{
  "schemaVersion": 1,
  "id": "mva-results-2026-10-10-n1002k-eqexp-v1",
  "dataAsOf": "2026-10-10",
  "publicationReview": "public-summary-reviewed",
  "scope": "Public literature, computational reanalyses and explicitly labeled synthetic software checks only. Wet-lab validation is deferred. No private genomic data are included. The GSE65145 summary and N1002K equal-expression audit were checked by the research assistant for source support, privacy and scientific limits; neither has received independent human scientific review.",
  "records": [
    {
      "id": "MVA-NMD-003",
      "title": "704-drug NMD screen: reporter specificity",
      "kind": "Reanalysis",
      "status": "Completed",
      "recordedOn": "2026-10-09",
      "evidence": "COMPUTATIONAL / PATHWAY EVIDENCE",
      "model": "Published mouse Neuro-2a AS-NMD isoform summaries; three reporter genes, not BUB1B.",
      "finding": "Montelukast has a published permutation q of 0.021150, but the response is reporter-dependent and confounded by non-NMD isoform changes. No hit establishes functional BUBR1 rescue.",
      "decision": "Conditional",
      "limitations": [
        "Normalized RNA ratios cannot isolate decay from splicing or isoform regulation.",
        "Replicate Ct values are unavailable. Published ratio SEM formulas do not provide valid replicate-based uncertainty; no error bars are shown.",
        "Translation inhibition is counterevidence for homoharringtonine. Statistical significance is not therapeutic suitability."
      ],
      "next": "Establish L737* residual function first; any NMD candidate then needs allele-specific RNA, protein synthesis, and separate checkpoint/segregation endpoints.",
      "sourceIds": [
        "zhao-2021"
      ],
      "provenance": {
        "artifact": "nmd_reanalysis_20261009/results/selected_candidates.csv",
        "sha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
        "method": "Extracted named compounds and ratios from the existing independently reconstructed Table S2/S4 analysis; published q values are not clinical probabilities.",
        "verification": "Imported an existing analysis artifact and computed its SHA-256. This snapshot build does not rerun the original analysis or validate biological efficacy."
      }
    },
    {
      "id": "MVA-RT-002",
      "title": "L737* readthrough: exact versus nearby contexts",
      "kind": "Reanalysis",
      "status": "Completed",
      "recordedOn": "2026-10-09",
      "evidence": "COMPUTATIONAL / PATHWAY EVIDENCE",
      "model": "Published 144-nt PTC reporters in human cells; nearest-context subset, not endogenous BUB1B.",
      "finding": "No exact L737* measurement or exact six-flanking-base match in the 5,837-PTC table. Twelve nearest contexts have a median paired gentamicin increment of 0.0165 percentage points.",
      "decision": "Deprioritized",
      "limitations": [
        "Neighboring-context values are not a prediction for L737* or the child.",
        "The main predictive analysis excluded gentamicin for weak signal.",
        "Readthrough does not guarantee native leucine, endogenous transcript survival, or functional BUBR1. Gentamicin plus mefloquine remains an experimental branch only."
      ],
      "next": "Use the exact L737* context with matched controls and independently test full-length protein, checkpoint response and segregation fidelity.",
      "sourceIds": [
        "toledano-2024",
        "omachi-2022"
      ],
      "provenance": {
        "artifact": "l737_readthrough_gate_2026-10-09/results/results.json",
        "sha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
        "method": "Extracted medians from the existing nearest-context reanalysis. The paired median increment is not the difference of group medians.",
        "verification": "Imported an existing analysis artifact and computed its SHA-256. This snapshot build does not rerun the original analysis or validate biological efficacy."
      }
    },
    {
      "id": "MVA-CTRL-006",
      "title": "BUBR1 functional controls: arrest duration",
      "kind": "Reanalysis",
      "status": "Completed",
      "recordedOn": "2026-10-09",
      "evidence": "COMPUTATIONAL / DIRECT-BUBR1",
      "model": "Published HeLa BUBR1 depletion/replacement with WT or engineered TPR variants under nocodazole challenge.",
      "finding": "Figure 4B source-data medians are 650 minutes for WT and 60 minutes for D137R. A control for checkpoint competence, not a drug-rescue result.",
      "decision": "Control only",
      "limitations": [
        "D137R is not N1002K; no tested drug or exact patient genotype.",
        "Cells in the displayed representative replicate are not independent biological replicates.",
        "Mitotic-arrest duration under spindle challenge is not chromosome-segregation fidelity in unperturbed divisions."
