Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28231844", "kind": "science-record", "revision": 8, "content_hash": "sha256:9556c9ba1e411eeca45ae88fc5f446b688b62a325897152ae7d5319420e3eba7", "created_at": "2026-11-01T15:40:22Z", "updated_at": "2026-11-01T22:42:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma.", "doi": "10.1186/s40659-017-0108-9", "pmid": "28231844", "authors": ["Xiaofen Wu", "Lei Ruan", "Yi Yang", "Qi Mei"], "journal": "Biological research", "year": 2017, "abstract": "BACKGROUND: This study aimed to investigate the gene expression changes associated with carcinoma-associated fibroblasts (CAFs) involving in non-small cell lung carcinoma (NSCLC).\nMETHODS: We downloaded the GEO series GSE22862, which contained matched gene expression values for 15 CAF and normal fibroblasts samples, and series GSE27289 containing SNP genotyping for four matched NSCLC samples. The differentially expressed genes in CAF samples were identified using the limma package in R. Then we performed gene ontology (GO) and pathway enrichment analysis and protein-protein interaction (PPI) network construction using the identified DEGs. Moreover, aberrant cell fraction, ploidy, allele-specific copy number, and loss of heterozygosity (LOH) within CAF cells were analyzed using the allele-specific copy number analysis.\nRESULTS: We obtained 545 differentially expressed genes between CAF and normal fibroblasts samples. The up-regulated genes are mainly involved in GO terms such as positive regulation of cell migration and extracellular region, while the down-regulated genes participate in the lung development and extracellular region. Multiple genes including bone morphogenetic protein 4 (BMP4) and transforming growth factor, beta 3 (TGFB3) are involved in the TGF-β signaling pathway. Genes including BMP4, TGFBI and matrix Gla protein (MGP) were hub genes. Moreover, no LOH event for BMP4 and MGP was found, that for sphingosine kinase 1 (SPHK1) was 70%, and for TGFBI was 40%.\nCONCLUSION: Our data suggested that BMP4, MGP, TGFBI, and SPHK1 may be important in CAFs-associated NSCLC, and the abnormal expression and high LOH frequency of them may be used as the diagnosis targets of CAFs in NSCLC.", "claims": [{"id": "claim-method", "statement": "We screened the DEGs between CAF and NF samples in GSE22862 series using the limma package in R (http://www.bioconductor.org).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28231844", "locator": "sections[5] \"Screening and functional enrichment analysis of DEGs\" paragraph 2", "quote": "We screened the DEGs between CAF and NF samples in GSE22862 series using the limma package in R (http://www.bioconductor.org)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data GSE22874 were downloaded from the GEO (Gene Expression Omnibus) database in NCBI (http://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28231844", "locator": "sections[18] \"Availability of data and materials\" paragraph 2", "quote": "The microarray data GSE22874 were downloaded from the GEO (Gene Expression Omnibus) database in NCBI (http://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used the limma package in R to analyze matched gene-expression data from GEO series GSE22862 and SNP genotyping data from GEO series GSE27289, identifying 545 differentially expressed genes between CAF and normal fibroblast samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28231844", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We downloaded the GEO series GSE22862, which contained matched gene expression values for 15 CAF and normal fibroblasts samples, and series GSE27289 containing SNP genotyping for four matched NSCLC samples. The differentially expressed genes in CAF samples were identified using the limma package in R."}, {"asset": "source:pmid:28231844", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We obtained 545 differentially expressed genes between CAF and normal fibroblasts samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used the limma package in R to analyze matched gene-expression data from GEO series GSE22862 and SNP genotyping data from GEO series GSE27289, identifying 545 differentially expressed genes between CAF and normal fibroblast samples.", "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:28231844"], "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:GSE22862"], "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:GSE22862"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28231844", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40659-017-0108-9", "sha256": 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copy number of B allele", "Proportion (%)", "Description", "Log2 FC"], ["TGFB3", "1.7", "0.3", "70", "Copy neutral LOH in 70%", "−0.96"], ["SPHK1", "0.3", "1.7", "70", "Copy neutral LOH in 70%", "0.6825"], ["NTS", "0.5", "1.5", "50", "Copy neutral LOH in 50%", "−0.7975"], ["CXCL10", "1.5", "0.5", "50", "Copy neutral LOH in 50%", "0.66"], ["F2RL1", "0.5", "1.5", "50", "Copy neutral LOH in 50%", "−1.375"], ["TGFBI", "0.6", "1.4", "40", "Loss of one allele in 40%", "−1.23"], ["COL3A1", "1.4", "0.6", "40", "Loss of one allele in 50%", "−1.12"], ["LUM", "1.2", "0.8", "20", "Loss of one allele in 20%", "−0.665"], ["IGF2", "0.8", "1.2", "20", "Loss of one allele in 20%", "1.07125"], ["GNG2", "0.9", "1.1", "10", "Imbalance in 10%", "−1.3775"], ["COL14A1", "1.1", "0.9", "10", "Imbalance in 10%", "−1.8125"], ["WNT2", "1.1", "1", "5", "Imbalance in 5%", "−1.1275"], ["MGP", "1", "1", "0", "Expected balance", "−2.3075"], ["BMP4", "1", "1", "0", "Expected balance", "−1.115"], ["PPARG", "1", "1", 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(LOH) frequency", "rows": [["Gene symbol", "The copy number of A allele", "The copy number of B allele", "Proportion (%)", "Description", "Log2 FC"], ["LXN", "2", "0", "100", "Loss of the one allele,gain of another allele", "−1.9225"], ["RASL11A", "2", "0", "100", "Loss of the one allele,gain of another allele", "−0.885"], ["KCNRG", "0", "2", "100", "Loss of the one allele,gain of another allele", "−0.6275"], ["TFAP2C", "0.3", "1.7", "70", "Copy neutral LOH in 70%", "0.9875"], ["SPHK1", "0.3", "1.7", "70", "Copy neutral LOH in 70%", "0.6825"], ["TP53INP1", "1.6", "0.4", "60", "Copy neutral LOH in 60%", "−0.795"], ["HOXD12", "1.5", "0.5", "50", "Copy neutral LOH in 50%", "0.87"], ["ERRFI1", "1.5", "0.5", "50", "Copy neutral LOH in 50%", "−1.195"], ["RPS6KA6", "0.6", "1.6", "50", "Loss of one allele in 50%", "−1.12"], ["DNAJB4", "0.4", "1.4", "50", "Copy neutral LOH in 50%", "−1.02"], ["ITGA7", "0.5", "1.5", "50", "Copy neutral LOH in 50%", "−0.925"]], "row_count": 12, "column_count": 6, 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