Molecular Differences between Squamous Cell Carcinoma and Adenocarcinoma Cervical Cancer Subtypes: Potential Prognostic Biomarkers.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35877232", "kind": "science-record", "revision": 5, "content_hash": "sha256:28958ad5d5a6cecd8957fab33b88dd19ff05b3bcaf37406e6cb9e05103ca4886", "created_at": "2026-11-01T18:14:58Z", "updated_at": "2026-11-01T22:49:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Molecular Differences between Squamous Cell Carcinoma and Adenocarcinoma Cervical Cancer Subtypes: Potential Prognostic Biomarkers.", "doi": "10.3390/curroncol29070372", "pmid": "35877232", "authors": ["Alma D Campos-Parra", "Milagros Pérez-Quintanilla", "Antonio Daniel Martínez-Gutierrez", "Delia Pérez-Montiel", "Jaime Coronel-Martínez", "Oliver Millan-Catalan", "David Cantú De León", "Carlos Pérez-Plasencia"], "journal": "Current oncology (Toronto, Ont.)", "year": 2022, "abstract": "The most frequently diagnosed histological types of cervical cancer (CC) are squamous cell carcinoma (SCC) and adenocarcinoma (ADC). Clinically, the prognosis of both types is controversial. A molecular profile that distinguishes each histological subtype and predicts the prognosis would be of great benefit to CC patients.\nMETHODS: The transcriptome of CC patients from The Cancer Genome Atlas (TCGA) was analyzed using the DESeq2 package to obtain the differentially expressed genes (DEGs) between ADC and SCC. The DEGs were validated on a publicly available Mexican-Mestizo patient transcriptome dataset (GSE56303). The global biological pathways involving the DEGs were obtained using the Webgestalt platform. The associations of the DEGs with Overall Survival (OS) were assessed. Finally, three DEGs were validated by RT-qPCR in an independent cohort of Mexican patients.\nRESULTS: The molecular profiles of ADC and SCC of the CC patients of the TCGA database and the Mexican-Mestizo cohort (GSE56303) were determined obtaining 1768 and 88 DEGs, respectively. Strikingly, 70 genes were concordant-with similar Log2FoldChange values-in both cohorts. The 70 DEGs were involved in IL-17, JAK/STAT, and Ras signaling. Kaplan-Meier OS analysis from the Mexican-Mestizo cohort showed that higher GABRB2 and TSPAN8 and lower TMEM40 expression were associated with better OS. Similar results were found in an independent Mexican cohort.\nCONCLUSIONS: Molecular differences were detected between the ADC and SCC subtypes; however, further studies are required to define the appropriate prognostic biomarker for each histological type.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was carried out using the DESeq2 package [20], where an adjusted (adj) p-value < 0.01 and a log2FoldChange >2 or <2 were considered significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35877232", "locator": "sections[3] \"2.1. Analysis of Differential Expression\" paragraph 2", "quote": "Differential expression analysis was carried out using the DESeq2 package [20], where an adjusted (adj) p-value < 0.01 and a log2FoldChange >2 or <2 were considered significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data used in the present study are publicly available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35877232", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "All data used in the present study are publicly available."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The transcriptome of CC patients from The Cancer Genome Atlas (TCGA) was analyzed using the DESeq2 package to obtain the differentially expressed genes (DEGs) between ADC and SCC.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Strikingly, 70 genes were concordant—with similar Log2FoldChange values—in both cohorts."}, "evidence": [{"asset": "source:pmid:35877232", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The transcriptome of CC patients from The Cancer Genome Atlas (TCGA) was analyzed using the DESeq2 package to obtain the differentially expressed genes (DEGs) between ADC and SCC."}, {"asset": "source:pmid:35877232", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Strikingly, 70 genes were concordant—with similar Log2FoldChange values—in both cohorts."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The transcriptome of CC patients from The Cancer Genome Atlas (TCGA) was analyzed using the DESeq2 package to obtain the differentially expressed genes (DEGs) between ADC and SCC.", "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:35877232"], "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:GSE56303"], "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:GSE56303"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35877232", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/curroncol29070372", "sha256": "sha256:a60ac983f936a390278534da1f296b13a810a04c86a369c7b55d6dd4ef1bb326", "bytes": 40935, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/curroncol29070372", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9322365", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE56303", "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=GSE56303", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE56303", "version": null, "note": "All data used in the present study are publicly available.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data used in the present study are publicly available.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1358650", "GSM1358651", "GSM1358652", "GSM1358653", "GSM1358654", "GSM1358655", "GSM1358656", "GSM1358657", "GSM1358658", "GSM1358659", "GSM1358660", "GSM1358661", "GSM1358662", "GSM1358663", "GSM1358664", "GSM1358665", "GSM1358666", "GSM1358667", "GSM1358668", "GSM1358669", "GSM1358670", "GSM1358671", "GSM1358672", "GSM1358673", "GSM1358674", "GSM1358675", "GSM1358676", "GSM1358677", "GSM1358678", "GSM1358679", "GSM1358680", "GSM1358681", "GSM1358682", "GSM1358683", "GSM1358684", "GSM1358685", "GSM1358686", "GSM1358687", "GSM1358688", "GSM1358689", "GSM1358690", "GSM1358691", "GSM1358692", "GSM1358693", "GSM1358694", "GSM1358695", "GSM1358696", "GSM1358697", "GSM1358698", "GSM1358699", "GSM1358700", "GSM1358701", "GSM1358702", "GSM1358703", "GSM1358704", "GSM1358705", "GSM1358706", "GSM1358707", "GSM1358708", "GSM1358709", "GSM1358710", "GSM1358711", "GSM1358712", "GSM1358713", "GSM1358714", "GSM1358715", "GSM1358716", "GSM1358717", "GSM1358718", "GSM1358719", "GSM1358720", "GSM1358721", "GSM1358722", "GSM1358723", "GSM1358724", "GSM1358725", "GSM1358726", "GSM1358727", "GSM1358728", "GSM1358729", "GSM1358730", "GSM1358731", "GSM1358732", "GSM1358733", "GSM1358734", "GSM1358735", "GSM1358736", "GSM1358737", "GSM1358738"], "sample_count": 89, "group_sizes": null, "group_sizes_basis": null, "platform": "10191;16025", "taxon": "Homo sapiens", "title": "Genome wide expression profile in cervical cancer patients (staged, locally advanced)", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE56303 not downloaded", "asset:data:geo:GSE56303 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differential expression analysis was carried out using the DESeq2 package [20], where an adjusted (adj) p-value < 0.01 and a log2FoldChange >2 or <2 were considered significant."}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "differential_expression", "specific": "deseq2", "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": 0.7, "band": "medium", "quote": "DESeq2"}}, {"id": "method-4", "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": 0.8, "band": "high", "quote": "limma"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 2.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. 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