E47 Governs the MYC-CDKN1B/p27KIP1-RB Network to Growth Arrest PDA Cells Independent of CDKN2A/p16INK4A and Wild-Type p53.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30003124", "kind": "science-record", "revision": 8, "content_hash": "sha256:62f43bf5f96b12d10e87dd31dd2951249f97ac4dbf0efe336b83a17c873ce434", "created_at": "2026-11-01T15:40:35Z", "updated_at": "2026-11-01T22:43:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "E47 Governs the MYC-CDKN1B/p27KIP1-RB Network to Growth Arrest PDA Cells Independent of CDKN2A/p16INK4A and Wild-Type p53.", "doi": "10.1016/j.jcmgh.2018.05.002", "pmid": "30003124", "authors": ["Kathleen M Scully", "Reyhaneh Lahmy", "Lia Signaevskaia", "Roman Sasik", "Rachel Medal", "Heejung Kim", "Randall French", "Brian James", "Yifan Wu", "Andrew M Lowy", "Pamela Itkin-Ansari"], "journal": "Cellular and molecular gastroenterology and hepatology", "year": 2018, "abstract": "BACKGROUND & AIMS: Oncogenic mutations in KRAS, coupled with inactivation of p53, CDKN2A/p16INK4A, and SMAD4, drive progression of pancreatic ductal adenocarcinoma (PDA). Overexpression of MYC and deregulation of retinoblastoma (RB) further promote cell proliferation and make identifying a means to therapeutically alter cell-cycle control pathways in PDA a significant challenge. We previously showed that the basic helix-loop-helix transcription factor E47 induced stable growth arrest in PDA cells in vitro and in vivo. Here, we identified molecular mechanisms that underlie E47-induced growth arrest in low-passage, patient-derived primary and established PDA cell lines.\nMETHODS: RNA sequencing was used to profile E47-dependent transcriptomes in 5 PDA cell lines. Gene Ontology analysis identified cell-cycle control as the most altered pathway. Small interfering RNA/short hairpin RNA knockdown, small-molecule inhibitors, and viral expression were used to examine the function of E47-dependent genes in cell-cycle arrest. Cell morphology, expression of molecular markers, and senescence-associated β-galactosidase activity assays identified cellular senescence.\nRESULTS: E47 uniformly inhibited PDA cell-cycle progression by decreasing expression of MYC, increasing the level of CDKN1B/p27KIP1, and restoring RB tumor-suppressor function. The molecular mechanisms by which E47 elicited these changes included altering both RNA transcript levels and protein stability of MYC and CDKN1B/p27KIP1. At the cellular level, E47 elicited a senescence-like phenotype characterized by increased senescence-associated β-galactosidase activity and altered expression of senescence markers.\nCONCLUSIONS: E47 governs a highly conserved network of cell-cycle control genes, including MYC, CDKN1B/p27KIP1, and RB, which can induce a senescence-like program in PDA cells that lack CDKN2A/p16INK4A and wild-type p53. RNA sequencing data are available at the National Center for Biotechnology Information GEO at https://www.ncbi.nlm.nih.gov/geo/; accession number: GSE100327.", "claims": [{"id": "claim-method", "statement": "Differential expression was assessed with an R package limma applied to log2-transformed counts. The statistical significance of each test was expressed in terms of local false discovery rate (lfdr) using the limma function Empirical Bayes Statistics for Differential Expression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30003124", "locator": "sections[15] \"RNA-Seq Analysis\" paragraph 2", "quote": "Differential expression was assessed with an R package limma applied to log2-transformed counts. The statistical significance of each test was expressed in terms of local false discovery rate (lfdr) using the limma function Empirical Bayes Statistics for Differential Expression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA sequencing data are available at the National Center for Biotechnology Information GEO at https://www.ncbi.nlm.nih.gov/geo/; accession number: GSE100327.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30003124", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "RNA sequencing data are available at the National Center for Biotechnology Information GEO at https://www.ncbi.nlm.nih.gov/geo/; accession number: GSE100327."}], "state": "complete"}, {"id": "claim-target-result", "statement": "E47 uniformly inhibited PDA cell-cycle progression by decreasing MYC expression, increasing CDKN1B/p27KIP1, and restoring RB tumor-suppressor function.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:30003124", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "E47 uniformly inhibited PDA cell-cycle progression by decreasing expression of MYC, increasing the level of CDKN1B/p27KIP1, and restoring RB tumor-suppressor function."}, {"asset": "source:pmid:30003124", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "RNA sequencing was used to profile E47-dependent transcriptomes in 5 PDA cell lines."}, {"asset": "source:pmid:30003124", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Gene Ontology analysis identified cell-cycle control as the most altered pathway."}, {"asset": "source:pmid:30003124", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "RNA sequencing data are available at the National Center for Biotechnology Information GEO at https://www.ncbi.nlm.nih.gov/geo/; accession number: GSE100327."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "E47 uniformly inhibited PDA cell-cycle progression by decreasing MYC expression, increasing CDKN1B/p27KIP1, and restoring RB tumor-suppressor function.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30003124"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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"Antibodies Used", "rows": [["Immunogen", "Source", "Supplier", "Dilution"], ["p53 ab-6 (clone DO-1)", "Mouse", "Thermofisher (Waltham, MA)/NeoMarkers (MS-187-P0)", "Western blot 1:1000"], ["p16", "Rabbit", "Abcam (Cambridge, MA) (ab81278)", "Western blot 1:10,000"], ["SMAD4", "Rabbit", "One World Lab (San Diego, CA) (ID 54398)", "Western blot 1:3000"], ["Vinculin", "Rabbit", "Cell Signaling Technology (Danvers, MA) (4650S)", "Western blot 1:2000"], ["p21", "Mouse", "Santa Cruz Biotech (Santa Cruz, CA) (sc-6246)", "Western blot 1:50"], ["P27", "Rabbit", "GeneTex (Irvine, CA) (GTX100446)", "Western blot 1:2000/ICC 1:400"], ["CEBP-α", "Rabbit", "Abcam (ab40761)", "Western blot 1:1000"], ["Lamin B1", "Rabbit", "Abcam (ab16048)", "Western blot 1:1000"], ["CENP-A", "Rabbit", "Cell Signaling Technology (2186P)", "Western blot 1:1000"], ["RB pSER807/811", "Rabbit", "Cell Signaling Technology (8516S)", "Western blot 1:2000"], ["RB pSER608", "Rabbit", "Cell Signaling Technology (2181S)", 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Here, we identified molecular mechanisms th"], "order_basis": "paper_text_order:593", "id": "assay:1"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ie E47-induced growth arrest in low-passage, patient-derived primary and established PDA cell lines. METH", "tus of PDA Driver Loci Determined in Primary Patient-Derived Cell Lines To begin mechanistic studies, we", "dies, we characterized 2 clinically relevant patient-derived cell lines that were recently generated from"], "order_basis": "paper_text_order:699", "id": "assay:2"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ary and established PDA cell lines. METHODS: RNA sequencing was used to profile E47-dependent transcript", "that lack CDKN2A/p16INK4A and wild-type p53. RNA sequencing data are available at the National Center fo", "sequencing was used to profile E47-dependent transcriptomes in 5 PDA cell lines. 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