The gene signature of tertiary lymphoid structures within ovarian cancer predicts the prognosis and immunotherapy benefit.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36704336", "kind": "science-record", "revision": 3, "content_hash": "sha256:37f8492ac0fb20568d284e2f2375645f020664f581780c734cc819a8c6098cad", "created_at": "2026-11-01T19:01:16Z", "updated_at": "2026-11-01T22:08:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The gene signature of tertiary lymphoid structures within ovarian cancer predicts the prognosis and immunotherapy benefit.", "doi": "10.3389/fgene.2022.1090640", "pmid": "36704336", "authors": ["Yue Hou", "Sijing Qiao", "Miao Li", "Xue Han", "Xuan Wei", "Yingxin Pang", "Hongluan Mao"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Ovarian cancer (OC) has the lowest survival rate among gynecologic malignancies. Ectopic lymphocyte aggregates, namely tertiary lymphoid structures (TLSs), have been reported as positive biomarkers for tumor prognosis. However, the related gene signature of tertiary lymphoid structure in ovarian cancer was less understood. Therefore, this study first exhibited the organizational patterns of tertiary lymphoid structure by H&E staining and immunohistochemistry (IHC), and confirmed the improved survival values of tertiary lymphoid structure and quantified tumor-infiltrating lymphocytes (CD20+ B cells and CD8+ T cells) in ovarian cancer patients. Secondly, we collected the genes involved in tertiary lymphoid structure from databases. By the univariate regression analysis, the tertiary lymphoid structure gene signature (CETP, CCR7, SELL, LAMP3, CCL19, CXCL9, CXCL10, CXCL11, and CXCL13) with prognostic value, characteristically of ovarian cancer, was constructed in the TCGA dataset and validated in the GSE140082 dataset. Thirdly, by performing CIBERSORT and Tumor Immune Dysfunction and Exclusion (TIDE) analysis, we found that the high expression of this gene signature was positively correlated with developed immune infiltration and reduced immune escape. The improved IPS score and application in the IMvigor210 dataset received PD-L1 proved the predictive value of immunotherapy for this gene signature. Furthermore, this signature showed a better correlation between tumor mutation burden and classical checkpoint genes. In conclusion, Tertiary lymphoid structure plays important role in tumor immunity and the gene signature can be evaluated as a biomarker for predicting prognosis and guiding immunotherapy in ovarian cancer.", "claims": [{"id": "claim-method", "statement": "Differences in Overall Survival (OS) and Progression-Free Survival (PFS) between different groups were evaluated by Kaplan—Meier survival curve and verified by the log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36704336", "locator": "sections[10] \"2.8 Statistical analysis\" paragraph 2", "quote": "Differences in Overall Survival (OS) and Progression-Free Survival (PFS) between different groups were evaluated by Kaplan—Meier survival curve and verified by the log-rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36704336", "locator": "sections[22] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TLS-positive ovarian cancer patients showed superior 5-year overall survival and progression-free survival.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36704336", "locator": "sections[13] \"3.2 The existence of TLSs represents a superior survival outcome\" paragraph 2", "quote": "As portrayed in Figures 2A, B, the TLS-positive group performed the superior 5-year overall survival and progression-free survival (5-year-OS: p = .0078; 5-year-PFS: p = .041)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TLS-positive ovarian cancer patients showed superior 5-year overall survival and progression-free survival.", "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:36704336"], "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:GSE140082"], "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:GSE140082"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36704336", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.1090640", "sha256": "sha256:dc161b45d72aa1d432f6c48c8f608655d1f286f842414ed57ad966a1c1e14f37", "bytes": 51894, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2022.1090640", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9871364", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE140082", "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=GSE140082", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE140082", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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