Proteomics Approach Highlights Early Changes in Human Fibroblasts-Pancreatic Ductal Adenocarcinoma Cells Crosstalk.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35406724", "kind": "science-record", "revision": 4, "content_hash": "sha256:b484275799cea0a4c94b6a1bbc6cc7eb0b4a3d4231e5c0fe4b690eef2bb9bc64", "created_at": "2026-11-01T18:14:13Z", "updated_at": "2026-11-01T22:06:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomics Approach Highlights Early Changes in Human Fibroblasts-Pancreatic Ductal Adenocarcinoma Cells Crosstalk.", "doi": "10.3390/cells11071160", "pmid": "35406724", "authors": ["Verena Damiani", "Maria Concetta Cufaro", "Maurine Fucito", "Beatrice Dufrusine", "Claudia Rossi", "Piero Del Boccio", "Luca Federici", "Maria Caterina Turco", "Michele Sallese", "Damiana Pieragostino", "Vincenzo De Laurenzi"], "journal": "Cells", "year": 2022, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer mortality worldwide. Non-specific symptoms, lack of biomarkers in the early stages, and drug resistance due to the presence of a dense fibrous stroma all contribute to the poor outcome of this disease. The extracellular matrix secreted by activated fibroblasts contributes to the desmoplastic tumor microenvironment formation. Given the importance of fibroblast activation in PDAC pathology, it is critical to recognize the mechanisms involved in the transformation of normal fibroblasts in the early stages of tumorigenesis. To this aim, we first identified the proteins released from the pancreatic cancer cell line MIA-PaCa2 by proteomic analysis of their conditioned medium (CM). Second, normal fibroblasts were treated with MIA-PaCa2 CM for 24 h and 48 h and their proteostatic changes were detected by proteomics. Pathway analysis indicated that treated fibroblasts undergo changes compatible with the activation of migration, vasculogenesis, cellular homeostasis and metabolism of amino acids and reduced apoptosis. These biological activities are possibly regulated by ITGB3 and TGFB1/2 followed by SMAD3, STAT3 and BAG3 activation. In conclusion, this study sheds light on the crosstalk between PDAC cells and associated fibroblasts. Data are available via ProteomeXchange with identifier PXD030974.", "claims": [{"id": "claim-method", "statement": "Moreover, in order to define the differential proteins significantly expressed between the HDF cells or supernatants exposed to MIA-PaCa2 CM or DMEM SF at 24 h or 48 h, a univariate statistical analysis was performed with a p-value threshold of 0.05, visualizing results as a Volcano Plot.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35406724", "locator": "sections[7] \"2.5. Bioinformatics and Proteomics Data Processing\" paragraph 2", "quote": "Moreover, in order to define the differential proteins significantly expressed between the HDF cells or supernatants exposed to MIA-PaCa2 CM or DMEM SF at 24 h or 48 h, a univariate statistical analysis was performed with a p-value threshold of 0.05, visualizing results as a Volcano Plot."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this study are available in this article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35406724", "locator": "sections[22] \"notes\" paragraph 1", "quote": "The data presented in this study are available in this article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Proteomic analysis identified 981 proteins in MIA-PaCa2 conditioned medium.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35406724", "locator": "sections[11] \"3.1. Analysis of Protein Secreted by PDAC Cells\" paragraph 4", "quote": "A total of 981 proteins were identified in MIA-PaCa2 CM (Figure 1A), of which 55% were cytoplasmic proteins, 21% were nuclear, 12% were known to be membrane bound and 11% were extracellular proteins (Figure 1A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Proteomic analysis identified 981 proteins in MIA-PaCa2 conditioned medium.", "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:35406724"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD030974"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD030974"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35406724", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cells11071160", "sha256": "sha256:3d3e869995d3ffd48d86f82ef73542016dc2eac10ad0c2cabe12495717198e6d", "bytes": 31866, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cells11071160", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8997741", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD030974", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD030974", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD030974", "version": null, "note": "The data presented in this study are available in this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available in this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomics approach unravels early changes in Human Fibro-blasts-Pancreatic Ductal Adenocarcinoma cells crosstalk", "resolution_checked_at": "2026-11-01T18:06:51Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD030974 not downloaded", "asset:data:geo:PXD030974 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "univariate statistical analysis with a p-value threshold of 0.05", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Moreover, in order to define the differential proteins significantly expressed between the HDF cells or supernatants exposed to MIA-PaCa2 CM or DMEM SF at 24 h or 48 h, a univariate statistical analysis was performed with a p-value threshold of 0.05, visualizing results as a Volcano Plot."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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