:0000269, not ECO:0000305, nothing - so they are curator statements and were NOT relied on. The Rohrmoser half is the founding localisation experiment and was fetched and read as an abstract; the immunofluorescence, fractionation and gradient methods are named in the abstract. NOT verified here: the 26 PDB entries were not opened and no structure is used for a domain boundary; the BRCT boundary 322-415 is UniProt's own feature and is the only domain asserted. SYSTEM: mammalian cell lines, no leukaemia, no fusion.

   ▸Evidence that argues against this (1)

   • Rohrmoser's central finding is that the complex is highly sensitive to Bop1 levels and that Bop1, not Pes1, is the integral subunit whose loss abolishes the other two subunits' co-purification. So a PES1-centred reading of PeBoW is the wrong emphasis on the complex's own biology, and a PES1 entry in this graph without BOP1 and WDR12 entries - neither of which exists - represents the complex by its least integral subunit. Rohrmoser M et al. 2007
5. E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   In DepMap release 26Q2 as served by Open Targets, PES1 (ENSG00000100029) has a mean gene effect of -1.0246 across 1,258 screens, a minimum of -2.228, 96.9% of lines below -0.5, and a mean of -1.0214 across the 57 leukaemia-annotated screens - a common-essential profile with no leukaemia selectivity.

   Open Targets Platform GraphQL, target.depMapEssentiality (DepMap 26Q2) · Open Targets Platform / DepMap 2026
   ▸What this evidence cannot show

   RELEASE RECORDED per rule 83: meta.dataVersion = {year: 26, month: 06} = DepMap 26Q2, fetched 2026-09-22. 1,258 is this gene's own screen count, not a corpus denominator. All 29 tissue blocks of depMapEssentiality were concatenated before averaging - reading block [0] is a registered trap. Ensembl id resolved through the HGNC primary ensembl_gene_id per rule 78, with the readback control passing (Open Targets returned approvedSymbol PES1). THE LEUKAEMIA SUBSET IS NOT A KMT2A SUBSET: it is a substring match on diseaseFromSource and was not stratified by KMT2A rearrangement, so this number cannot speak to fusion selectivity in either direction. NO NULL-DISTRIBUTION TEST was run and none is needed - the claim is absolute pan-essentiality, not a median-split proportion, which this project's rule 84 forbids reporting.

   ▸Evidence that argues against this (1)

   • Pan-essentiality is the strongest single argument AGAINST this protein mattering to the project, and it is also the reason a co-purification with it is uninformative: a protein required by 96.9% of cell lines is present in every nucleus at high abundance, which is the condition under which AP-MS co-purification is least interpretable. The same number therefore both rules out the target and weakens the interaction evidence. Open Targets Platform / DepMap 2026
6. E6strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   PubMed esearch 2026-09-22, each operand separately tagged: PES1[tiab] = 136, pescadillo[tiab] = 67, PeBoW[tiab] = 20, PES1[tiab] AND KMT2A[tiab] = 0, PES1[tiab] AND MLL[tiab] = 0, pescadillo[tiab] AND MLL[tiab] = 0 (three parsed zeros), PES1[tiab] AND leukemia[tiab] = 3 and pescadillo[tiab] AND leukemia[tiab] = 1; and ten sampled records from the head of PES1[tiab] were title-checked with only two being the human gene, the rest being plant Phytyl Ester Synthase, bacteriophage PES-1, a Candida albicans study and omics gene lists.

   NCBI PubMed esearch, bounded-absence queries with querytranslation and warninglist recorded · NCBI E-utilities 2026
   ▸What this evidence cannot show

   Every zero carries a non-empty querytranslation (e.g. `"PES1"[Title/Abstract] AND "KMT2A"[Title/Abstract]`) and warninglist.outputmessages = ["No items found."]. Each operand separately tagged; no `(A OR B)[tiab]` form used, per rule 94. BOTH KMT2A SYMBOL GENERATIONS were run and both name generations of the gene (PES1 and pescadillo) were paired with MLL, so the zero is not an artefact of either symbol choice. THE 136-RECORD COUNT IS A CONTAMINATED CEILING and must never be quoted as the PES1 literature: 8 of 10 sampled records are not the human gene. NAME LIST TRIED: PES1, pescadillo, PeBoW, KMT2A, MLL, leukemia. NOT TRIED: Nop7 (the yeast/trypanosomatid orthologue name, which a third literature uses and which neither PES1 nor pescadillo reaches), BOP1, WDR12, 'MLL-AF4', 'MLL-AF9', '"t(4;11)"'. Bounded by TITLES AND ABSTRACTS ONLY. data/symbol-collisions.json (147 rows) was grepped for PES1, pescadillo, PeBoW, BOP1 and WDR12 before the first query per rule 88: no row exists for any of them, so this is a NEW trap and not a rediscovery.

   ▸Evidence that argues against this (1)

   • The Nop7 name generation is the unclosed hole in this bounded absence. Nop7 is the yeast and trypanosomatid orthologue name and a 2026 J Proteomics paper on Nop7 protein interactions appeared in the PES1 sample, so a Nop7 literature exists that neither PES1 nor pescadillo retrieves. Any claim about what is known of this protein's interactions is bounded by two of its three name generations, not three. Nepomuceno-Mejia T et al. 2026

• co-occurs with →AFF4 — the textbook SEC scaffold that KMT2A::AFF1 cells need LESS than other leukemias

  two BioPlex rows (28514442, 33961781) - one screening programme seen twice; PES1 is the BAIT and AFF4 the prey in both; HEK293T; IntAct MI-score 0.53, the joint-highest in the read queue and still below IntAct's 0.6 high-confidence cut

• related to →The nucleolus — the one compartment with direct published images of a KMT2A fusion inside it

  nucleolar by immunofluorescence, fractionation and sucrose gradient - the compartment the fusion is reported to occupy; co-localisation with the fusion has never been tested

• related to →PA2G4 / EBP1 (Q9UQ80) - the best-evidenced member of the MLL-fusion nucleolar block in the index fusion's own column (p = 0.014), and the only one with a published AML phenotype

  both ribosome-biogenesis factors in this graph, reached by DISJOINT routes: PA2G4 via the Skucha MLL-fusion AP-MS nucleolar block, PES1 via BioPlex/AFF4. PES1, BOP1 and WDR12 are absent from the Skucha 960-protein network

• refutes →The differentiation block — what it actually is, operationally, in KMT2A::AFF1 leukaemia

  NEGATIVE: in murine 32D myeloid cells ectopic PES1 increased cell size and altered the cell cycle but did NOT confer IL-3 independence and did NOT block granulocytic differentiation

• ← supportsIn all 24 read-queue rows inspected, the candidate is the BAIT and this project's protein is the prey - nobody has ever tagged KMT2A, AFF4, menin or PSIP1 and found any of them; plus seven bounded rejections

  both PES1 rows read per row: candidate bait, AFF4 prey, HEK293T, MI-score 0.53