Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38521905", "kind": "science-record", "revision": 5, "content_hash": "sha256:1d036d2a479be5b4cd834a123102bac60c9f4dd64d9d0e0e5475b05814b94f23", "created_at": "2026-11-01T19:20:28Z", "updated_at": "2026-11-01T22:53:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.", "doi": "10.1186/s12967-024-05092-z", "pmid": "38521905", "authors": ["Jingtong Wu", "Yinyin Lv", "Pei Hao", "Ziyi Zhang", "Yongtian Zheng", "Ermei Chen", "Yanyun Fan"], "journal": "Journal of translational medicine", "year": 2024, "abstract": "BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.\nMETHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.\nRESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.\nCONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.", "claims": [{"id": "claim-method", "statement": "LASSO regression was implemented using the “glmNETs” R package to filter down to 11 genes. Random Forest classifier and Support Vector Machine (SVM) analyses were implemented using the “randomForest” and “kernlab” R packages, and the top 10 genes were retained.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38521905", "locator": "sections[4] \"Identification of lactylation-related hub genes in CD patients\" paragraph 2", "quote": "LASSO regression was implemented using the “glmNETs” R package to filter down to 11 genes. Random Forest classifier and Support Vector Machine (SVM) analyses were implemented using the “randomForest” and “kernlab” R packages, and the top 10 genes were retained."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding authors upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38521905", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding authors upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified six Lactylation-related hub genes that are highly associated with CD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38521905", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified six Lactylation-related hub genes that are highly associated with CD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We identified six Lactylation-related hub genes that are highly associated with CD.", "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:38521905"], "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:GSE112366"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:machine_learning_random_forest", "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:GSE112366"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:machine_learning_random_forest"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38521905", "role": "manuscript", "format": "xml", "media_type": "application/xml", 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