Transcriptome analysis of mammary epithelial cell gene expression reveals novel roles of the extracellular matrix.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28955800", "kind": "science-record", "revision": 8, "content_hash": "sha256:8b490ed4d170dcc8cc66c04fdeaf1d35b7b3c5f5b91fee3c36df0ca1ab515f4c", "created_at": "2026-11-01T15:40:28Z", "updated_at": "2026-11-01T22:43:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome analysis of mammary epithelial cell gene expression reveals novel roles of the extracellular matrix.", "doi": "10.1016/j.bbrep.2017.08.013", "pmid": "28955800", "authors": ["Stephen S Wanyonyi", "Amit Kumar", "Ryan Du Preez", "Christophe Lefevre", "Kevin R Nicholas"], "journal": "Biochemistry and biophysics reports", "year": 2017, "abstract": "BACKGROUND: The unique lactation strategy of the tammar wallaby (Macropus eugeni) has been invaluable in evaluating the role of lactogenic hormones and the extracellular matrix (ECM) in the local control of mammary gland function. However molecular pathways through which hormones and ECM exert their effect on wallaby mammary gland function remain unclear. This study undertakes transcriptome analysis of wallaby mammary epithelial cells (WallMEC) following treatment with mammary ECM from two distinct stages of lactation.\nMETHODS: WallMEC from MID lactation mammary glands were cultured on ECM from MID or LATE lactation and treated for 5 days with 1 μg/ml cortisol, 1 μg/ml insulin, 0.2 µg/ml prolactin, 650 pg/ml triodothyronine and 1 pg/ml estradiol to induce lactation. WallMEC RNA from triplicate ECM treatments was used to perform RNAseq.\nRESULTS: ECM from MID and LATE lactation differentially regulated key genes in sugar and lipid metabolism. Seven pathways including galactose metabolism, lysosome, cell adhesion molecules (CAM), p53 signaling, the complement and coagulation and Nod-like receptor signaling pathways were only significantly responsive to ECM in the presence of hormones. The raw RNA-seq data for this project are available on the NCBI Gene Expression Omnibus (GEO) browser (accession number GSE81210).\nCONCLUSIONS: A potential role of ECM in regulation of the caloric content of milk, among other functions including apoptosis, cell proliferation and differentiation has been identified.\nGENERAL SIGNIFICANCE: This study has used a non-eutherian lactation model to demonstrate the synergy between ECM and hormones in the local regulation of mammary function.", "claims": [{"id": "claim-method", "statement": "Statistical analysis of qPCR data from replicate samples was performed using one way ANOVA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28955800", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "Statistical analysis of qPCR data from replicate samples was performed using one way ANOVA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw RNA-seq data for this project are available on the NCBI Gene Expression Omnibus (GEO) browser (accession number GSE81210).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28955800", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The raw RNA-seq data for this project are available on the NCBI Gene Expression Omnibus (GEO) browser (accession number GSE81210)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used RNA-seq to assess ECM- and hormone-dependent differential gene expression in WallMECs, with the raw RNA-seq source data available through NCBI GEO under accession GSE81210.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28955800", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "WallMEC RNA from triplicate ECM treatments was used to perform RNAseq."}, {"asset": "source:pmid:28955800", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "ECM from MID and LATE lactation differentially regulated key genes in sugar and lipid metabolism."}, {"asset": "source:pmid:28955800", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The raw RNA-seq data for this project are available on the NCBI Gene Expression Omnibus (GEO) browser (accession number GSE81210)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used RNA-seq to assess ECM- and hormone-dependent differential gene expression in WallMECs, with the raw RNA-seq source data available through NCBI GEO under accession GSE81210.", "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:28955800"], "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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number GSE81210).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw RNA-seq data for this project are available on the NCBI Gene Expression Omnibus (GEO) browser (accession number GSE81210).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2144708", "GSM2144709", "GSM2144710", "GSM2144711"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "21832", "taxon": "Notamacropus eugenii", "title": "Transcriptome analysis of extracellular matrix (ECM)-induced changes in mammary epithelial cell gene expression", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:28955800:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ffd7bb020cbb6768a23d977946bedfe3b9acbb5f2b2065913ad404ed866f8668", "bytes": 480, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#t0005", "version": null, "note": ": Genes down-regulated by ECM grouped according to functional pathways.", "structure": {"pmcid": "PMC5613237", "section_index": 14, "section_title": "Differentially regulated functional pathways", "row_count": 6, "column_count": 2}, "table": {"label": "Table 1A", "caption": ": Genes down-regulated by ECM grouped according to functional pathways.", "rows": [["MID_ NH versus LATE_NH", "Regulated genes"], ["No pathway", "–"], ["MID_H versus LATE_H", "Regulated genes"], ["Lysosome", "cathepsins, ACP5, ASAH1, LAPTM"], ["Complement and coagulation pathway", "C1S, C2, C3,"], ["Cell adhesion molecules", "PVRL1, CNTN1, CDH3,"]], "row_count": 6, "column_count": 2, "numeric_cells": 0, "header_rows": 1, "locator": "section[14]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:28955800:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f2e97bdb3aaf5f146e545d9454fbc3a171feddb1b61849b28d6f43769861eaa6", "bytes": 1831, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#t0010", "version": null, "note": ": Genes up-regulated by ECM grouped according to functional pathways.", "structure": {"pmcid": "PMC5613237", "section_index": 14, "section_title": "Differentially regulated functional pathways", "row_count": 23, "column_count": 2}, "table": {"label": "Table 1B", "caption": ": Genes up-regulated by ECM grouped according to functional pathways.", "rows": [["MID_ NH versus LATE_NH", "Regulated genes"], ["Jak-STAT signaling pathway", "IL6, CytokineR, PI3K, CycD"], ["Cytokine-cytokine receptor interaction", "IL6, IL11, LIF, BSF3, CSF3, GHR, CSF2RB, 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This study undertakes transcriptome analysis of wallaby mammary epithelial cells", "riplicate ECM treatments was used to perform RNAseq. RESULTS: ECM from MID and LATE lactation di", "to ECM in the presence of hormones. The raw RNA-seq data for this project are available on the N"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ent of milk, among other functions including apoptosis, cell proliferation and differentiation has"], "order_basis": "paper_text_order:1517", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Statistical analysis Statistical analysis of qPCR data from replicate samples was performed us"], "order_basis": "paper_text_order:2126", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical analysis of qPCR data from replicate samples was performed using one way ANOVA."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}