      ],
      "next": "Require independent checkpoint and chromosome-segregation readouts in future equal-expression assays.",
      "sourceIds": [
        "bubr1-tpr-2026"
      ],
      "provenance": {
        "artifact": "bubr1_checkpoint_kinetics_2026-10-09/results.json",
        "sha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
        "method": "Selected the Figure 4B rows from a completed deterministic source-workbook reanalysis; no kinetic rate or new confidence interval inferred.",
        "verification": "Imported an existing analysis artifact and computed its SHA-256. This snapshot build does not rerun the original analysis or validate biological efficacy."
      }
    },
    {
      "id": "MVA-N1002K-GATE-002",
      "title": "N1002K stabilization: equal-expression gate",
      "kind": "Evidence audit",
      "status": "Completed",
      "recordedOn": "2026-10-10",
      "evidence": "DIRECT-BUBR1 COMPARATORS / RELATED-VARIANT IN VIVO / TARGETED AUDIT",
      "model": "Published human-cell BUBR1 depletion/replacement studies, MVA fibroblast rescue and a mouse L1012P comparator model; none tests N1002K.",
      "finding": "No exact-N1002K functional experiment was located. I909T/L1012P checkpoint rescue at matched abundance makes an abundance-limited mechanism plausible, but equally expressed B56-binding mutants still failed chromosome-congression rescue and mouse L1012P showed allelic effects beyond total protein level. Stabilization remains conditional; no drug is promoted.",
      "decision": "Conditional",
      "limitations": [
        "This targeted audit is not a systematic review; failure to locate an exact-N1002K study does not prove that none exists.",
        "I909T and L1012P are comparator variants, not substitutes for N1002K.",
        "B56-binding mutants lie in a different region and demonstrate only that equal abundance is not universally sufficient.",
        "Mouse L1002P models human L1012P, not human N1002K.",
        "Checkpoint-only rescue must not be relabeled as chromosome-alignment or segregation rescue.",
        "The published 6% versus 13% titration is cell-line-specific, not a universal functional or clinical threshold."
      ],
      "next": "At measured matched abundance, compare WT, N1002K and L1012P in one depletion-replacement system; report nocodazole checkpoint arrest separately from chromosome alignment and missegregation per completed division. Wet-lab work is deferred.",
      "sourceIds": [
        "suijkerbuijk-2010",
        "xu-2013",
        "sieben-2020"
      ],
      "provenance": {
        "artifact": "n1002k_equal_expression_audit_2026-10-10/audit.json",
        "sha256": "30a149370a4bd736fbe39618c2e0ed549008066ea004bd24a5e699308657c73d",
        "method": "Targeted exact-variant search plus primary-study comparison of abundance-matched BUBR1 rescue and counterexamples; no biological simulation was executed.",
        "verification": "Primary-source claims were checked against PMID 20516114 Figures 2D/3/4D, PMID 23789096 Figures 2/4 and PMID 31738183 Figures 1-3. Artifact bytes were hashed directly. No independent human scientific review or biological efficacy validation is claimed."
      }
    },
    {
      "id": "MVA-L737-NMD-FIRST-001",
      "title": "L737* NMD-first: test truncated-protein function",
      "kind": "Evidence audit",
      "status": "Completed",
      "recordedOn": "2026-10-09",
      "evidence": "DIRECT-BUBR1 COMPARATOR / OUR INFERENCE",
      "model": "Published 731X/753X BUBR1 constructs and a proposed exact-L737* validation design.",
      "finding": "A related 731X construct motivates testing whether L737* retains useful function when NMD is bypassed. The exact L737* experiment has not been performed.",
      "decision": "Conditional",
      "limitations": [
        "731X is a frameshift product with about 715 native residues, not a clean L737* surrogate.",
        "NMD sensitivity is predicted, not measured for this child.",
        "More nonsense transcript can increase nonfunctional protein; NMD inhibition does not itself remove a stop codon."
