Landscape of the immune infiltration and identification of molecular diagnostic markers associated with immune cells in patients with kidney transplantation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39433868", "kind": "science-record", "revision": 4, "content_hash": "sha256:4b5079d80c0c6aa800e044e607c260bcdbdde4e8da93111a34856ec4251aed11", "created_at": "2026-11-01T20:29:41Z", "updated_at": "2026-11-01T22:55:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Landscape of the immune infiltration and identification of molecular diagnostic markers associated with immune cells in patients with kidney transplantation.", "doi": "10.1038/s41598-024-75052-6", "pmid": "39433868", "authors": ["Zhangxiao Xu", "Xun Sun", "Xiaobo Ma", "Bo Tao", "Jian Wu", "Yunpeng He", "Yuan Zhao", "Hexiang Mao", "Jie Yang", "Dehui Jiang", "Lijun Wang", "Chao Song"], "journal": "Scientific reports", "year": 2024, "abstract": "Rejection seriously affects the success of kidney transplantations. However, the molecular mechanisms underlying this rejection remain unclear. The GSE21374 and GSE36059 datasets were downloaded from the Gene Expression Omnibus (GEO) database. Next, the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was used to infer the proportions of 22 immune cells. Moreover, infiltrating immune cell-related genes were identified using weighted gene co-expression network analysis (WGCNA), and enrichment analysis was conducted to observe their biological functions. Extreme Gradient Boosting (XGBoost) and Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression algorithms were used to screen hub genes. Quantitative real-time PCR was conducted to verify the number of immune cells and hub gene expression levels. The rejection and non-rejection groups showed significantly different distributions (P < 0.05) of eight immune cells (B cell memory, Plasma cells, mast cells, follicular helper T cells, T CD8 cells, Macrophages M1, T Cells CD4 memory activated, and gamma delta T cells). Subsequently, CD8A, CRTAM, GBP2, WARS, and VAMP5 were screened as hub genes using the XGBoost and LASSO algorithms and could be used as diagnostic biomarkers. Finally, differential analysis and quantitative real-time PCR suggested that CD8A, CRTAM, GBP2, WARS, and VAMP5 were upregulated in rejection samples compared to non-rejection samples. The present study identified five key infiltrating immune cell-related genes (CD8A, CRTAM, GBP2,WARS, and VAMP5) involved in kidney transplant rejection, which may explain the molecular mechanism of rejection in kidney transplantation development.", "claims": [{"id": "claim-method", "statement": "To distinguish hub genes from prognostic genes, extreme gradient boosting (XGBoost)53 and least absolute shrinkage and selection operator (LASSO) logistic regression algorithms54 were applied to the GSE21374 dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39433868", "locator": "sections[20] \"Identification of hub genes by machine learning algorithms\" paragraph 2", "quote": "To distinguish hub genes from prognostic genes, extreme gradient boosting (XGBoost)53 and least absolute shrinkage and selection operator (LASSO) logistic regression algorithms54 were applied to the GSE21374 dataset."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data analyzed in this study were obtained from public databases with the following relevant links: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21374, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36059.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39433868", "locator": "sections[32] \"notes\" paragraph 1", "quote": "The data analyzed in this study were obtained from public databases with the following relevant links: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21374, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36059."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the publicly downloaded GSE21374 and GSE36059 datasets, the study applied CIBERSORT, WGCNA, Kaplan–Meier survival analysis, XGBoost, and LASSO logistic regression to identify five diagnostic biomarkers—CD8A, CRTAM, GBP2, WARS, and VAMP5—that were upregulated in kidney transplant rejection samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39433868", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The GSE21374 and GSE36059 datasets were downloaded from the Gene Expression Omnibus (GEO) database."}, {"asset": "source:pmid:39433868", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Extreme Gradient Boosting (XGBoost) and Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression algorithms were used to screen hub genes."}, {"asset": "source:pmid:39433868", "locator": "sections[7] \"Identification of hub genes by machine learning algorithms\" paragraph 2", "quote": "Finally, by overlapping genes obtained by the XGBoost and LASSO algorithms, a total of five hub genes, including WARS, CD8A, CRTAM, GBP2, and VAMP5, were identified (Fig. 5G)."}, {"asset": "source:pmid:39433868", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Finally, differential analysis and quantitative real-time PCR suggested that CD8A, CRTAM, GBP2, WARS, and VAMP5 were upregulated in rejection samples compared to non-rejection samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the publicly downloaded GSE21374 and GSE36059 datasets, the study applied CIBERSORT, WGCNA, Kaplan–Meier survival analysis, XGBoost, and LASSO logistic regression to identify five diagnostic biomarkers—CD8A, CRTAM, GBP2, WARS, and VAMP5—that were upregulated in kidney transplant rejection samples.", "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:39433868"], "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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