PRKAR1A (P10644) - a PKA regulatory subunit in the pan-MLL-fusion core with no catalytic subunit anywhere in the network, and a fusion oncogene in variant APL

{
  "bait": "MLL-AF4 (= KMT2A::AFF1)",
  "p_value": 0.048,
  "spectral_counts": "3|3",
  "n_fusions_of_seven": 7,
  "negative_control_counts": "0|0",
  "per_bait": {
    "MLL-AF1p": "0.0139 (8|3)",
    "MLL-AF4": "0.048 (3|3)",
    "MLL-AF9": "0.00601 (10|8)",
    "MLL-CBP": "0.02 (3|5)",
    "MLL-EEN": "0.0361 (10|5)",
    "MLL-ENL": "0.000321 (14|17)",
    "MLL-GAS7": "0.0208 (11|6)"
  },
  "af4_spectral_rank_of_seven": 7,
  "af4_p_rank_within_the_42_pan_fusion": 35,
  "index_bait_note": "0.048 clears the conventional line by four percent. Six of seven baits are above 0.006, so this is a broadly weak row across the whole panel, not just in the index column - which distinguishes it from ZNF512 and LUZP1, where the index column alone is weak.",
  "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"
}

{
  "answer": "YES, but to RARA and not to KMT2A",
  "fusion": "PRKAR1A-RARA, variant acute promyelocytic leukaemia",
  "n_published_cases": "1 index case (Catalano 2007); the fifth variant APL with an identified RARA partner",
  "functional_validation": "transforms mouse bone-marrow progenitor/stem cells; binds RAREs as homodimer and RXRalpha heterodimer; transformation depends on RXRalpha and NOT on the RIIa dimerisation domain (Qiu 2010)",
  "why_it_is_recorded_here": "It establishes that PRKAR1A has a nuclear, DNA-associated capability when fused, which is the only thing making a nuclear pool of the wild-type protein plausible - UniProt annotates none. It is NOT evidence for the MLL-fusion interaction and must not be cited as such.",
  "the_negative_that_matters": "The PRKAR1A dimerisation domain is DISPENSABLE for transformation in the one fusion it forms. A graph that reasons about coiled-coil and dimerisation partners should carry that."
}

{
  "complex": "cAMP-dependent protein kinase (PKA) holoenzyme; A-kinase anchoring",
  "partners_in_the_960": {
    "AKAP8 (AKAP95)": "n=4, NO MLL-AF4 value, neg 0|0 - a nuclear/chromatin AKAP",
    "AKAP8L (HA95)": "n=5, NO MLL-AF4 value, neg 0|0 - inside the post-filter 128",
    "PRKAR1B": "n=1, MLL-AF9 only",
    "PRKAR2A": "n=1, MLL-EEN only"
  },
  "absent_from_the_960": [
    "PRKACA (catalytic alpha)",
    "PRKACB (catalytic beta)",
    "PRKAR2B",
    "AKAP1",
    "AKAP9"
  ],
  "reading": "NO HOLOENZYME, AND A SUBTYPE-MISMATCHED ANCHOR. Neither catalytic subunit is in the network, so this is not PKA co-purifying. The two nuclear AKAPs are present while the membrane and mitochondrial ones are absent, which is the strongest pro-interaction observation available - but neither appears in the MLL-AF4 column, and AKAP95 is a type II anchor while PRKAR1A is type I-alpha. No PKA or AKAP module was tested in analyses/mll-fusion-interactome-complexes/, and this pairing has NOT been tested against a background, so it is an observation and not an enrichment claim (rule 84)."
}

[
  "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",
  "human adult APL marrow - the PRKAR1A-RARA index patient, 88% hypergranular promyelocytes",
  "mouse bone marrow, retroviral transduction/transformation - the PRKAR1A-RARalpha functional work",
  "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": "PRKAR1A"
}

{
  "query": "PRKAR1A[tiab] AND (KMT2A[tiab] OR MLL[tiab] OR \"MLL-AF4\"[tiab] OR \"MLL-AF9\"[tiab] OR \"t(4;11)\"[tiab])",
  "querytranslation": "\"PRKAR1A\"[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,
  "date": "2026-09-21",
  "tool": "NCBI esearch db=pubmed",
  "names_tried": [
    "PRKAR1A",
    "RIalpha (run separately, unscoped, 24 records - none in a KMT2A context)"
  ],
  "bare_operand_control": "PRKAR1A[tiab] AND leukemia[tiab] returns 6, all APL/variant-RARA or thyroid; PRKAR1A[tiab] AND \"Carney complex\"[tiab] returns 350. So the gene clause reaches a large literature and the zero against the KMT2A clause is a real zero.",
  "positive_control": "MEN1[tiab] AND the identical five-term KMT2A clause returns 85.",
  "complex_level_query_not_run": "The complex/pathway forms - 'protein kinase A', 'cAMP signalling' - were NOT run against the KMT2A clause, and rule 64 says a complex subunit's absence needs the complex form. This bound is therefore incomplete and a later beat should close it.",
  "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 PRKACA and PRKACB peptides below the 300-per-bait rank cutoff. Public data. If the catalytic subunits are there sub-threshold this is PKA carryover; if they are genuinely absent, a kinase-independent RI-alpha interaction becomes the interesting hypothesis.",
  "Nuclear/cytoplasmic fractionation blot of PRKAR1A in any human haematopoietic cell. There is no published one, which is remarkable for a protein this well studied, and it is one gel.",
  "Do AKAP8 and AKAP8L have MLL-AF4 values below the rank cutoff? Their absence from the index column is the single fact that kills the nuclear-anchoring story, and it may be a cutoff artefact rather than a real absence."
]