      ],
      "next": "Test WT, clean L737*, 731X and 753X at matched abundance; advance NMD modulation only if the exact truncation retains useful function.",
      "sourceIds": [
        "suijkerbuijk-2010"
      ],
      "provenance": {
        "artifact": "l737_nmd_first_gate_2026-10-09/experiment.json",
        "sha256": "68b890531733aec6fc1f4a6cace8ce8e85bdcccf63bb61900688b831aa383a69",
        "method": "Imported an evidence-supported proposed design. Completed refers to the audit, not execution of the wet-lab validation.",
        "verification": "Imported an existing analysis artifact and computed its SHA-256. This snapshot build does not rerun the original analysis or validate biological efficacy."
      }
    },
    {
      "id": "MVA-ARI-007",
      "title": "Arimoclomol: target engagement and exposure gap",
      "kind": "Evidence audit",
      "status": "Completed",
      "recordedOn": "2026-10-09",
      "evidence": "PATHWAY EVIDENCE / COMPUTATIONAL / OUR INFERENCE",
      "model": "Human-cell heat-shock studies and a nominal molar conversion of FDA-label serum concentrations.",
      "finding": "No direct BUBR1 or N1002K rescue evidence was located in the audit. Heat-shock responses are context-dependent; arimoclomol is not promoted to lead candidate.",
      "decision": "Deprioritized",
      "limitations": [
        "Published human-cell systems report both conditional induction and negative responses.",
        "Total serum exposure and nominal cell-culture concentration are not pharmacokinetically interchangeable.",
        "Approval for a different disease does not establish MVA efficacy."
      ],
      "next": "Require target engagement at relevant exposure plus exact-variant functional rescue before reconsidering prioritization.",
      "sourceIds": [
        "deane-2016",
        "steurer-2022",
        "arimoclomol-label"
      ],
      "provenance": {
        "artifact": "arimoclomol_n1002k_gate_2026-10-09/results.json",
        "sha256": "6ce51099f036cd0082358c22176f9f58e3065fc545a32781d40014c020233764",
        "method": "Imported the existing nominal concentration conversion; no tissue distribution, free-drug exposure or rescue model was calculated.",
        "verification": "Imported an existing analysis artifact and computed its SHA-256. This snapshot build does not rerun the original analysis or validate biological efficacy."
      }
    },
    {
      "id": "MVA-FUNC-005",
      "title": "Cytostasis confounding: denominator unit test",
      "kind": "Software test",
      "status": "Completed",
      "recordedOn": "2026-10-08",
      "evidence": "SYNTHETIC SOFTWARE FIXTURE",
      "model": "Invented test counts used only to test code; not an experiment or a biological simulation.",
      "finding": "The synthetic fixture flags fewer raw error-positive divisions without a lower error rate per completed division. It does not measure sirolimus activity.",
      "decision": "Control only",
      "limitations": [
        "All fixture counts are synthetic.",
        "No drug response, BUBR1 rescue, or patient outcome can be inferred from a passing software test."
      ],
      "next": "Reuse the denominator checks with prospectively designed real measurements when wet-lab work becomes available.",
      "sourceIds": [],
      "provenance": {
        "artifact": "mitosis_adjudicator_2026-10-08/examples/cytostasis_results.json",
        "sha256": "dfb5fa29aa719fc59d206cf34a8d33b1ce59bda41d5665f685a219c6770a753b",
        "method": "Imported the labeled fixture output, checked the synthetic flag, and excluded synthetic quantities from the scientific charts.",
        "verification": "Imported an existing analysis artifact and computed its SHA-256. This snapshot build does not rerun the original analysis or validate biological efficacy."
