DHX16 / hPRP2 (O60231) - the spliceosomal catalytic-activation helicase, pan-MLL-fusion, and one of only two in the 42 whose index-fusion p-value exceeds 0.05

{
  "bait": "MLL-AF4 (= KMT2A::AFF1)",
  "p_value": 0.0929,
  "above_conventional_threshold": true,
  "spectral_counts": "5|1",
  "n_fusions_of_seven": 7,
  "negative_control_counts": "0|0",
  "per_bait": {
    "MLL-AF1p": "0.0838 (5|3)",
    "MLL-AF4": "0.0929 (5|1)",
    "MLL-AF9": "0.0393 (6|5)",
    "MLL-CBP": "0.0336 (2|12)",
    "MLL-EEN": "0.0113 (9|12)",
    "MLL-ENL": "0.00372 (11|11)",
    "MLL-GAS7": "0.0569 (7|7)"
  },
  "af4_spectral_rank_of_seven": 7,
  "af4_p_rank_within_the_42_pan_fusion": 38,
  "weak_everywhere": "THREE of seven baits exceed 0.05 and the best p across the panel is 0.00372. This distinguishes DHX16 from LUZP1, whose index column is weak (0.127) but which reaches 2.63e-10 under MLL-ENL.",
  "written_precedent_at_worse_p": "SMC3 0.174 (gene-smc3, moderate), NOLC1 0.134 (gene-nolc1, weak), TRIM28 0.129 (gene-trim28, weak) - all three already in this graph. Measured 2026-09-21 by reading each entry's data.skucha_2018 block.",
  "source": "analyses/skucha-mll-fusion-interactome/results.json, re-derived from the cached MOESM4 xlsx 2026-09-21; run.py re-run, both controls PASS"
}

{
  "complex": "spliceosome, catalytic activation (Bact -> B* transition)",
  "partners_in_the_960": {
    "SF3A3": "n=7, MLL-AF4 p 0.000595 (15|12), neg 0|3 - and this is the paper's own named NON-SELECTIVITY control",
    "SF3B2": "n=5, MLL-AF4 p 0.113 (15|11), neg 6|4",
    "SF3B1": "n=1, no MLL-AF4 value, neg 8|4"
  },
  "absent_from_the_960": [
    "AQR (Aquarius, the partner helicase)",
    "PPIL4",
    "SNW1/SKIP",
    "PRPF8",
    "SNRNP200",
    "DHX15",
    "DHX8",
    "CDC5L",
    "PLRG1",
    "RBM22",
    "BUD31",
    "ISY1"
  ],
  "reading": "ISOLATED FROM ITS OWN MACHINE, AND THE COMPANY IT DOES KEEP IS THE PAPER'S NEGATIVE CONTROL. Everything DHX16 works with structurally is absent; the U2 SF3 module is present and its pan-fusion representative SF3A3 is the protein the authors used to show that a pan-fusion interactor can be generically essential. analyses/mll-fusion-interactome-complexes/ scores U2 snRNP at q = 0.062 - NOT significant - against a 5,754-protein nuclear background; it is one of the seven of twelve complexes that lose significance once the background is corrected."
}

{
  "observation": "PPIL4 is in direct structural contact with the DHX16 N-terminal domain in the human BAQR spliceosome (Schmitzová 2023), and this graph holds `gene-ppil4` from the proximity-interactome beat - but PPIL4 is ABSENT from the Skucha 960 at any n, and DHX16 was absent from this graph until now.",
  "why_it_matters": "Two independent experiments each recovered one half of a direct structural contact and neither saw the other half. That is a worked example of rule 93's point about instrument coverage, in this project's own data."
}

[
  "Jurkat (human T-ALL) - the AP-MS host, nuclear lysate, tagged single-copy transgene",
  "MOLM-13 (human MLL-AF9 AML) - shRNA screen host, six shRNAs, per-gene score unpublished",
  "HeLa and HeLa nuclear extract - the in vitro splicing and dominant-negative work",
  "reconstituted human spliceosome intermediates - the cryo-EM",
  "no B-lineage cell, no infant cell, and no KMT2A::AFF1 cell of any kind"
]

