CEACAM1 as a molecular target in oral cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37589542", "kind": "science-record", "revision": 4, "content_hash": "sha256:4a3ca843bddd046d82ac4cf88bc6ca35056a2615aaa7d48711410de8ef5b170b", "created_at": "2026-11-01T19:02:23Z", "updated_at": "2026-11-01T22:52:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CEACAM1 as a molecular target in oral cancer.", "doi": "10.18632/aging.204960", "pmid": "37589542", "authors": ["Sai Ma", "Zhonghua Wang", "Chao Li", "Zhenli Liu", "Xuan Zhang", "Liheng Li", "Feng An", "Xiaoli Qiao"], "journal": "Aging", "year": 2023, "abstract": "OBJECTIVE: The majority of oral cancer is caused by malignant transformation of squamous cells in surface of the oral mucosa. However, the relationship between CEACAM1 and oral cancer is unclear.\nMETHODS: GSE23558 and GSE25099 profiles were downloaded from gene expression omnibus (GEO). Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. Construction and analysis of protein-protein interaction (PPI) Network. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG), gene set enrichment analysis (GSEA), gene expression heatmap, immune infiltration analysis, comparative toxicogenomics database (CTD) were performed. TargetScan screened miRNAs that regulated central DEGs. Western blotting (WB) experiment was performed.\nRESULTS: 1269 DEGs were identified. According to GO analysis, they were mainly enriched in same protein binding, signal receptor binding, cell surface, epithelial cell development. KEGG analysis showed that they were mainly enriched in cancer pathways, PI3K Akt signaling pathway, TNF signaling pathway, NF kappa B signaling pathway, TGF beta signaling pathway. PPI network showed that 11 genes (CDCA8, CCNA2, MELK, KIF2C, CDC45, HMMR, TPX2, CENPF, CDK1, CEP55, CEACAM1) were obtained. Gene expression heatmap showed that CEP55 and MELK were highly expressed in oral cancer samples. CEACAM1 was lowly expressed in oral cancer samples. CEACAM1, CEP55 and MELK were involved in tumor, inflammation, necrosis, and proliferation. Western blotting (WB) showed that CEACAM1 in oral cancer samples was lower than that in normal samples, after CEACAM1 knockdown, it was lower than that in oral cancer samples.\nCONCLUSION: CEACAM1 is lowly expressed in oral cancer, the lower CEACAM1, the worse prognosis.", "claims": [{"id": "claim-method", "statement": "Probe aggregation and background correction of merge matrix of GSE23558 and GSE25099 using R package “limma”. P value were adjusted using Benjamini-Hochberg method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37589542", "locator": "sections[4] \"Screening of differentially expressed genes (DEGs)\" paragraph 2", "quote": "Probe aggregation and background correction of merge matrix of GSE23558 and GSE25099 using R package “limma”. P value were adjusted using Benjamini-Hochberg method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37589542", "locator": "sections[14] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CEACAM1 is lowly expressed in oral cancer, the lower CEACAM1, the worse prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37589542", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Conclusion: CEACAM1 is lowly expressed in oral cancer, the lower CEACAM1, the worse prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CEACAM1 is lowly expressed in oral cancer, the lower CEACAM1, the worse prognosis.", "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:37589542"], "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:GSE23558"], "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:GSE23558"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37589542", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.204960", "sha256": "sha256:d1daca9849f26a6fc3a0e77efd421c4c083e9296444e7418365bac9a23d4f4c4", "bytes": 30375, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.204960", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10497000", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE23558", "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=GSE23558", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23558", "version": null, "note": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM577914", "GSM577915", "GSM577916", "GSM577917", "GSM577918", "GSM577919", "GSM577920", "GSM577921", "GSM577922", "GSM577923", "GSM577924", "GSM577925", "GSM577926", "GSM577927", "GSM577928", "GSM577929", "GSM577930", "GSM577931", "GSM577932", "GSM577933", "GSM577934", "GSM577935", "GSM577936", "GSM577937", "GSM577938", "GSM577939", "GSM577940", "GSM577941", "GSM577942", "GSM577943", "GSM577944", "GSM577945"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Oral Squamous Cell Carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE25099", "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=GSE25099", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25099", "version": null, "note": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM616583", "GSM616584", "GSM616585", "GSM616586", "GSM616587", "GSM616588", "GSM616589", "GSM616590", "GSM616591", "GSM616592", "GSM616593", "GSM616594", "GSM616595", "GSM616596", "GSM616597", "GSM616598", "GSM616599", "GSM616600", "GSM616601", "GSM616602", "GSM616603", "GSM616604", "GSM616605", "GSM616606", "GSM616607", "GSM616608", "GSM616609", "GSM616610", "GSM616611", "GSM616612", "GSM616613", "GSM616614", "GSM616615", "GSM616616", "GSM616617", "GSM616618", "GSM616619", "GSM616620", "GSM616621", "GSM616622", "GSM616623", "GSM616624", "GSM616625", "GSM616626", "GSM616627", "GSM616628", "GSM616629", "GSM616630", "GSM616631", "GSM616632", "GSM616633", "GSM616634", "GSM616635", "GSM616636", "GSM616637", "GSM616638", "GSM616639", "GSM616640", "GSM616641", "GSM616642", "GSM616643", "GSM616644", "GSM616645", "GSM616646", "GSM616647", "GSM616648", "GSM616649", "GSM616650", "GSM616651", "GSM616652", "GSM616653", "GSM616654", "GSM616655", "GSM616656", "GSM616657", "GSM616658", "GSM616659", "GSM616660", "GSM616661"], "sample_count": 79, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Expression data from 57 patients with oral cancer and 22 normal persons", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE23558 not downloaded", "asset:data:geo:GSE23558 licence not read", "asset:data:geo:GSE25099 not downloaded", "asset:data:geo:GSE25099 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Probe aggregation and background correction of merge matrix of GSE23558 and GSE25099 using R package “limma”. 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Western blotting (WB) experiment was performed. RESULTS: 1269", ", inflammation, necrosis, and proliferation. Western blotting (WB) showed that CEACAM1 in oral cancer samp"], "order_basis": "paper_text_order:760", "id": "assay:1"}, {"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": ["r than that in normal samples, after CEACAM1 knockdown, it was lower than that in oral cancer sampl"], "order_basis": "paper_text_order:1652", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Probe aggregation and background correction of merge matrix of GSE23558 and GSE25099 using R package “limma”. P value were adjusted using Benjamini-Hochberg method."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}