Pain-Related Gene Solute Carrier Family 24 Member 3 Is a Prognostic Biomarker and Correlated with Immune Infiltrates in Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma: A Study via Integrated Bioinformatics Analyses and Experimental Verification.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36798148", "kind": "science-record", "revision": 4, "content_hash": "sha256:0d72874a62994e817f35ebe08b435d5ce2ff089f9a85043029374923790cbb37", "created_at": "2026-11-01T19:01:23Z", "updated_at": "2026-11-01T22:51:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Pain-Related Gene Solute Carrier Family 24 Member 3 Is a Prognostic Biomarker and Correlated with Immune Infiltrates in Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma: A Study via Integrated Bioinformatics Analyses and Experimental Verification.", "doi": "10.1155/2023/4164232", "pmid": "36798148", "authors": ["Shuguang Zhou", "Qinqin Jin", "Hui Yao", "Jie Ying", "Lu Tian", "Xiya Jiang", "Yinting Yang", "Xiaomin Jiang", "Wei Gao", "Weiyu Zhang", "Yuting Zhu", "Wujun Cao"], "journal": "Computational and mathematical methods in medicine", "year": 2023, "abstract": "The aim of this study was to explore cervical carcinoma and screen a suitable gene as the biomarker used for prognosis evaluation as well as pain therapy. Low expression levels of solute carrier family 24 member 3 (SLC24A3) was involved in the appearance and development of numerous malignancies. Nevertheless, the prognostic value of SLC24A3 expression with cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) patients remains uncertain. During the present study, SLC24A3 expression in CESC was retrieved from TCGA, GEO, and MSigDB databases. Based on TCGA and GEO profiles, we performed survival and difference analyses about SLC24A3 both in two GEO (GSE44001 and GSE63514) and TCGA-CESC cohorts (all p < 0.05), indicating that SLC24A3 was low expressed in tumors and associated with higher overall survival in CESC patients. Additionally, we programmed a series of analyses, including genomic profiling, enrichment analysis, immune infiltration analysis, and therapy-related analysis to identify the mechanism of the SLC24A3 in the process of cancer in CESC. Meanwhile, qRT-PCR was used to validate that the expression of SLC24A3 mRNA in Hela and SiHa cell lines was significantly lower than in PANC-1 and HUCEC cell lines. Our finding elucidated that the SLC24A3, a sodium-calcium regulator of cells, is an indispensable factor which can significantly influence the prognosis of patients with CESC and could provide novel clinical evidence to serve as a potential biological indicator for future diagnosis and pain therapy.", "claims": [{"id": "claim-method", "statement": "Differential expression genes (DEGs) were screened via “edgeR” R package by comparing SLC24A3 expression of the tumor and normal cases. We calculated the Spearman coefficients of the DEGs and key pain candidate genes, while defining DEGs with p value < 0.05 as key pain candidate genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36798148", "locator": "sections[4] \"2.2. Identification of SLC24A3-Related Genes\" paragraph 2", "quote": "Differential expression genes (DEGs) were screened via “edgeR” R package by comparing SLC24A3 expression of the tumor and normal cases."}, {"asset": "source:pmid:36798148", "locator": "sections[4] \"2.2. Identification of SLC24A3-Related Genes\" paragraph 2", "quote": "We calculated the Spearman coefficients of the DEGs and key pain candidate genes, while defining DEGs with p value < 0.05 as key pain candidate genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Collection and Description. The Cancer Genome Atlas (TCGA) database (http://xena.ucsc.edu/) was applied to download gene expression quantification data and clinical information of female with CESC. Nevertheless, because the TCGA database lacks normal tissue data matched with cervical cancer, the total number of samples is only three. Hence, the Genotype-Tissue Expression (GTEx) Portal was applied to obtain the expression values of the normal cervix tissue. The Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) was applied to download gene expression and clinical data of patients in GSE44001 and GSE63514 cohorts. The Molecular Signatures Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/index.jsp) was used to extract pain-related genes. Since the data were downloaded from public databases, there is no need to get approval from ethics committee.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36798148", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "Data Collection and Description. The Cancer Genome Atlas (TCGA) database (http://xena.ucsc.edu/) was applied to download gene expression quantification data and clinical information of female with CESC. Nevertheless, because the TCGA database lacks normal tissue data matched with cervical cancer, the total number of samples is only three. Hence, the Genotype-Tissue Expression (GTEx) Portal was applied to obtain the expression values of the normal cervix tissue. The Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) was applied to download gene expression and clinical data of patients in GSE44001 and GSE63514 cohorts. The Molecular Signatures Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/index.jsp) was used to extract pain-related genes. Since the data were downloaded from public databases, there is no need to get approval from ethics committee."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SLC24A3 was low expressed in tumors and associated with higher overall survival in CESC patients.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Based on TCGA and GEO profiles, we performed survival and difference analyses about SLC24A3 both in two GEO (GSE44001 and GSE63514) and TCGA-CESC cohorts (all p < 0.05), indicating that SLC24A3 was low expressed in tumors and associated with higher overall survival in CESC patients."