Mass spectrometry analysis of adipose-derived stem cells reveals a significant effect of hypoxia on pathways regulating extracellular matrix.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27075204", "kind": "science-record", "revision": 7, "content_hash": "sha256:6cf432b3feddbafd45d5d715bb5cfb1d1ca3d872671833df5fe986af2c393ea3", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T21:59:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Mass spectrometry analysis of adipose-derived stem cells reveals a significant effect of hypoxia on pathways regulating extracellular matrix.", "doi": "10.1186/s13287-016-0310-7", "pmid": "27075204", "authors": ["Simone Riis", "Allan Stensballe", "Jeppe Emmersen", "Cristian Pablo Pennisi", "Svend Birkelund", "Vladimir Zachar", "Trine Fink"], "journal": "Stem cell research & therapy", "year": 2016, "abstract": "BACKGROUND: Adipose-derived stem cells (ASCs) are being increasingly recognized for their potential to promote tissue regeneration and wound healing. These effects appear to be partly mediated by paracrine signaling pathways, and are enhanced during hypoxia. Mass spectrometry (MS) is a valuable tool for proteomic profiling of cultured ASCs, which may help to reveal the identity of the factors secreted by the cells under different conditions. However, serum starvation which is essentially required to obtain samples compatible with secretome analysis by MS can have a significant influence on ASCs. Here, we present a novel and optimized culturing approach based on the use of a clinically relevant serum-free formulation, which was used to assess the effects of hypoxia on the ASC proteomic profile.\nMETHODS: Human ASCs from three human donors were expanded in StemPro® MSC SFM XenoFree medium. Cells were cultured for 24 h in serum- and albumin-free supplements in either normoxic (20 %) or hypoxic (1 %) atmospheres, after which the cells and conditioned medium were collected, subfractionated, and analyzed using MS. Prior to analysis, the secreted proteins were further subdivided into a secretome (>30 kDa) and a peptidome (3-30 kDa) fraction.\nRESULTS: MS analysis revealed the presence of 342, 98, and 3228 proteins in the normoxic ASC secretome, peptidome, and proteome, respectively. A relatively small fraction of the proteome (9.6 %) was significantly affected by hypoxia, and the most regulated proteins were those involved in extracellular matrix (ECM) synthesis and cell metabolism. No proteins were found to be significantly modulated by hypoxic treatment across all cultures for the secretome and peptidome samples.\nCONCLUSIONS: This study highlights ECM remodeling as a significant mechanism contributing to the ASC regenerative effect after hypoxic preconditioning, and further underscores considerable inter-individual differences in ASC response to hypoxia. The novel culture paradigm provides a basis for future proteomic studies under conditions that do not induce a stress response, so that the best responders can be accurately identified for prospective therapeutic use. Data are available via ProteomeXchange with identifier PXD003550.", "claims": [{"id": "claim-method", "statement": "MS measurements were grouped preservation-method wise, and two-sided t tests were performed to identify statistically significant changing proteins. The statistical tests were corrected for multiple hypothesis testing using permutation-based FDR, and the parameters were chosen to provide sufficient input in the subsequent analysis (FDR = 0.05, s0 = 0.1, and 250 randomizations). The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium [74] via the PRIDE partner repository with the dataset identifier PXD003550.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27075204", "locator": "sections[15] \"Data analysis\" paragraph 3", "quote": "MS measurements were grouped preservation-method wise, and two-sided t tests were performed to identify statistically significant changing proteins."}, {"asset": "source:pmid:27075204", "locator": "sections[15] \"Data analysis\" paragraph 3", "quote": "The statistical tests were corrected for multiple hypothesis testing using permutation-based FDR, and the parameters were chosen to provide sufficient input in the subsequent analysis (FDR = 0.05, s0 = 0.1, and 250 randomizations)."}, {"asset": "source:pmid:27075204", "locator": "sections[25] \"Availability of data\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium [74] via the PRIDE partner repository with the dataset identifier PXD003550."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium [74] via the PRIDE partner repository with the dataset identifier PXD003550.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27075204", "locator": "sections[25] \"Availability of data\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium [74] via the PRIDE partner repository with the dataset identifier PXD003550."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A small fraction (9.6%) of the ASC proteome was significantly affected by hypoxia, with no proteins significantly modulated across all cultures in the secretome and peptidome; protein-level comparisons used label-free quantitative MS analyzed with two-sided t tests, and the source proteomics data are available through ProteomeXchange under identifier PXD003550.", "kind": "quantitative", "target": {"value": 9.6, "unit": "per cent", "tolerance": null, "source": "A relatively small fraction of the proteome (9.6 %) was significantly affected by hypoxia, and the most regulated proteins were those involved in extracellular matrix (ECM) synthesis and cell metabolism."}, "evidence": [{"asset": "source:pmid:27075204", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A relatively small fraction of the proteome (9.6 %) was significantly affected by hypoxia, and the most regulated proteins were those involved in extracellular matrix (ECM) synthesis and cell metabolism."}, {"asset": "source:pmid:27075204", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "No proteins were found to be significantly modulated by hypoxic treatment across all cultures for the secretome and peptidome samples."}, {"asset": "source:pmid:27075204", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "Data are available via ProteomeXchange with identifier PXD003550."}, {"asset": "source:pmid:27075204", "locator": "sections[18] \"Identification of proteins\" paragraph 2", "quote": "Using reverse-phase UPLC, the peptides were separated according to their hydrophobicity."}, {"asset": "source:pmid:27075204", "locator": "sections[21] \"Effect of hypoxic treatment on the ASC proteome\" paragraph 2", "quote": "Statistical analysis of the difference between label-free samples of the proteome fraction from hypoxic preconditioned ASC 21 against the proteome fraction from normoxic preconditioned ASC21 with a two-sided t test."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A small fraction (9.6%) of the ASC proteome was significantly affected by hypoxia, with no proteins significantly modulated across all cultures in the secretome and peptidome; protein-level comparisons used label-free quantitative MS analyzed with two-sided t tests, and the source proteomics data are available through ProteomeXchange under identifier PXD003550.", "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:27075204"], "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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Mass spectrometry (MS) is a valuable tool for proteomic profil", "to assess the effects of hypoxia on the ASC proteomic profile. METHODS: Human ASCs from three huma", "ass spectrometry (MS) is a valuable tool for proteomic profiling of cultured ASCs, which may help t"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Methods Cell culture The cells were cultured in polystyrene tissue flasks (CELLSTAR®, Greine", "tachment. Unless stated otherwise, ASCs were cultured in StemPro+. 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