Integrated analysis of bulk and single-cell RNA sequencing reveals the impact of nicotinamide and tryptophan metabolism on glioma prognosis and immunotherapy sensitivity.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39468708", "kind": "science-record", "revision": 3, "content_hash": "sha256:896cc04078ce53fb2c83885f200fb7b18e2fbb53a571961f6fed1da263c448e2", "created_at": "2026-11-01T20:29:43Z", "updated_at": "2026-11-01T22:13:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated analysis of bulk and single-cell RNA sequencing reveals the impact of nicotinamide and tryptophan metabolism on glioma prognosis and immunotherapy sensitivity.", "doi": "10.1186/s12883-024-03924-5", "pmid": "39468708", "authors": ["Sen Wang", "Shen Gao", "Shaochong Lin", "Xiaofeng Fang", "Haopeng Zhang", "Man Qiu", "Kai Zheng", "Yupeng Ji", "Baijun Xiao", "Xiangtong Zhang"], "journal": "BMC neurology", "year": 2024, "abstract": "BACKGROUND: Nicotinamide and tryptophan metabolism play important roles in regulating tumor synthesis metabolism and signal transduction functions. However, their comprehensive impact on the prognosis and the tumor immune microenvironment of glioma is still unclear. The purpose of this study was to investigate the association of nicotinamide and tryptophan metabolism with prognosis and immune status of gliomas and to develop relevant models for predicting prognosis and sensitivity to immunotherapy in gliomas.\nMETHODS: Bulk and single-cell transcriptome data from TCGA, CGGA and GSE159416 were obtained for this study. Gliomas were classified based on nicotinamide and tryptophan metabolism, and PPI network associated with differentially expressed genes was established. The core genes were identified and the risk model was established by machine learning techniques, including univariate Cox regression and LASSO regression. Then the risk model was validated with data from the CGGA. Finally, the effects of genes in the risk model on the biological behavior of gliomas were verified by in vitro experiments.\nRESULTS: The high nicotinamide and tryptophan metabolism is associated with poor prognosis and high levels of immune cell infiltration in glioma. Seven of the core genes related to nicotinamide and tryptophan metabolism were used to construct a risk model, and the model has good predictive ability for prognosis, immune microenvironment, and response to immune checkpoint therapy of glioma. We also confirmed that high expression of TGFBI can lead to an increased level of migration, invasion, and EMT of glioma cells, and the aforementioned effect of TGFBI can be reduced by FAK inhibitor PF-573,228.\nCONCLUSIONS: Our study evaluated the effects of nicotinamide and tryptophan metabolism on the prognosis and tumor immune microenvironment of glioma, which can help predict the prognosis and sensitivity to immunotherapy of glioma.", "claims": [{"id": "claim-method", "statement": "The core genes were identified and the risk model was established by machine learning techniques, including univariate Cox regression and LASSO regression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39468708", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The core genes were identified and the risk model was established by machine learning techniques, including univariate Cox regression and LASSO regression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets TCGA-GBM and TCGA-LGG analyzed in the current study can be found in the Cancer Genome Atlas database (https://portal.gdc.cancer.gov/projects). Datasets CGGA mRNAseq_693, CGGA mRNAseq_125, and CGGA mRNA array_101 were collected in Chinese Glioma Genome Atlas (http://www.cgga.org.cn/). GSE159416 were downloaded from Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159416).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39468708", "locator": "sections[35] \"notes\" paragraph 1", "quote": "The datasets TCGA-GBM and TCGA-LGG analyzed in the current study can be found in the Cancer Genome Atlas database (https://portal.gdc.cancer.gov/projects). Datasets CGGA mRNAseq_693, CGGA mRNAseq_125, and CGGA mRNA array_101 were collected in Chinese Glioma Genome Atlas (http://www.cgga.org.cn/). GSE159416 were downloaded from Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159416)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seven of the core genes related to nicotinamide and tryptophan metabolism were used to construct a risk model, and the model has good predictive ability for prognosis, immune microenvironment, and response to immune checkpoint therapy of glioma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39468708", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Seven of the core genes related to nicotinamide and tryptophan metabolism were used to construct a risk model, and the model has good predictive ability for prognosis, immune microenvironment, and response to immune checkpoint therapy of glioma."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Seven of the core genes related to nicotinamide and tryptophan metabolism were used to construct a risk model, and the model has good predictive ability for prognosis, immune microenvironment, and response to immune checkpoint therapy of glioma.", "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:39468708"], "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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