Resonance of fatty acid metabolism and immune infiltration in anti-PD-1 monotherapy for breast cancer.

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The breast cancer samples from the TCGA database were used as the training set, and samples from GSE42568 were employed as the validation set for constructing a model to identify a signature associated with fatty acid metabolism through Lasso Cox regression. And the changes in immune related signatures and risk score before and after anti-PD-1 monotherapy were caught by the differential analysis in GSE225078. A 14-gene prognostic risk scoring model identifying by fatty acid metabolism relevant signature was conducted, and the high risk group had shorter overall survival and progression free survival than low risk group. Many metabolism-related pathways were enriched in the high risk group, and many immune-related pathways were enriched in low risk group. The crucial differentially expressed genes between the high/low risk groups, CYP4F8 and CD52, were found to be strongly associated with SUCLA2 and ACOT4 of 14-gene model, and strongly related to immune infiltration. Immune related signatures, fatty acid metabolism-risk score and the expression level of ALDH1A1 (in 14-gene-model) changed after anti-PD-1 monotherapy. And the mice model results also showed anti-PD-1 mAb could significantly reduce the expression level of ALDH1A1 (p < 0.01). These results brought up the crosstalk between immune components and fatty acid metabolism in breast cancer microenvironment, which provided a new possibility of targeting fatty acid metabolism for combination therapy in breast cancer immunotherapy.", "claims": [{"id": "claim-method", "statement": "The prognostic genes were further processed using the \"glmnet\" R package, and the prognostic risk score model for predicting overall survival (OS) in breast cancer samples was developed using LASSO Cox regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38604109", "locator": "sections[4] \"Development and validation of prognostic risk score model\" paragraph 2", "quote": "The prognostic genes were further processed using the \"glmnet\" R package, and the prognostic risk score model for predicting overall survival (OS) in breast cancer samples was developed using LASSO Cox regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the results and conclusions of this study were downloaded from the TCGA (http://tcga-data.nci.nih.gov/tcga/) and GEO (http://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38604109", "locator": "sections[22] \"Data availability\" paragraph 2", "quote": "The datasets supporting the results and conclusions of this study were downloaded from the TCGA (http://tcga-data.nci.nih.gov/tcga/) and GEO (http://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A 14-gene prognostic risk scoring model identifying by fatty acid metabolism relevant signature was conducted, and the high risk group had shorter overall survival and progression free survival than low risk group.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38604109", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "A 14-gene prognostic risk scoring model identifying by fatty acid metabolism relevant signature was conducted, and the high risk group had shorter overall survival and progression free survival than low risk group."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A 14-gene prognostic risk scoring model identifying by fatty acid metabolism relevant signature was conducted, and the high risk group had shorter overall survival and progression free survival than low risk group.", "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:38604109"], "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 mice were sacrificed and transplanted tumors were taken for immun", "ong University. Seven-week-old female Balb/c mice were obtained from the Laboratory Animal Center o", "eatment and control groups respectively. The mice were sacrificed and transplanted tumors were take", "d \"ggplot2″ R packages. Clinical samples and in vivo experiments Paraffin sections of human tissu"], "order_basis": "paper_text_order:3426", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ficed and transplanted tumors were taken for immunohistochemical staining after 21 days. 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