Tryptophan metabolism-related gene CYP1B1 serves as a shared biomarker for both Parkinson's disease and insomnia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39779759", "kind": "science-record", "revision": 4, "content_hash": "sha256:4a2bc2d4628c15bdba51d1f449bf5c5611deb2efa94684d4a6419bd29605ec39", "created_at": "2026-11-01T20:30:06Z", "updated_at": "2026-11-01T22:55:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Tryptophan metabolism-related gene CYP1B1 serves as a shared biomarker for both Parkinson's disease and insomnia.", "doi": "10.1038/s41598-024-84362-8", "pmid": "39779759", "authors": ["Xin-Yu Li", "Wen-Kai Yu", "Jing-Hao Wu", "Wen-Jun He", "Yu-Nan Cheng", "Kai Gao", "Yi-Han Wei", "Yu-Sheng Li"], "journal": "Scientific reports", "year": 2025, "abstract": "Parkinson's disease (PD) and insomnia are prevalent neurological disorders, with emerging evidence implicating tryptophan (TRP) metabolism in their pathogenesis. However, the precise mechanisms by which TRP metabolism contributes to these conditions remain insufficiently elucidated. This study explores shared tryptophan metabolism-related genes (TMRGs) and molecular mechanisms underlying PD and insomnia, aiming to provide insights into their shared pathogenesis. We analyzed datasets for PD (GSE100054) and insomnia (GSE208668) obtained from the Gene Expression Omnibus (GEO) database. TMRGs were obtained from the Molecular Signatures Database (MSigDB) and the Genecards database. Tryptophan metabolism-related differentially expressed genes (TM-DEGs) were identified by intersecting TMRGs with shared differentially expressed genes (DEGs) from these datasets. Through Protein-Protein Interaction (PPI) network analysis, Support Vector Machine-Recursive Feature Elimination (SVM-RFE) , and Extreme Gradient Boosting (XGBoost) machine learning, we identified Cytochrome P4501B1 (CYP1B1) and Electron Transfer Flavoprotein Alpha (ETFA) as key hub genes. Subsequently, we employed CIBERSORT and single-sample gene set enrichment analysis (ssGSEA) to further investigate the association between hub genes and peripheral immune activation and inflammatory response. Additionally, gene interaction, Drug-mRNA, Transcription Factor (TF)-mRNA, and competing endogenous RNA (ceRNA) networks centered on these hub genes were constructed to explore regulatory mechanisms and potential drug interactions. Finally, validation through bioinformatics and animal experiments identified CYP1B1 as a promising biomarker associated with both PD and insomnia.", "claims": [{"id": "claim-method", "statement": "DEGs were identified using the ‘limma’ package (v3.54.2)32, with selection criteria of p-value < 0.05 and absolute log2 fold change (|log2FC|) > 0.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39779759", "locator": "sections[4] \"Identification of TM-DEGs in PD and insomnia\" paragraph 2", "quote": "DEGs were identified using the ‘limma’ package (v3.54.2)32, with selection criteria of p-value < 0.05 and absolute log2 fold change (|log2FC|) > 0.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets used in this study are publicly available. The RNA-seq data were obtained from the following GEO datasets: GSE100054, GSE208668, GSE165082, GSE198273, and GSE49036. These datasets are accessible at the NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39779759", "locator": "sections[33] \"notes\" paragraph 1", "quote": "All datasets used in this study are publicly available. The RNA-seq data were obtained from the following GEO datasets: GSE100054, GSE208668, GSE165082, GSE198273, and GSE49036. These datasets are accessible at the NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After intersecting results, we finally identified 2 hub genes (CYP1B1, ETFA) shared across PPI network analysis, SVM-RFE, and XGBoost algorithms.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39779759", "locator": "sections[20] \"Identification of hub genes using PPI network analysis and machine learning\" paragraph 2", "quote": "After intersecting results, we finally identified 2 hub genes (CYP1B1, ETFA) shared across PPI network analysis, SVM-RFE, and XGBoost algorithms (Fig. 3F)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After intersecting results, we finally identified 2 hub genes (CYP1B1, ETFA) shared across PPI network analysis, SVM-RFE, and XGBoost algorithms.", "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:39779759"], "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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Ten-week-old C57BL/6 J mice were obtained from Beijing Vital River Laboratory", "ogy Co., Ltd. (Beijing, China). Six of these mice were subjected to a chronic sleep deprivation app", "one week to model clinical insomnia. Control mice were housed in identical apparatuses to maintain", "al apparatuses to maintain normal sleep. All mice were kept under standard laboratory conditions: 2"], "order_basis": "paper_text_order:2429", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ate our conclusions, we employed qRT-PCR and Western blotting to assess transcriptional changes in CYP1B1", "pheral blood compared to controls (Fig. 8A). Western blotting similarly confirmed increased protein expres", "d compared to controls (Fig. 8C). Subsequent Western blotting confirmed these results, consistent with the", "genes in mouse peripheral blood samples. (B) Western blot validation of differential protein expressio"], "order_basis": "paper_text_order:7047", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["DEGs were identified using the ‘limma’ package (v3.54.2)32, with selection criteria of p-value < 0.05 and absolute log2 fold change (|log2FC|) > 0.5."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}