Prediction and Verification of Potential Therapeutic Targets for Non-Responders to Infliximab in Ulcerative Colitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37215377", "kind": "science-record", "revision": 4, "content_hash": "sha256:11e20407d63eb07398b9607344f082ce6c434ff88d7208a582b78c8d9e8d51f2", "created_at": "2026-11-01T19:01:55Z", "updated_at": "2026-11-01T22:51:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prediction and Verification of Potential Therapeutic Targets for Non-Responders to Infliximab in Ulcerative Colitis.", "doi": "10.2147/JIR.S409290", "pmid": "37215377", "authors": ["Xue Lyu", "Zhe Zhang", "Xia Liu", "Li Geng", "Muhan Zhang", "Baisui Feng"], "journal": "Journal of inflammation research", "year": 2023, "abstract": "Background: Infliximab (IFX) has been widely used in ulcerative colitis (UC) patients. However, the subsequent effective treatment of IFX non-response in UC patients remains a challenge. This study aims to predict potential therapeutic targets for non-responders by performing a bioinformatic analysis of the data in the Gene Expression Omnibus (GEO) database and validation by biopsies.\nMethods: Colonic mucosal biopsies expression profiles of IFX-treated UC patients (GSE73661, GSE16879) were utilized to predict potential therapeutic targets. Bioinformatics analyses were used to explore potential biological mechanisms. CytoHubba was performed to screen hub genes. We used a validation dataset and colonic mucosal biopsies of UC patients to validate hub genes.\nResults: A total of 147 DEGs were identified (119 upregulated genes and 28 downregulated genes). GSEA showed that DEGs in GSE73661 were enriched in the pathways of the cytokine-cytokine receptor, the chemokine, and the adhesion molecules system. Based on the PPI network analysis, we identified four hub genes (and the transcription factor NF-κB). Then, we validate the expression of hub genes by reverse transcription-polymerase chain reaction (RT-PCR). We found higher expression of IL-6, IL1B, CXCL8, and CCL2 in non-responders compared to responders.\nConclusion: In summary, four potential targets (IL-6, IL1B, CXCL8, and CCL2) were finally identified by performing a bioinformatics analysis of the datasets in the GEO database. Their expression was confirmed in colonic mucosal biopsies of patients with UC. These results can help to further explore the mechanism of non-responders to IFX in UC and to provide potential targets for their subsequent treatment.", "claims": [{"id": "claim-method", "statement": "Responders to IFX and non-responders to IFX were analyzed using the limma package, and statistically significant altered and DEGs were identified. The significant DEGs were identified with the threshold: adjust P value <0.05 and |log2 (Fold Change) |>1.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37215377", "locator": "sections[3] \"Datasets Selection and Identification of DEGs\" paragraph 2", "quote": "Responders to IFX and non-responders to IFX were analyzed using the limma package, and statistically significant altered and DEGs were identified. The significant DEGs were identified with the threshold: adjust P value <0.05 and |log2 (Fold Change) |>1.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO) datasets (https://www.ncbi.nlm.nih.gov/geo/). And the authors confirm that the data supporting the findings of this study are available within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37215377", "locator": "sections[20] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO) datasets (https://www.ncbi.nlm.nih.gov/geo/). And the authors confirm that the data supporting the findings of this study are available within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 147 DEGs were identified (119 upregulated genes and 28 downregulated genes).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37215377", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 147 DEGs were identified (119 upregulated genes and 28 downregulated genes)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 147 DEGs were identified (119 upregulated genes and 28 downregulated genes).", "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:37215377"], "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:GSE16879"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE16879"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37215377", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S409290", "sha256": "sha256:10bfd94b7270cb88cdc63a48ec88761a551d3ced454f72f455a45b1cef73be2d", "bytes": 31488, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JIR.S409290", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10198282", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16879", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16879", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16879", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO) datasets (https://www.ncbi.nlm.nih.gov/geo/). And the authors confirm that the data supporting the findings of this study are available within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO) datasets (https://www.ncbi.nlm.nih.gov/geo/). 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And the authors confirm that the data supporting the findings of this study are available within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO) datasets (https://www.ncbi.nlm.nih.gov/geo/). 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