{
  "screened": true,
  "shrnas_for_this_gene": 6,
  "design": "Supplementary Table 6 / MOESM5 is the shRNA library for the negative-selection screen: 768 data rows, 128 unique gene symbols, EXACTLY 6 shRNAs each - counted with openpyxl by this beat on 2026-09-21. Host is MLL-AF9-expressing MOLM-13, a human myeloid line.",
  "set_identity_measured_by_this_beat": "The 128 symbols in the shRNA library are the SAME SET as the 128 rows of MOESM4 with n_fusions >= 5, checked by set difference on 2026-09-21: the only four mismatches are alias spellings (JADE2/PHF15, JADE3/PHF16, KMT2A/MLL, NIFK/MKI67IP). This matters for the contamination question. The paper says 'Seven proteins were manually removed as these were either frequently observed contaminants or were not detected in human hematopoietic cell lines. The final set was comprised of 128 proteins.' Because the table's >=5 set is already exactly 128, those seven are NOT recoverable from Supplementary Table 5 - and every protein in this tranche is in the post-removal 128 and was carried into the functional screen.",
  "what_this_does_NOT_establish": "A per-gene result. Scores are presented only as heatmaps (Fig. 2c/2d); no per-gene depletion value is tabulated anywhere in the paper or its supplementary files, so for any individual gene the outcome is measured-not-reported. It is also MLL-AF9 MOLM-13, a myeloid line, not the index fusion and not B-lineage.",
  "the_filter_is_leaky_and_here_is_the_proof": "'Survived the authors' manual contaminant removal' is weaker than it sounds. CCT3 is also in the 128 and was also screened, and the CCT/TRiC chaperonin is the canonical AP-MS contaminant - the companion analysis analyses/mll-fusion-interactome-complexes/ uses it as its NEGATIVE control and it is still significant against a nuclear background (q = 2.7e-05, 8 of 9 subunits in the MLL-AF4 column). The authors' own named essentiality controls were RFC1, SF3A3 and CCT3. So the manual removal did not remove a canonical contaminant complex, and membership in the 128 is not the authors certifying a protein as a real partner.",
  "absence_class_for_the_per_gene_score": "measured-not-reported",
  "library_symbol": "DHX16"
}

{
  "query": "DHX16[tiab] AND (KMT2A[tiab] OR MLL[tiab] OR \"MLL-AF4\"[tiab] OR \"MLL-AF9\"[tiab] OR \"t(4;11)\"[tiab])",
  "querytranslation": "\"DHX16\"[Title/Abstract] AND (\"KMT2A\"[Title/Abstract] OR \"MLL\"[Title/Abstract] OR \"MLL-AF4\"[Title/Abstract] OR \"MLL-AF9\"[Title/Abstract] OR \"t 4 11\"[Title/Abstract])",
  "count": 0,
  "second_query": "PRP2[tiab] AND the identical KMT2A clause",
  "second_querytranslation": "\"PRP2\"[Title/Abstract] AND (\"KMT2A\"[Title/Abstract] OR \"MLL\"[Title/Abstract] OR \"MLL-AF4\"[Title/Abstract] OR \"MLL-AF9\"[Title/Abstract] OR \"t 4 11\"[Title/Abstract])",
  "second_count": 0,
  "date": "2026-09-21",
  "tool": "NCBI esearch db=pubmed",
  "names_tried": [
    "DHX16",
    "PRP2",
    "hPRP2 and DDX16 and DBP2 NOT run separately - a residual gap, though all three are heavily contaminated strings"
  ],
  "bare_operand_control": "DHX16[tiab] alone returns 29 records and DHX16[tiab] AND spliceosome[tiab] returns 8, so the gene clause reaches its literature.",
  "positive_control": "MEN1[tiab] AND the identical five-term KMT2A clause returns 85.",
  "complex_level_query": "The complex form WAS run by a sibling entry in this corpus: `(spliceosome[tiab] OR \"splicing factor\"[tiab] OR \"RNA splicing\"[tiab])` against the same KMT2A clause returns 19 - NOT zero - of which MBNL1 (PMID 32398749) and PTBP1 (PMID 42637878) are real splicing dependencies in this disease. Neither is in the Skucha network. So the complex-level literature exists and is about different proteins (rule 64 satisfied by re-use of a checked sibling result, not by assumption).",
  "bound": "Titles and abstracts only; supporting figures not searched (rule 80). Cytogenetic term quoted, querytranslation read back with no injected [UID] term (rule 95). One tag per term (rule 94)."
}

[
  "Search PXD009338 for AQR, PRPF8, SNRNP200 and PPIL4 peptides below the 300-per-bait rank cutoff. If the catalytic spliceosome is there sub-threshold, this is a truncated module; if not, DHX16's isolation is real and stranger.",
  "The PPIL4 asymmetry is a free experiment: two of this graph's datasets each hold one half of a direct structural contact and neither sees the other. Ask what each instrument could not reach.",
  "Ask the authors for the per-gene MOLM-13 shRNA score. Measured-not-reported, an afternoon, and for a protein this close to the selectivity question it is worth more than most."
]