Explorative study of stimulated saliva proteome in head and neck cancer patients pre- and post-treatment.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39640734", "kind": "science-record", "revision": 2, "content_hash": "sha256:15654bec4f5f474995251504d4007d769435dd50c43e351f41df484e101fe7ad", "created_at": "2026-11-01T20:29:55Z", "updated_at": "2026-11-01T21:34:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Explorative study of stimulated saliva proteome in head and neck cancer patients pre- and post-treatment.", "doi": "10.1016/j.heliyon.2024.e39033", "pmid": "39640734", "authors": ["Ulrica Almhöjd", "Amela Fisic", "Hülya Cevik-Aras", "Lisa Tuomi", "Caterina Finizia", "Annica Almståhl"], "journal": "Heliyon", "year": 2024, "abstract": "Objectives: to compare saliva proteome of patients before treatment of head and neck cancer and six months post-treatment with controls.\nDesign: Five dentate patients and five age and gender-matched controls were included. The stimulated salivary secretion rate was determined, and saliva was stored at -80 °C. After thawing, 30 mg of each sample and a reference (aliqouts of all samples) was trypsin digested. The digested peptides were analyzed by mass spectrometry. The relative abundances were transformed to log2 and significant differences determined. Relative abundances of mucins were compared with patient's problems with dry mouth, sticky saliva and swallowing. Data are available via ProteomeXchange with identifier PXD047500.\nResults: 966 proteins with ≥2 unique peptides were found. Compared with controls, 30 proteins were found in significantly lower relative abundances and 65 in higher at pre-treatment and 38 proteins in significantly lower relative abundances and 34 proteins in higher post-treatment. Regarding proteins from the salivary glands, a significantly lower relative abundance of Cystatins was detected pre-treatment and significantly lower relative abundances of Cystatin, Cysteine-rich secretory protein 3, Lactoperoxidase, Prolactin-inducible protein and Proline-rich protein 4 post-treatment. No clear relation between relative abundance of mucins and dry mouth, sticky saliva and problems with swallowing was detected.\nConclusion: Decreases in several salivary gland proteins post cancer treatment might lead to a reduced defense against oral disorders. Knowledge about changes in saliva proteins in connection with oral cancer treatment is important for planning dental care for these patients.", "claims": [{"id": "claim-method", "statement": "The abundance ratios were transformed to log2 and statistical differences between the healthy persons and the cancer patients at pre-treatment and six months post-treatment as well as for the cancer patients at pre-treatment and at six months post-treatment were calculated using Students' unpaired t-test. Correlations between patients' problems with dry mouth, sticky saliva, taste and swallowing of liquids, mashed food, solid food, and choking (score 1–4) and the relative abundances of mucins MUC5B and MUC7 at six months post-treatment were analyzed using Spearman's correlation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39640734", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "The abundance ratios were transformed to log2 and statistical differences between the healthy persons and the cancer patients at pre-treatment and six months post-treatment as well as for the cancer patients at pre-treatment and at six months post-treatment were calculated using Students' unpaired t-test."}, {"asset": "source:pmid:39640734", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Correlations between patients' problems with dry mouth, sticky saliva, taste and swallowing of liquids, mashed food, solid food, and choking (score 1–4) and the relative abundances of mucins MUC5B and MUC7 at six months post-treatment were analyzed using Spearman's correlation."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXChange Consortium via the PRIDE partner repository with the dataset identifier PXD047500.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39640734", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXChange Consortium via the PRIDE partner repository with the dataset identifier PXD047500."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Compared with controls, 30 proteins were found in significantly lower relative abundances and 65 in higher at pre-treatment and 38 proteins in significantly lower relative abundances and 34 proteins in higher post-treatment.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39640734", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Compared with controls, 30 proteins were found in significantly lower relative abundances and 65 in higher at pre-treatment and 38 proteins in significantly lower relative abundances and 34 proteins in higher post-treatment."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Compared with controls, 30 proteins were found in significantly lower relative abundances and 65 in higher at pre-treatment and 38 proteins in significantly lower relative abundances and 34 proteins in higher post-treatment.", "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:39640734"], "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:PXD047500"], "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:PXD047500"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39640734", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e39033", "sha256": "sha256:fddda78abc2f68eb0af23008fdf2fd18d26e61c0288310c4e9c8d33f0a77706a", "bytes": 40815, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e39033", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11620125", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD047500", "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=PXD047500", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD047500", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXChange Consortium via the PRIDE partner repository with the dataset identifier PXD047500.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXChange Consortium via the PRIDE partner repository with the dataset identifier PXD047500.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Explorative study of stimulated saliva proteome in head and neck cancer patients pre-and post-treatment", "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD047500 not downloaded", "asset:data:geo:PXD047500 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The abundance ratios were transformed to log2 and statistical differences between the healthy persons and the cancer patients at pre-treatment and six months post-treatment as well as for the cancer patients at pre-treatment and at six months post-treatment were calculated using Students' unpaired t-test. 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