The Secretome Profiling of a Pediatric Airway Epithelium Infected with hRSV Identified Aberrant Apical/Basolateral Trafficking and Novel Immune Modulating (CXCL6, CXCL16, CSF3) and Antiviral (CEACAM1) Proteins.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32075873", "kind": "science-record", "revision": 7, "content_hash": "sha256:d296b9b7fcdc90278446aba4caaaa66e6beb4c18731d6f599c56ee50f84f491c", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T22:01:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Secretome Profiling of a Pediatric Airway Epithelium Infected with hRSV Identified Aberrant Apical/Basolateral Trafficking and Novel Immune Modulating (CXCL6, CXCL16, CSF3) and Antiviral (CEACAM1) Proteins.", "doi": "10.1074/mcp.RA119.001546", "pmid": "32075873", "authors": ["Olivier Touzelet", "Lindsay Broadbent", "Stuart D Armstrong", "Waleed Aljabr", "Elaine Cloutman-Green", "Ultan F Power", "Julian A Hiscox"], "journal": "Molecular & cellular proteomics : MCP", "year": 2020, "abstract": "The respiratory epithelium comprises polarized cells at the interface between the environment and airway tissues. Polarized apical and basolateral protein secretions are a feature of airway epithelium homeostasis. Human respiratory syncytial virus (hRSV) is a major human pathogen that primarily targets the respiratory epithelium. However, the consequences of hRSV infection on epithelium secretome polarity and content remain poorly understood. To investigate the hRSV-associated apical and basolateral secretomes, a proteomics approach was combined with an ex vivo pediatric human airway epithelial (HAE) model of hRSV infection (data are available via ProteomeXchange and can be accessed at https://www.ebi.ac.uk/pride/ with identifier PXD013661). Following infection, a skewing of apical/basolateral abundance ratios was identified for several individual proteins. Novel modulators of neutrophil and lymphocyte activation (CXCL6, CSF3, SECTM1 or CXCL16), and antiviral proteins (BST2 or CEACAM1) were detected in infected, but not in uninfected cultures. Importantly, CXCL6, CXCL16, CSF3 were also detected in nasopharyngeal aspirates (NPA) from hRSV-infected infants but not healthy controls. Furthermore, the antiviral activity of CEACAM1 against RSV was confirmed in vitro using BEAS-2B cells. hRSV infection disrupted the polarity of the pediatric respiratory epithelial secretome and was associated with immune modulating proteins (CXCL6, CXCL16, CSF3) never linked with this virus before. In addition, the antiviral activity of CEACAM1 against hRSV had also never been previously characterized. This study, therefore, provides novel insights into RSV pathogenesis and endogenous antiviral responses in pediatric airway epithelium.", "claims": [{"id": "claim-method", "statement": "The significantly enriched apical and basolateral proteins were highlighted with volcano plots (two-sample t test with a permutation-based FDR method) and further selected using an adjusted p value <0.05 and a fold change >2 as filtering criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32075873", "locator": "sections[20] \"Experimental Design and Statistical Rationale\" paragraph 3", "quote": "The significantly enriched apical and basolateral proteins were highlighted with volcano plots (two-sample t test with a permutation-based FDR method) and further selected using an adjusted p value <0.05 and a fold change >2 as filtering criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (28) partner repository with the data set identifier PXD013661. Data can be accessed at https://www.ebi.ac.uk/pride/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32075873", "locator": "sections[31] \"DATA AVAILABILITY\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (28) partner repository with the data set identifier PXD013661. Data can be accessed at https://www.ebi.ac.uk/pride/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:32075873"], "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:PXD013661"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:PXD013661"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32075873", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1074/mcp.RA119.001546", "sha256": "sha256:ef0655a0d4ad90fcfea6d8e2940bb299b3af6bf129d8d28a11c6553a1feea130", "bytes": 73650, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1074/mcp.RA119.001546", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7196588", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD013661", "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=PXD013661", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD013661", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (28) partner repository with the data set identifier PXD013661. Data can be accessed at https://www.ebi.ac.uk/pride/.", "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 (28) partner repository with the data set identifier PXD013661. Data can be accessed at https://www.ebi.ac.uk/pride/.