      }
    },
    {
      "id": "MVA-RAP-GSE65145-001",
      "title": "Rapamycin in human fibroblasts: BUB1B locus RNA signal",
      "kind": "Reanalysis",
      "status": "Completed",
      "recordedOn": "2026-10-10",
      "evidence": "Public human perturbation data; descriptive locus-level RNA reanalysis, not functional rescue.",
      "model": "Normal 2DD fibroblasts: proliferative vehicle, 0.5% serum, or 500 nM rapamycin for five days; two biological replicates per condition.",
      "finding": "The primary BUB1B-spanning feature has a Rap/Pro mean ratio of 0.585706 (41.43% lower); reduced-serum/Pro is 0.186191. Three nearly full-span features give the same direction. This does not support an RNA-abundance-increase rationale for sirolimus in this model.",
      "decision": "Conditional",
      "limitations": [
        "Unstranded genomic-span features, not direct BUBR1 protein measurements or validated mature transcript isoform estimates.",
        "Three overlapping features are sensitivity views of the same locus, not independent biological replicates.",
        "Two biological replicates per condition from one normal cell line; no MVA genotype and no donor-level replication.",
        "Serum reduction is a useful control but is not matched to rapamycin for cell-cycle distribution; no causal proliferation adjustment is claimed.",
        "Continuous 500 nM/five-day treatment; no washout, transient exposure, aneuploidy, mitotic checkpoint or rescue endpoint.",
        "Published normalized RPKM values are used as deposited without re-alignment, count-based differential expression, an added pseudocount, p-values or rescue probabilities.",
        "149122 rows were observed in each deposited track; the paper states 149135 probes. The 13-row difference is not resolved here.",
        "This does not establish that BUBR1 protein falls, rule out post-transcriptional effects, or predict clinical harm or benefit."
      ],
      "next": "Keep sirolimus conditional. Proposed: compare full-length BUBR1 protein and segregation errors per completed division after transient exposure and washout at matched cell-cycle distribution. Wet-lab work is deferred.",
      "sourceIds": [
        "gillespie-2015"
      ],
      "provenance": {
        "artifact": "MVA_GSE65145_BUB1B_2026-10-10.zip/gse65145_bub1b_results.json",
        "sha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
        "method": "Parse six deposited hg19 RPKM tracks; require >=99% reciprocal overlap with RefSeq NM_001211.6; select minimum boundary-distance feature and calculate ratios of arithmetic means. Check all three qualifying features.",
        "verification": "All six coordinate arrays match; each has 149122 rows. Eighteen rows overlap the anchor and three qualify. GEO sample titles and artifact hashes verified. Complete reproducible package saved separately; no human scientific review or new biological experiment is claimed."
      }
    }
  ],
  "sources": [
    {
      "id": "zhao-2021",
      "title": "Zhao et al. — molecular profiling of NMD modulators",
      "pmid": "35024243",
      "doi": "10.1016/j.omtn.2021.12.003",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8718828/",
      "model": "Mouse Neuro-2a; three AS-NMD isoform reporters",
      "location": "Tables S1/S2/S4; Figures 2–5 and 7"
    },
    {
      "id": "toledano-2024",
      "title": "Toledano et al. — genome-scale PTC readthrough",
      "pmid": "39174735",
      "doi": "10.1038/s41588-024-01878-5",
      "url": "https://www.nature.com/articles/s41588-024-01878-5",
      "model": "Human HEK293T landing-pad reporters; not endogenous BUB1B",
      "location": "Supplementary Table 3; Extended Data Figure 4"
    },
    {
      "id": "omachi-2022",
      "title": "Omachi et al. — COL4A5 readthrough reporters",
      "pmid": "35243249",
      "doi": "10.1016/j.isci.2022.103891",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8866893/",
      "model": "HEK293 COL4A5 cDNA reporters; different gene and context",
      "location": "Figure 6: gentamicin plus mefloquine"
    },
    {
      "id": "suijkerbuijk-2010",
      "title": "Suijkerbuijk et al. — molecular causes of BUBR1 dysfunction",
      "pmid": "20516114",
      "doi": "10.1158/0008-5472.CAN-09-4319",
      "url": "https://doi.org/10.1158/0008-5472.CAN-09-4319",
