Focal Adhesion-Related Signatures Predict the Treatment Efficacy of Chemotherapy and Prognosis in Patients with Gastric Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35600404", "kind": "science-record", "revision": 4, "content_hash": "sha256:114287f80e89021b5c94109da1f888b4b3c44aaee8e6ce940d6c8d69f559f91d", "created_at": "2026-11-01T18:14:30Z", "updated_at": "2026-11-01T22:06:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Focal Adhesion-Related Signatures Predict the Treatment Efficacy of Chemotherapy and Prognosis in Patients with Gastric Cancer.", "doi": "10.3389/fonc.2022.808817", "pmid": "35600404", "authors": ["Xiaohuan Tang", "Xiaolong Wu", "Ting Guo", "Fangzhou Jia", "Ying Hu", "Xiaofang Xing", "Xiangyu Gao", "Ziyu Li"], "journal": "Frontiers in oncology", "year": 2022, "abstract": "Background: The current tumor-node-metastasis (TNM) staging system is insufficient for predicting the efficacy of chemotherapy in patients with gastric cancer (GC). This study aimed to analyze the association between the focal adhesion pathway and therapeutic efficacy of chemotherapy in patients with GC.\nMethods: RNA sequencing was performed on 33 clinical samples from patients who responded or did not respond to treatment prior to neoadjuvant chemotherapy. The validation sets containing 696 GC patients with RNA data from three cohorts (PKUCH, TCGA, and GSE14210) were analyzed. A series of machine learning and bioinformatics approaches was combined to build a focal adhesion-related signature model to predict the treatment efficacy and prognosis of patients with GC.\nResults: Among the various signaling pathways associated with cancer, focal adhesion was identified as a risk factor related to the treatment efficacy of chemotherapy and prognosis in patients with GC. The focal adhesion-related gene model (FAscore) discriminated patients with a high FAscore who are insensitive to neoadjuvant chemotherapy in our training cohort, and the predicted value was further verified in the GSE14210 cohort. Survival analysis also demonstrated that patients with high FAscores had a relatively shorter survival compared to those with low FAscores. In addition, we found that the levels of tumor mutation burden (TMB) and microsatellite instability (MSI) increased with an increase in FAscore, and the tumor microenvironment (TME) also shifted to a pro-tumor immune microenvironment.\nConclusion: The FAscore model can be used to predict the treatment efficacy of chemotherapy and select appropriate treatment strategies for patients with GC.", "claims": [{"id": "claim-method", "statement": "A predictive model was constructed using the LASSO Cox regression model with the R package ‘LASSO’.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35600404", "locator": "sections[6] \"Bioinformatics and Statistical Analysis\" paragraph 2", "quote": "A predictive model was constructed using the LASSO Cox regression model with the R package ‘LASSO’."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: GSE14210 at https://www.ncbi.nlm.nih.gov/geo/ and TCGA stomach cancer (STAD) at https://xenabrowser.net/datapages/. The original data presented in this study are included in the article or supplement materials, further inquires can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35600404", "locator": "sections[15] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: GSE14210 at https://www.ncbi.nlm.nih.gov/geo/ and TCGA stomach cancer (STAD) at https://xenabrowser.net/datapages/. The original data presented in this study are included in the article or supplement materials, further inquires can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The focal adhesion-related FAscore model discriminated chemotherapy-insensitive gastric cancer patients, predicted prognosis, and was associated with higher TMB, MSI, and a pro-tumor immune microenvironment.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35600404", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Among the various signaling pathways associated with cancer, focal adhesion was identified as a risk factor related to the treatment efficacy of chemotherapy and prognosis in patients with GC."}, {"asset": "source:pmid:35600404", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The focal adhesion-related gene model (FAscore) discriminated patients with a high FAscore who are insensitive to neoadjuvant chemotherapy in our training cohort, and the predicted value was further verified in the GSE14210 cohort."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The focal adhesion-related FAscore model discriminated chemotherapy-insensitive gastric cancer patients, predicted prognosis, and was associated with higher TMB, MSI, and a pro-tumor immune microenvironment.", "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:35600404"], "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:GSE14210"], "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:GSE14210"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35600404", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2022.808817", "sha256": "sha256:18e64eb0a6316c33137681a06f047d3a53ce9530eac9fb25f8df561f3051ae97", "bytes": 28279, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2022.808817", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9115387", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14210", "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=GSE14210", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14210", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: GSE14210 at https://www.ncbi.nlm.nih.gov/geo/ and TCGA stomach cancer (STAD) at https://xenabrowser.net/datapages/. The original data presented in this study are included in the article or supplement materials, further inquires can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: GSE14210 at https://www.ncbi.nlm.nih.gov/geo/ and TCGA stomach cancer (STAD) at https://xenabrowser.net/datapages/. 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Methods: RNA sequencing was performed on 33 clinical samples from pa", "S-1; XELEX: oxaliplatin + capecitabine). The RNA-seq data and clinical parameters of patients wit", "esponded poorly with less than 20% necrosis. RNA sequencing was performed on the pre-treatment tumor sam", "ients with gastric cancer. We then performed RNA sequencing of these 33 gastric biopsy samples during ga"], "order_basis": "paper_text_order:398", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["A predictive model was constructed using the LASSO Cox regression model with the R package ‘LASSO’."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}