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "The secretome profiling of a pediatric airway epithelium infected with hRSV identified aberrant apical/basolateral trafficking and novel immune modulating (CXCL6, CXCL16, CSF3) and antiviral (CEACAM1) proteins.", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32075873:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27c3a31bb340b280bb36f87d1170b506f7fd9ead22236d848abc4864964e0ad2", "bytes": 725, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[1]#TI", "version": null, "note": "hRSV proteins detected by LC-MS/MS at 96 hpi in the apical washes or basolateral medium of hRSV-infected WD-PBECs", "structure": {"pmcid": "PMC7196588", "section_index": 24, "section_title": "hRSV Growth Kinetics, Cell Tropism, and Viral Protein Detection", "row_count": 8, "column_count": 6}, "table": {"label": "Table I", "caption": "hRSV proteins detected by LC-MS/MS at 96 hpi in the apical washes or basolateral medium of hRSV-infected WD-PBECs", "rows": [["Protein name", "Apical", "Basolateral"], ["% protein abundancea/replicatesb", "Unique peptidesc", "% cov.d", "LFQe/replicatesb", "Unique peptidesc"], ["Matrix", "63.5/3", "25", "81.2", "24.36/1", "1"], ["Fusion (F0)", "11.6/3", "25", "53.3", "N.D.f", "N.D."], ["Phosphoprotein", "9.3/3", "12", "85.9", "N.D.", "N.D."], ["Nucleoprotein", "9.4/3", "22", "64.7", "N.D.", "N.D."], ["Matrix M2-1", "5.9/3", "5", "60.3", "N.D.", "N.D."], ["RNA-dependent RNA polymerase L", "0.38/2", "4", "4.4", "N.D.", "N.D."]], "row_count": 8, "column_count": 6, "numeric_cells": 21, "header_rows": 2, "locator": "section[24]/table-wrap[1]#TI"}}], "gaps": ["asset:data:geo:PXD013661 not downloaded", "asset:data:geo:PXD013661 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t test"}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-3", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-4", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-5", "family": null, "specific": null, "label": "Two-sample t test with a permutation-based false discovery rate method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The significantly enriched apical and basolateral proteins were highlighted with volcano plots (two-sample t test with a permutation-based FDR method) and further selected using an adjusted p value <0.05 and a fold change >2 as filtering criteria."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD013661"], "resolved_accessions": ["PXD013661"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (28) partner repository with the data set identifier PXD013661. Data can be accessed at https://www.ebi.ac.uk/pride/."], "basis": "The paper names PXD013661 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32075873", "data:geo:PXD013661", "asset:table:pmid:32075873:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD013661"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:24Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 58510, "completion_tokens": 1352, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32075873", "type": "paper", "label": "pmid:32075873"}, {"id": "source:pmid:32075873", "type": "manuscript", "label": "PMID 32075873 full text"}, {"id": "data:geo:PXD013661", "type": "dataset", "label": "GEO PXD013661"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32075873", "type": "paper", "label": "pmid:32075873"}, {"id": "source:pmid:32075873", "type": "manuscript", "label": "PMID 32075873 full text"}, {"id": "data:geo:PXD013661", "type": "dataset", "label": "GEO PXD013661"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32075873", "type": "extraction", "used": ["source:pmid:32075873"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD013661", "type": "accession_resolution", "used": ["data:geo:PXD013661"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32075873", "parent_hash": "sha256:d1e0fdf7893c6ad73def28b5afb56e48482a02cbf509f25db48492eb675cfa27", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD013661 licence not read", "asset:data:geo:PXD013661 not downloaded", "execution.not_run", "method.reader_named_unmapped", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ociated apical and basolateral secretomes, a proteomics approach was combined with an ex vivo pediat", "e performed with intermittent vortex-mixing. Proteomic-grade trypsin (Sigma) was added (0.2 μg) and", "at 95 °C. Sample Preparation for Label-free Mass Spectrometry Apical (135 μl) and basolateral (180 μl) sam", "repared for analysis by NanoLC MS ESI MS/MS (LC-MS/MS). Soluble proteins were precipitated by addi"], "order_basis": "paper_text_order:685", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["k-treated or infected) was also validated by Western blotting, whereas the corresponding cultures (fixed a"], "order_basis": "paper_text_order:5764", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["cultures (fixed at 120 hpi) were analyzed by immunofluorescence. For ELISA quantification in samples from WD"], "order_basis": "paper_text_order:5853", "id": "assay:3"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["pi) were analyzed by immunofluorescence. For ELISA quantification in samples from WD-PBECs cult"], "order_basis": "paper_text_order:5877", "id": "assay:4"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Student's t test"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}