      "model": "U2OS/HeLa BUBR1 depletion and replacement",
      "location": "Figures 4D and 5; comparator variants, not N1002K"
    },
    {
      "id": "xu-2013",
      "title": "Xu et al. — BUBR1 recruits PP2A-B56 for chromosome congression",
      "pmid": "23789096",
      "doi": "10.1242/bio.20134051",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3654266/",
      "model": "HeLa BUBR1 depletion/reconstitution and BUB1B-mutated MVA fibroblast rescue",
      "location": "Figures 2 and 4; equally expressed B56-binding mutants are functional counterexamples"
    },
    {
      "id": "sieben-2020",
      "title": "Sieben et al. — allelic effects in MVA progeria syndrome",
      "pmid": "31738183",
      "doi": "10.1172/JCI126863",
      "url": "https://www.jci.org/articles/view/126863",
      "model": "Mouse BubR1 L1002P ortholog model of human L1012P with hypomorphic or truncating alleles",
      "location": "Abstract and Figures 1-3; related variant, not N1002K"
    },
    {
      "id": "bubr1-tpr-2026",
      "title": "BUBR1 TPR / MCC–APC/C functional controls",
      "pmid": "42477419",
      "doi": "10.1038/s42003-026-10384-9",
      "url": "https://www.nature.com/articles/s42003-026-10384-9",
      "model": "HeLa endogenous BUBR1 RNAi and RNAi-resistant YFP replacement",
      "location": "Figure 4B; supplementary source-data workbook, Sheet1"
    },
    {
      "id": "deane-2016",
      "title": "Deane and Brown — conditional heat-shock co-induction",
      "pmid": "27273088",
      "doi": "10.1007/s12192-016-0708-2",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5003800/",
      "model": "Differentiated human SH-SY5Y cells; arimoclomol plus celastrol",
      "location": "Figures 2–5; not a BUBR1 study"
    },
    {
      "id": "steurer-2022",
      "title": "Steurer et al. — HSF1 reporter evaluation",
      "pmid": "35218516",
      "doi": "10.1007/s12033-022-00467-3",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9259536/",
      "model": "Human HSF-responsive reporter and endogenous target systems",
      "location": "Table 1 and Figure 4: negative arimoclomol response in this system"
    },
    {
      "id": "arimoclomol-label",
      "title": "FDA — MIPLYFFA prescribing information (2024)",
      "pmid": null,
      "doi": null,
      "url": "https://www.accessdata.fda.gov/drugsatfda_docs/label/2024/214927s000lbl.pdf",
      "model": "Regulatory label; human serum pharmacokinetics, different indication",
      "location": "Clinical pharmacology; historical label used by the 2026-10-09 audit"
    },
    {
      "id": "gillespie-2015",
      "title": "Gillespie et al. — rapamycin and normal human fibroblast transcription",
      "pmid": "26652669",
      "doi": "10.1080/19491034.2015.1128610",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4915505/",
      "model": "2DD normal human foreskin fibroblasts; two biological replicates per condition",
      "location": "GSE65145 processed tracks; Figures 1 and 3; Figure S2; Cell culture and RNA-seq methods"
    }
  ],
  "charts": [
    {
      "id": "nmd-reporters",
      "title": "One drug, three different reporter responses",
      "recordId": "MVA-NMD-003",
      "unit": "NMD / non-NMD normalized RNA ratio",
      "baseline": 1,
      "series": [
        "Ptbp2",
        "Hnrnpl",
        "Tra2b"
      ],
      "rows": [
        {
          "label": "Montelukast sodium",
          "values": [
            1.3153820850896314,
            3.406494677098417,
            1.7654686351224798
          ],
          "note": "Published permutation q = 0.02115; not a BUBR1 endpoint."
        },
        {
          "label": "Artesunate",
          "values": [
            1.718112969537028,
            1.0078988102818638,
            4.2875477079256585
          ],
          "note": "Published permutation q = 0.010071; not a BUBR1 endpoint."
        },
        {
          "label": "Cladribine",
          "values": [
            2.126124275101715,
            2.0820411294900216,
            1.6377191943091594
          ],
          "note": "Published permutation q = 0.010071; not a BUBR1 endpoint."
        },
        {
          "label": "Albendazole",
          "values": [
            1.5634627380948676,
            1.701726223666598,
            3.2992143735876955
          ],
          "note": "Published permutation q = 0.015667; not a BUBR1 endpoint."
