Identification of collagen genes related to immune infiltration and epithelial-mesenchymal transition in glioma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34034744", "kind": "science-record", "revision": 6, "content_hash": "sha256:eeb183f2333ad4a8dcb23b10159bb945a114f3bf0610dcc7d17a6392bfafeca8", "created_at": "2026-11-01T15:41:36Z", "updated_at": "2026-11-01T21:25:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of collagen genes related to immune infiltration and epithelial-mesenchymal transition in glioma.", "doi": "10.1186/s12935-021-01982-0", "pmid": "34034744", "authors": ["Wen Yin", "Hecheng Zhu", "Jun Tan", "Zhaoqi Xin", "Quanwei Zhou", "Yudong Cao", "Zhaoping Wu", "Lei Wang", "Ming Zhao", "Xingjun Jiang", "Caiping Ren", "Guihua Tang"], "journal": "Cancer cell international", "year": 2021, "abstract": "BACKGROUND: Gliomas account for the majority of fatal primary brain tumors, and there is much room for research in the underlying pathogenesis, the multistep progression of glioma, and how to improve survival. In our study, we aimed to identify potential biomarkers or therapeutic targets of glioma and study the mechanism underlying the tumor progression.\nMETHODS: We downloaded the microarray datasets (GSE43378 and GSE7696) from the Gene Expression Omnibus (GEO) database. Then, we used weighted gene co-expression network analysis (WGCNA) to screen potential biomarkers or therapeutic targets related to the tumor progression. ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumors using Expression data) algorithm and TIMER (Tumor Immune Estimation Resource) database were used to analyze the correlation between the selected genes and the tumor microenvironment. Real-time reverse transcription polymerase chain reaction was used to measure the selected gene. Transwell and wound healing assays were used to measure the cell migration and invasion capacity. Western blotting was used to test the expression of epithelial-mesenchymal transition (EMT) related markers.\nRESULTS: We identified specific module genes that were positively correlated with the WHO grade but negatively correlated with OS of glioma. Importantly, we identified that 6 collagen genes (COL1A1, COL1A2, COL3A1, COL4A1, COL4A2, and COL5A2) could regulate the immunosuppressive microenvironment of glioma. Moreover, we found that these collagen genes were significantly involved in the EMT process of glioma. Finally, taking COL3A1 as a further research object, the results showed that knockdown of COL3A1 significantly inhibited the migration, invasion, and EMT process of SHG44 and A172 cells.\nCONCLUSIONS: In summary, our study demonstrated that collagen genes play an important role in regulating the immunosuppressive microenvironment and EMT process of glioma and could serve as potential therapeutic targets for glioma management.", "claims": [{"id": "claim-method", "statement": "The coefficients of correlation were calculated by Pearson correlation analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34034744", "locator": "sections[17] \"Statistical analysis\" paragraph 2", "quote": "The coefficients of correlation were calculated by Pearson correlation analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in the current study are included within the article. Other data and materials are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34034744", "locator": "sections[35] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used in the current study are included within the article. Other data and materials are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:34034744"], "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:GSE43378"], "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:GSE43378"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34034744", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-021-01982-0", "sha256": "sha256:8aaf861969d438d794a3ccd4f10a0b8351a6f4c5fd4836f66609af594ac83478", "bytes": 60837, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-021-01982-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8147444", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE43378", "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=GSE43378", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43378", "version": null, "note": "The datasets used in the current study are included within the article. Other data and materials are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in the current study are included within the article. 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Other data and materials are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in the current study are included within the article. 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"section[20]/table-wrap[1]#Tab1", "version": null, "note": "Hub genes ranked in cytoHubba", "structure": {"pmcid": "PMC8147444", "section_index": 20, "section_title": "Screening collagen genes", "row_count": 22, "column_count": 5}, "table": {"label": "Table 1", "caption": "Hub genes ranked in cytoHubba", "rows": [["Category", "Rank methods in cytoHubba"], ["Degree", "EPC", "Closeness", "Radiality"], ["Genes top 20", "FN1", "FN1", "FN1", "FN1"], ["", "CD44", "COL4A1", "COL4A1", "COL4A1"], ["", "COL4A1", "ANGPT2", "ANXA2", "ANXA2"], ["", "ANXA2", "COL5A2", "CD44", "ANGPT2"], ["", "COL5A2", "ANXA2", "ANGPT2", "LAMB1"], ["", "ANGPT2", "COL3A1", "LAMB1", "COL1A1"], ["", "COL3A1", "COL1A1", "SERPINH1", "SERPINH1"], ["", "COL1A1", "CALD1", "COL5A2", "CALD1"], ["", "CLIC1", "CD44", "COL1A1", "CD44"], ["", "CALD1", "SERPINH1", "CALD1", "NAMPT"], ["", "LAMB1", "COL1A2", "COL1A2", "LAMC1"], ["", "SERPINH1", "NAMPT", "LAMC1", "COL5A2"], ["", "COL1A2", "LAMB1", "NAMPT", "COL1A2"], ["", "LAMC1", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE43378", "GSE7696"], "resolved_accessions": ["GSE43378", "GSE7696"], "statements": ["The datasets used in the current study are included within the article. Other data and materials are available from the corresponding author on reasonable request."], "basis": "The paper names GSE43378, GSE7696 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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METHODS: We downloaded the microarray datasets (GSE43378 and GSE7696) from the Gen", "and glioma grades were executed on a cancer microarray data-mining database: Oncomine [25]. The res", "ain dataset [26], a maximal sample size mRNA microarray that could be grouped by glioma grade in his"], "order_basis": "paper_text_order:452", "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": ["re the cell migration and invasion capacity. Western blotting was used to test the expression of epithelia"], "order_basis": "paper_text_order:1146", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["her research object, the results showed that knockdown of COL3A1 significantly inhibited the migrat"], "order_basis": "paper_text_order:1743", "id": "assay:3"}, {"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": ["ere analyzed by R language. Cell culture and real-time quantitative PCR (qRT-PCR) SHG44 and A172 glioma cells were p"], "order_basis": "paper_text_order:2964", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["angsha, China. The SHG44 and A172 cells were cultured in DMEM high glucose medium (Gibco/Thermo Fishe"], "order_basis": "paper_text_order:3145", "id": "assay:5"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e increases. From the UCSC database, level 3 RNA-Seq datasets (TCGA-GBMLGG) and their clinical in"], "order_basis": "paper_text_order:5589", "id": "assay:6"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["CGGA (B) datasets. **** p < 0.0001 Moreover, immunohistochemistry (IHC) datasets retrieved from the Human Prot", "n genes in the Human Protein Atlas database (immunohistochemistry). The translational expression level of the", "IL6 in WHO II-IV grade glioma tissues using immunofluorescence. Additional file 7: Fig. S7. The correlation", "* p < 0.0001 Moreover, immunohistochemistry (IHC) datasets retrieved from the Human Protein A"], "order_basis": "paper_text_order:7747", "id": "assay:7"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The coefficients of correlation were calculated by Pearson correlation analysis."], "order_basis": "consumes_earlier_output", "id": "assay:8"}]}