Characterization of Genetic and Chemical Drivers in the Pathogenesis of DRESS Syndrome: In Silico Study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41017862", "kind": "science-record", "revision": 3, "content_hash": "sha256:58d4ef7a215bb469262792d8c033202815f137a87349e403dd2f427fbe7dbf65", "created_at": "2026-11-01T20:31:05Z", "updated_at": "2026-11-01T22:14:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterization of Genetic and Chemical Drivers in the Pathogenesis of DRESS Syndrome: In Silico Study.", "doi": "10.1002/hsr2.71283", "pmid": "41017862", "authors": ["Ahmed I AbdElneam", "Mohammed S Al-Dhubaibi", "Saleh S Bahaj", "Ghada F Mohammed", "Lina M Atef", "Walaa A Siam", "Amany A E Elshemally", "Ali I A Abdel Rhaim", "Sameh S Aziz"], "journal": "Health science reports", "year": 2025, "abstract": "Background and Aims: The pathophysiology of drug rash with eosinophilia and systemic symptoms (DRESS) syndrome is complex and poorly understood. Genetic predispositions play a significant role. We aimed to explore the genetic factors and molecular mechanisms driving DRESS, focusing on gene expression, transcription factors (TFs), microRNAs (miRNAs), and chemical interactions.\nMethods: We utilized RNA-seq data from the GSE160369 data set in the gene expression omnibus (GEO) database to identify differentially expressed genes (DEGs) related to DRESS. The analysis was conducted using GEO2R for identifying upregulated and downregulated genes. Protein-protein interaction (PPI) networks were constructed using STRING and further analyzed with Cytoscape and CytoHubba. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify biological pathways. miRNAs and TFs were predicted using bioinformatics tools like TargetScan, miRDB, and ChEA3, while chemical interactions with key genes were explored using CTDbase.\nResults: A total of 336 DEGs were identified, including 239 upregulated and 97 downregulated genes. The PPI network highlighted TNF, IL2, and CD40 as central genes involved in immune-related pathways. Functional enrichment analyses revealed significant pathways related to immune activation, such as leukocyte-mediated immunity. We predicted 15 miRNAs, including hsa-miR-1296-5p, and identified 10 TFs, such as MTF1 and NFKB2, which regulate the expression of key genes. Chemical interaction analysis revealed decitabine and tetradecanoylphorbol acetate as prominent agents modulating gene expression.\nConclusion: miRNAs, TFs, and chemical modulators, which play a key role in the development of DRESS syndrome. Knowledge of the molecular underpinnings of DRESS, imperative for therapeutic targets.", "claims": [{"id": "claim-method", "statement": "The GSE160369 data set was examined utilizing the GEO2R analytical tool accessible via the NCBI platform at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60481.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41017862", "locator": "sections[4] \"Analysis of RNA‐seq‐Seq GSE60481\" paragraph 2", "quote": "The GSE160369 data set was examined utilizing the GEO2R analytical tool accessible via the NCBI platform at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60481."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions. “All authors have read and approved the final version of the manuscript [Saleh S. Bahaj] had full access to all of the data in this study and takes complete responsibility for the integrity of the data and the accuracy of the data analysis.”", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41017862", "locator": "sections[27] \"Data Availability Statement\" paragraph 2", "quote": "The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions. “All authors have read and approved the final version of the manuscript [Saleh S. Bahaj] had full access to all of the data in this study and takes complete responsibility for the integrity of the data and the accuracy of the data analysis.”"}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 336 DEGs were identified, including 239 upregulated and 97 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41017862", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 336 DEGs were identified, including 239 upregulated and 97 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 336 DEGs were identified, including 239 upregulated and 97 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:41017862"], "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:GSE160369"], "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:GSE160369"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41017862", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/hsr2.71283", "sha256": "sha256:b63a0f902601f83db52989c0dd222c1c7463bf6f4eaf52ed0e4d9a178dc885f9", "bytes": 35994, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/hsr2.71283", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12464728", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE160369", "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=GSE160369", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE160369", "version": null, "note": "The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions. “All authors have read and approved the final version of the manuscript [Saleh S. Bahaj] had full access to all of the data in this study and takes complete responsibility for the integrity of the data and the accuracy of the data analysis.”", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions. “All authors have read and approved the final version of the manuscript [Saleh S. Bahaj] had full access to all of the data in this study and takes complete responsibility for the integrity of the data and the accuracy of the data analysis.”", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4872323", "GSM4872324", "GSM4872325", "GSM4872326", "GSM4872327", "GSM4872328", "GSM4872329", "GSM4872330", "GSM4872331", "GSM4872332"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "RNA sequencing data from patients with drug reaction with eosinophilia and systemic symptoms to antibiotics", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE160369 not downloaded", "asset:data:geo:GSE160369 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The GSE160369 data set was examined utilizing the GEO2R analytical tool accessible via the NCBI platform at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60481."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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