        },
        {
          "label": "Topotecan hydrochloride",
          "values": [
            3.9533398228039465,
            2.3994174963086077,
            0.6542839291174242
          ],
          "note": "Published permutation q = 0.0 (finite-sampling zero, not zero uncertainty); not a BUBR1 endpoint."
        },
        {
          "label": "Homoharringtonine",
          "values": [
            5.0039366160196295,
            24.97590928901173,
            11.672927661494484
          ],
          "note": "Published permutation q = 0.0 (finite-sampling zero, not zero uncertainty); not a BUBR1 endpoint."
        },
        {
          "label": "Mefloquine hydrochloride",
          "values": [
            1.181600971576268,
            1.3075083215610865,
            1.5102164979716604
          ],
          "note": "Published permutation q = 0.061224; not a BUBR1 endpoint."
        },
        {
          "label": "Nicotinic acid",
          "values": [
            1.1859031685137231,
            1.4152893426077033,
            0.9171679519898492
          ],
          "note": "Published permutation q = 0.08225; not a BUBR1 endpoint."
        }
      ],
      "note": "Selected compounds from a 704-drug mouse-cell screen, not a therapeutic ranking. Ratios can rise when the denominator falls. No BUB1B was measured; no valid replicate-based ratio error bars are available."
    },
    {
      "id": "nearby-readthrough",
      "title": "Nearby contexts are not the exact variant",
      "recordId": "MVA-RT-002",
      "unit": "Median reporter readthrough (%)",
      "baseline": null,
      "series": [
        "Median"
      ],
      "rows": [
        {
          "label": "Untreated",
          "values": [
            0.1745
          ],
          "note": "12 nearest measured six-base contexts; exact L737* context absent."
        },
        {
          "label": "Gentamicin",
          "values": [
            0.1985
          ],
          "note": "Same 12 contexts, not BUB1B efficacy or a patient prediction."
        }
      ],
      "note": "Median paired increment: 0.0165 percentage points; it is not the difference of the two medians. The six-base analogy ignores the rest of the reporter sequence. No rescue probability is computed."
    },
    {
      "id": "checkpoint-controls",
      "title": "Checkpoint competence needs its own control",
      "recordId": "MVA-CTRL-006",
      "unit": "Median NEBD-to-exit time (minutes)",
      "baseline": null,
      "series": [
        "Median"
      ],
      "rows": [
        {
          "label": "Wild type",
          "values": [
            650
          ],
          "note": "27 cells; representative replicate, not independent biological replicates."
        },
        {
          "label": "D137R",
          "values": [
            60
          ],
          "note": "39 cells; representative replicate, not independent biological replicates."
        }
      ],
      "note": "Published Figure 4B under nocodazole challenge. WT and D137R are not drug-treatment arms. These cell counts do not establish between-replicate precision; no confidence interval is inferred."
    },
    {
      "id": "rapamycin-bub1b-locus",
      "title": "BUB1B-spanning RNA feature in normal human fibroblasts",
      "recordId": "MVA-RAP-GSE65145-001",
      "unit": "RPKM as deposited; genomic-span RNA feature",
      "note": "GSE65145; two biological replicates per condition from one normal cell line. Continuous rapamycin for five days; no washout. The selected unstranded feature spans chr15:40453238–40513321 (hg19). No protein, checkpoint-rescue or statistical-significance claim. Overlapping features are not extra replicates.",
      "baseline": null,
      "series": [
        "Biological replicate 1",
        "Biological replicate 2"
      ],
      "rows": [
        {
          "label": "Proliferative vehicle",
          "values": [
            6.227185,
            5.570779
          ],
          "note": "10% FBS; DMSO vehicle."
        },
        {
          "label": "Reduced serum",
          "values": [
            1.2674783,
            0.9291951
          ],
          "note": "0.5% FBS for five days; not matched for cell-cycle distribution."
        },
        {
          "label": "Rapamycin 500 nM",
          "values": [
            3.7114706,
            3.198672
          ],
          "note": "500 nM for five days; 10% FBS. Mean is 0.585706 times proliferative control."
        }
      ]
    }
  ]
}