Identification of Significant Secreted or Membrane-Located Proteins in Laryngeal Squamous Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35655921", "kind": "science-record", "revision": 5, "content_hash": "sha256:c46c7bcb18911071198cab9c380c1f2f4574cd305766fb4c7c08a9e4e1651815", "created_at": "2026-11-01T18:14:35Z", "updated_at": "2026-11-01T22:49:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Significant Secreted or Membrane-Located Proteins in Laryngeal Squamous Cell Carcinoma.", "doi": "10.1155/2022/9089397", "pmid": "35655921", "authors": ["Li Yan", "Chunyan Hu", "Yangyang Ji", "Lifen Zou", "Yang Zhao", "Yi Zhu", "Xiaoshen Wang"], "journal": "Journal of immunology research", "year": 2022, "abstract": "Background: This study is aimed at investigating the expressions and prognostic values of secreted or membrane-located proteins (SMPs) in laryngeal squamous cell carcinoma (LSCC). The correlations between the expressions of SMPs and immune cells' infiltrations were also investigated.\nMethods: The expression data of normal laryngeal and LSCC samples were obtained from the TCGA and GEO datasets. The differentially expressed SMPs were identified, and their prognostic values were analyzed. The biological functions of differentially expressed and worse-survival-related SMPs were explored. LASSO regression, Cox multivariate analysis, and nomogram were used to construct a model to predict the survival. Then, the infiltrations of the 24 immune cell populations were calculated using the GSVA method, and the correlations between the expression of SMPs and the immune infiltration were investigated.\nResults: 122 samples (12 normal and 120 LSCC) of the TCGA database and 114 samples (57 normal and 57 LSCC) of GSE127165 were included. We identified that 138 SMPs were significantly upregulated in LSCC samples of both the TCGA and GEO datasets, among which 52 SMPs were significantly correlated with worse survival. GO and KEGG analyses revealed those 52 SMPs significantly participate in tumor microenvironment and immune cells' communication. Nine of 52 SMPs (ABCC5, ATP1B3, CLEC11A, FLNA, FSTL3, MMP1, NME1, OAS3, and PHLDB2) were included in the nomogram to effectively and accurately predict the LSCC patients' survival. The expressions of most SMPs, such as MMP1 and FSTL3, were significantly positively correlated with the immune infiltration of LSCC.\nConclusions: In this study, the expression, prognostic values, and correlations with immune infiltration of SMPs were analyzed in LSCC samples. Our analyses identified several significant SMPs differentially expressed between normal laryngeal and LSCC samples, correlated with worse survival, and related to the immune infiltration.", "claims": [{"id": "claim-method", "statement": "Genes differentially expressed between normal laryngeal and LSCC samples were identified with a threshold of Log2 (fold change) > 0.5 or Log2 (fold change) < −0.5, as well as both p value and adjusted p value < 0.05 using the limma package of the R software (version 4.0.3) [10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35655921", "locator": "sections[5] \"2.3. Identification of Differentially Expressed SMPs\" paragraph 2", "quote": "Genes differentially expressed between normal laryngeal and LSCC samples were identified with a threshold of Log2 (fold change) > 0.5 or Log2 (fold change) < −0.5, as well as both p value and adjusted p value < 0.05 using the limma package of the R software (version 4.0.3) [10]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data can be obtained from the UCSC Xena browser (https://gdc.xenahubs.net) and the GEO database (https://www.ncbi.nlm.nih.gov/gds/) under the accession numbers GSE127165.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35655921", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "Data can be obtained from the UCSC Xena browser (https://gdc.xenahubs.net) and the GEO database (https://www.ncbi.nlm.nih.gov/gds/) under the accession numbers GSE127165."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 138 SMPs upregulated in LSCC in both the TCGA and GEO datasets, found 52 associated with worse survival, and incorporated nine into a survival-prediction nomogram.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35655921", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified that 138 SMPs were significantly upregulated in LSCC samples of both the TCGA and GEO datasets, among which 52 SMPs were significantly correlated with worse survival."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 138 SMPs upregulated in LSCC in both the TCGA and GEO datasets, found 52 associated with worse survival, and incorporated nine into a survival-prediction nomogram.", "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:35655921"], "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:GSE127165"], "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:GSE127165"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35655921", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/9089397", "sha256": 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