Identification of Novel Prognostic Markers Associated With Laryngeal Squamous Cell Carcinoma Using Comprehensive Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35087752", "kind": "science-record", "revision": 4, "content_hash": "sha256:e789abf1500ebcc88f1e8f1e39b744f96d1992d346c1c82fd1d66175cc1c41cd", "created_at": "2026-11-01T17:36:49Z", "updated_at": "2026-11-01T21:27:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Novel Prognostic Markers Associated With Laryngeal Squamous Cell Carcinoma Using Comprehensive Analysis.", "doi": "10.3389/fonc.2021.779153", "pmid": "35087752", "authors": ["Chao Huang", "Jun He", "Yi Dong", "Li Huang", "Yichao Chen", "Anquan Peng", "Hao Huang"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "BACKGROUND: Laryngeal squamous cell carcinoma (LSCC) is a leading malignant cancer of the head and neck. Patients with LSCC, in which the cancer has infiltrated and metastasized, have a poor prognosis. Therefore, there is an urgent need to identify more potential targets for drugs and biomarkers for early diagnosis.\nMETHODS: RNA sequence data from LSCC and patients' clinical traits were obtained from the Gene Expression Omnibus (GEO) (GSE142083) and The Cancer Genome Atlas (TCGA) database. Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify hub genes. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, prognostic value analysis, receiver operating characteristic (ROC) curve analysis, gene mutation analysis, tumor-infiltrating immune cell abundance profile estimation, gene set variation analysis (GSVA), and gene set enrichment analysis (GSEA) were performed. Single-gene RNA sequencing data were obtained from the GSE150321 dataset. Cell proliferation and viability were confirmed by the CCK-8 assay and real-time PCR.\nRESULTS: A total of 701 DEGs, including 329 upregulated and 372 downregulated genes, were screened in the GSE142083 dataset. Using WGCNA, three modules were identified to be closely related to LSCC. After intersecting the DEGs and performing univariate and multivariate Cox analyses, a novel prognostic model based on three genes (SLC35C1, HOXB7, and TEDC2) for LSCC was established. Interfering TEDC2 expression inhibited tumor cell proliferation and migration.\nCONCLUSIONS: Our results show that SLC35C1, HOXB7, and TEDC2 have the potential to become new therapeutic targets and prognostic biomarkers for LSCC.", "claims": [{"id": "claim-method", "statement": "Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify hub genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35087752", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify hub genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35087752", "locator": "sections[28] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After intersecting the DEGs and performing univariate and multivariate Cox analyses, a novel prognostic model based on three genes (SLC35C1, HOXB7, and TEDC2) for LSCC was established.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35087752", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "After intersecting the DEGs and performing univariate and multivariate Cox analyses, a novel prognostic model based on three genes (SLC35C1, HOXB7, and TEDC2) for LSCC was established."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After intersecting the DEGs and performing univariate and multivariate Cox analyses, a novel prognostic model based on three genes (SLC35C1, HOXB7, and TEDC2) for LSCC was established.", "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:35087752"], "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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Single-gene RNA sequencing data were obtained from the GSE150321 datase", "Methods Data Collection and Single-Cell RNA-Sequencing Data Processing The workflow used in this st", "set variation analysis. The gene expression RNA-Seq data and the corresponding clinical data fro"], "order_basis": "paper_text_order:1063", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["feration and viability were confirmed by the CCK-8 assay and real-time PCR. RESULTS: A total of"], "order_basis": "paper_text_order:1179", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["bility were confirmed by the CCK-8 assay and real-time PCR. RESULTS: A total of 701 DEGs, including 329"], "order_basis": "paper_text_order:1195", "id": "assay:3"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ta Cruz (UCSC) Xena (http://xena.ucsc.edu/). scRNA-Seq data from the GSE150321 dataset were obtaine", ".0.2) was used to process the data (26). The scRNA-Seq data of GSM4546857 and GSM4546858 from two L"], "order_basis": "paper_text_order:3667", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["icance was set at p < 0.05. Cell Culture and Transfection The laryngeal cancer cell line AMC-HN-8 and", "y RiboBio Inc. (Guangzhou, China). SiRNA was transfected into cells using Lipofectamine 3000 Reagent", "humidified incubator with 5% CO2. The TEDC2 siRNA (siTEDC2 #1 and siTEDC2 #2) was produced by", "produced by RiboBio Inc. (Guangzhou, China). 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