Transcriptome analysis reveals the link between lncRNA-mRNA co-expression network and tumor immune microenvironment and overall survival in head and neck squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32228580", "kind": "science-record", "revision": 7, "content_hash": "sha256:2b79e75b4044797f01c3084ee4347e7329b2995e990c15e16f310f49c55c7058", "created_at": "2026-11-01T15:40:58Z", "updated_at": "2026-11-01T22:44:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome analysis reveals the link between lncRNA-mRNA co-expression network and tumor immune microenvironment and overall survival in head and neck squamous cell carcinoma.", "doi": "10.1186/s12920-020-0707-0", "pmid": "32228580", "authors": ["Zhaoming Zhong", "Min Hong", "Xiao Chen", "Yan Xi", "Yuanyuan Xu", "Deyu Kong", "Jun Deng", "Yun Li", "Rui Hu", "Chuanzheng Sun", "Jin Liang"], "journal": "BMC medical genomics", "year": 2020, "abstract": "BACKGROUND: As the sixth most common cancer worldwide, head and neck squamous cell carcinoma (HNSCC) develops visceral metastases during the advanced stage of the disease and exhibits a low five-year survival rate. The importance of tumor microenvironment (TME) in tumor initiation and metastasis is widely recognized. In addition, accumulating evidence indicates that long non-coding RNA (lncRNA) is involved in crosstalk between TME and tumor cells. However, the lncRNA-associated regulators modulating the HNSCC microenvironment and progression remain largely unknown.\nMETHODS: The publicly available transcriptome data and matched clinical HNSCC data were collected from The Cancer Genome Atlas (TCGA). Immune scores (ISs) and stromal scores (SSs) of HNSCC TME were calculated using ESTIMATE algorithm. Weighted gene co-expression network analysis (WGCNA) was conducted to determine the co-expressed lncRNAs and protein-coding mRNAs.\nRESULTS: Results showed that the high IS HNSCC male patient subgroup exhibited improved survival. Additionally, we identified 169 lncRNAs and 825 protein-coding mRNAs that were differentially expressed in high IS HNSCC samples, with the up-regulated mRNAs displaying enrichment in immune-related biological processes. Notably, we identified a high co-expression lncRNA-mRNA module (i.e., purple module) that showed strong correlation with ISs. This module contained 79 lncRNAs and 442 mRNAs, including 26 lncRNAs and 215 mRNAs showing association between expression and male HNSCC survival. Consistently, 207 of the 215 mRNAs were up-regulated in high IS HNSCC group and were enriched in immune-related signaling pathways. Based on bioinformatics analyses and previous functional assays, certain lncRNAs (e.g., AL365361.1 and PCED1B-AS1) in the purple module likely contributed to the modification of tumor immune microenvironment (TIME) in the high IS HNSCC patients, achieved by regulating transcription of abundant immune-related genes (e.g., CCR7 and TLR8).\nCONCLUSIONS: In summary, we ascertained a HNSCC male patient subgroup that displayed high ISs and good survival probability. We identified hundreds of genes with specific expression patterns in this HNSCC subgroup as well as a highly co-expressed lncRNA-mRNA module with great potential for the modulation of TIME of HNSCC. Our study provides evidence of a link between the lncRNA-associated gene network, TIME, and HNSCC progression, and highlights potential therapeutic targets for this disease.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier analysis was conducted to calculate the association between overall survival of HNSCC patients and various features (e.g., IS/SS, gene expression, and gender) using the R survival package. Samples were first separated into two subgroups according to the upper and lower quartile values of each feature. A log-rank test was used to calculate the P-value and the R survminer package was used to draw the survival curves.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32228580", "locator": "sections[7] \"Survival analysis\" paragraph 2", "quote": "Kaplan-Meier analysis was conducted to calculate the association between overall survival of HNSCC patients and various features (e.g., IS/SS, gene expression, and gender) using the R survival package. Samples were first separated into two subgroups according to the upper and lower quartile values of each feature. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32228580", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-020-0707-0", "sha256": "sha256:00029551c814dcc076aae7f089aec5589c45b0ede3fb7f24b01f5f9b9222bc6a", "bytes": 25553, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-020-0707-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7104528", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32228580:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:254b60c52338fa48592020ddfd7f6520cd218ae34bc0a3773ec58a2ee899ebda", "bytes": 592, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab1", "version": null, "note": "Clinical information on high and low IS HNSCC samples", "structure": {"pmcid": "PMC7104528", "section_index": 12, "section_title": "DEGs between HNSCC male patient subgroups with high or low ISs", "row_count": 15, "column_count": 3}, "table": {"label": "Table 1", "caption": "Clinical information on high and low IS HNSCC samples", "rows": [["Clinical variable", "High IS HNSCC", "Low IS HNSCC"], ["Number", "92", "92"], ["Age (years)", "61.5 ± 10.8", "58.8 ± 11.0"], ["Gender", "male", "male"], ["IS range", "537.8–2034.8", "−1745.3–-473.5"], ["Clinical stage"], ["Stage I-III", "34", "41"], ["Stage IV", "56", "46"], ["Unknown", "2", "5"], ["Race"], ["White", "84", "72"], ["Other", "8", "20"], ["Vital status"], ["Alive", "62", "43"], ["Dead", "30", "39"]], "row_count": 15, "column_count": 3, "numeric_cells": 20, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab1"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan-Meier analysis was conducted to calculate the association between overall survival of HNSCC patients and various features (e.g., IS/SS, gene expression, and gender) using the R survival package. 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METHODS: The publicly available transcriptome data and matched clinical HNSCC data were co", "teristics of HNSCC patients We collected the RNA-seq profile data of 500 HNSCC and 44 normal samp"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan-Meier analysis was conducted to calculate the association between overall survival of HNSCC patients and various features (e.g., IS/SS, gene expression, and gender) using the R survival package. Samples were first separated into two subgroups according to the upper and lower quartile values of each feature. 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