Gene Expression Profiling and Immune Pathway Dysregulation in Ribonucleoprotein Autoantibody-Positive Systemic Lupus Erythematosus Patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39596553", "kind": "science-record", "revision": 4, "content_hash": "sha256:c813d8bbe107272991b5bea93ee805978f3925dccbfa67d5b40464f6400cbab3", "created_at": "2026-11-01T20:29:52Z", "updated_at": "2026-11-01T22:55:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene Expression Profiling and Immune Pathway Dysregulation in Ribonucleoprotein Autoantibody-Positive Systemic Lupus Erythematosus Patients.", "doi": "10.3390/genes15111353", "pmid": "39596553", "authors": ["Siyuan Tan", "Tirupapuliyur Damodaran"], "journal": "Genes", "year": 2024, "abstract": "BACKGROUND: Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by immune dysregulation and chronic inflammation across various organ systems. While anti-dsDNA and anti-Sm antibodies are commonly associated with SLE, the presence of anti-RNP antibodies is often linked to unique gene expression profiles and immune responses. This study aims to investigate the gene expression profiles in ribonucleoprotein (RNP) autoantibody-positive SLE patients by analyzing publicly available transcriptomic data.\nMETHODS: This study analyzed transcriptomic data from the GEO dataset GSE61635, which includes gene expression profiles from 79 anti-RNP-positive SLE patients and 30 healthy controls. Differentially expressed genes (DEGs) were identified using the GEO2R tool with a p-value < 0.05 and |log2fold change| > 1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Tissue-specific and cell-type enrichment analyses highlighted the involvement of immune tissues.\nRESULTS: A total of 1891 DEGs were identified between anti-RNP-positive SLE patients and healthy controls. Among the identified DEGs, SLC4A1 and EPB42 were notably downregulated, while PIP4K2A was highly upregulated. Enrichment analyses revealed significant dysregulation in antiviral response and immune regulation pathways. PPI network analysis highlighted key hub genes, suggesting a heightened antiviral state in these patients. Tissue-specific enrichment and cell-type enrichment identified the bone marrow and immune tissues as being highly affected by the altered gene expression. Additionally, gene frequency analysis highlighted RASD2 as being recurrently significant across multiple studies.\nCONCLUSIONS: The findings suggest that anti-RNP-positive SLE patients exhibit distinct gene expression and immune dysregulation profiles, particularly in antiviral and immune regulation pathways. These results provide insights into the molecular mechanisms driving SLE in this patient subset and may guide future therapeutic interventions.", "claims": [{"id": "claim-method", "statement": "GEO2R uses the Limma (Linear Models for Microarray Data) package to identify DEGs by comparing expression levels across different conditions.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39596553", "locator": "sections[4] \"2.2. Data Processing\" paragraph 2", "quote": "GEO2R uses the Limma (Linear Models for Microarray Data) package to identify DEGs by comparing expression levels across different conditions."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors declare that the data supporting the findings of this study are available within the paper.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39596553", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "The authors declare that the data supporting the findings of this study are available within the paper."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 1891 DEGs (p-value < 0.05, |log2fold change| > 1) were identified between RNP autoantibody+ SLE patients and healthy blood donors.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "A total of 1891 DEGs (p-value < 0.05, |log2fold change| > 1) were identified between RNP autoantibody+ SLE patients and healthy blood donors."}, "evidence": [{"asset": "source:pmid:39596553", "locator": "sections[11] \"3.1. Differential Gene Expression Analysis\" paragraph 2", "quote": "A total of 1891 DEGs (p-value < 0.05, |log2fold change| > 1) were identified between RNP autoantibody+ SLE patients and healthy blood donors."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 1891 DEGs (p-value < 0.05, |log2fold change| > 1) were identified between RNP autoantibody+ SLE patients and healthy blood donors.", "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:39596553"], "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:GSE61635"], "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:GSE61635"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39596553", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/genes15111353", "sha256": "sha256:c1a2785b9103c5aecc7d2234d5e477a72634e129b5f95007158831a7a529cfca", "bytes": 27590, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/genes15111353", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11593874", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE61635", "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=GSE61635", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61635", "version": null, "note": "The authors declare that the data supporting the findings of this study are available within the paper.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The authors declare that the data supporting the findings of this study are available within the paper.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1509610", "GSM1509611", "GSM1509612", "GSM1509613", "GSM1509614", "GSM1509615", "GSM1509616", "GSM1509617", "GSM1509618", "GSM1509619", "GSM1509620", "GSM1509621", "GSM1509622", "GSM1509623", "GSM1509624", "GSM1509625", "GSM1509626", "GSM1509627", "GSM1509628", "GSM1509629", "GSM1509630", "GSM1509631", "GSM1509632", "GSM1509633", "GSM1509634", "GSM1509635", "GSM1509636", "GSM1509637", "GSM1509638", "GSM1509639", "GSM1509640", "GSM1509641", "GSM1509642", "GSM1509643", "GSM1509644", "GSM1509645", "GSM1509646", "GSM1509647", "GSM1509648", "GSM1509649", "GSM1509650", "GSM1509651", "GSM1509652", "GSM1509653", "GSM1509654", "GSM1509655", "GSM1509656", "GSM1509657", "GSM1509658", "GSM1509659", "GSM1509660", "GSM1509661", "GSM1509662", "GSM1509663", "GSM1509664", "GSM1509665", "GSM1509666", "GSM1509667", "GSM1509668", "GSM1509669", "GSM1509670", "GSM1509671", "GSM1509672", "GSM1509673", "GSM1509674", "GSM1509675", "GSM1509676", "GSM1509677", "GSM1509678", "GSM1509679", "GSM1509680", "GSM1509681", "GSM1509682", "GSM1509683", "GSM1509684", "GSM1509685", "GSM1509686", "GSM1509687", "GSM1509688", "GSM1509689", "GSM1509690", "GSM1509691", "GSM1509692", "GSM1509693", "GSM1509694", "GSM1509695", "GSM1509696", "GSM1509697", "GSM1509698", "GSM1509699", "GSM1509700", "GSM1509701", "GSM1509702", "GSM1509703", "GSM1509704", "GSM1509705", "GSM1509706", "GSM1509707", "GSM1509708", "GSM1509709", "GSM1509710", "GSM1509711", "GSM1509712", "GSM1509713", "GSM1509714", "GSM1509715", "GSM1509716", "GSM1509717", "GSM1509718", "GSM1509719", "GSM1509720", "GSM1509721", "GSM1509722", "GSM1509723", "GSM1509724", "GSM1509725", "GSM1509726", "GSM1509727", "GSM1509728", "GSM1509729", "GSM1509730", "GSM1509731", "GSM1509732", "GSM1509733", "GSM1509734", "GSM1509735", "GSM1509736", "GSM1509737", "GSM1509738"], "sample_count": 129, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression in RNP autoantibody+ systemic lupus erythematosus (SLE) patient blood", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE61635 not downloaded", "asset:data:geo:GSE61635 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "GEO2R uses the Limma (Linear Models for Microarray Data) package to identify DEGs by comparing expression levels across different conditions."}}, {"id": "method-2", "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": "PPI"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 2.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. 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