}, "evidence": [{"asset": "source:pmid:36798148", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Based on TCGA and GEO profiles, we performed survival and difference analyses about SLC24A3 both in two GEO (GSE44001 and GSE63514) and TCGA-CESC cohorts (all p < 0.05), indicating that SLC24A3 was low expressed in tumors and associated with higher overall survival in CESC patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SLC24A3 was low expressed in tumors and associated with higher overall survival in CESC patients.", "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:36798148"], "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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The Cancer Genome Atlas (TCGA) database (http://xena.ucsc.edu/) was applied to download gene expression quantification data and clinical information of female with CESC. Nevertheless, because the TCGA database lacks normal tissue data matched with cervical cancer, the total number of samples is only three. Hence, the Genotype-Tissue Expression (GTEx) Portal was applied to obtain the expression values of the normal cervix tissue. The Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) was applied to download gene expression and clinical data of patients in GSE44001 and GSE63514 cohorts. The Molecular Signatures Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/index.jsp) was used to extract pain-related genes. 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The Molecular Signatures Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/index.jsp) was used to extract pain-related genes. 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The Cancer Genome Atlas (TCGA) database (http://xena.ucsc.edu/) was applied to download gene expression quantification data and clinical information of female with CESC. Nevertheless, because the TCGA database lacks normal tissue data matched with cervical cancer, the total number of samples is only three. Hence, the Genotype-Tissue Expression (GTEx) Portal was applied to obtain the expression values of the normal cervix tissue. The Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) was applied to download gene expression and clinical data of patients in GSE44001 and GSE63514 cohorts. The Molecular Signatures Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/index.jsp) was used to extract pain-related genes. Since the data were downloaded from public databases, there is no need to get approval from ethics committee.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Collection and Description. The Cancer Genome Atlas (TCGA) database (http://xena.ucsc.edu/) was applied to download gene expression quantification data and clinical information of female with CESC. Nevertheless, because the TCGA database lacks normal tissue data matched with cervical cancer, the total number of samples is only three. Hence, the Genotype-Tissue Expression (GTEx) Portal was applied to obtain the expression values of the normal cervix tissue. The Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) was applied to download gene expression and clinical data of patients in GSE44001 and GSE63514 cohorts. The Molecular Signatures Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/index.jsp) was used to extract pain-related genes. 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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": ["GSE44001", "GSE63514"], "resolved_accessions": ["GSE44001", "GSE63514"], "statements": ["Data Collection and Description. The Cancer Genome Atlas (TCGA) database (http://xena.ucsc.edu/) was applied to download gene expression quantification data and clinical information of female with CESC. Nevertheless, because the TCGA database lacks normal tissue data matched with cervical cancer, the total number of samples is only three. Hence, the Genotype-Tissue Expression (GTEx) Portal was applied to obtain the expression values of the normal cervix tissue. The Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) was applied to download gene expression and clinical data of patients in GSE44001 and GSE63514 cohorts. The Molecular Signatures Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/index.jsp) was used to extract pain-related genes. Since the data were downloaded from public databases, there is no need to get approval from ethics committee."], "basis": "The paper names GSE44001, GSE63514 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36798148", "data:geo:GSE44001"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE44001"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:27:50Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10219, "completion_tokens": 2999, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36798148", "type": "paper", "label": "pmid:36798148"}, {"id": "source:pmid:36798148", "type": "manuscript", "label": "PMID 36798148 full text"}, {"id": "data:geo:GSE44001", "type": "dataset", "label": "GEO GSE44001"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36798148", "type": "paper", "label": "pmid:36798148"}, {"id": "source:pmid:36798148", "type": "manuscript", "label": "PMID 36798148 full text"}, {"id": "data:geo:GSE44001", "type": "dataset", "label": "GEO GSE44001"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36798148", "type": "extraction", "used": ["source:pmid:36798148"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE44001", "type": "accession_resolution", "used": ["data:geo:GSE44001"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:36798148", "parent_hash": "sha256:2084fa1a0263f60da8bb8d428ad02d6bce14a5acb23f16f060ca8815fed9e4af", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE44001 licence not read", "asset:data:geo:GSE44001 not downloaded", "asset:data:geo:GSE63514 licence not read", "asset:data:geo:GSE63514 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["idate that the expression of SLC24A3 mRNA in Hela and SiHa cell lines was significantly lower"], "order_basis": "paper_text_order:1380", "id": "assay:1"}, {"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": ["Differential expression genes (DEGs) were screened via “edgeR” R package by comparing SLC24A3 expression of the tumor and normal cases. We calculated the Spearman coefficients of the DEGs and key pain candidate genes, while defining DEGs with p value < 0.05 as key pain candidate genes."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}