Identification of potential regulatory long non-coding RNA-associated competing endogenous RNA axes in periplaque regions in multiple sclerosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36324503", "kind": "science-record", "revision": 4, "content_hash": "sha256:4c4cee3e09f8fbba5260b9b63776cd73c333b5133739e8fa6f2e049fa3671232", "created_at": "2026-11-01T18:15:45Z", "updated_at": "2026-11-01T22:08:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential regulatory long non-coding RNA-associated competing endogenous RNA axes in periplaque regions in multiple sclerosis.", "doi": "10.3389/fgene.2022.1011350", "pmid": "36324503", "authors": ["Hani Sabaie", "Sharareh Khorami Rouz", "Ghazal Kouchakali", "Samaneh Heydarzadeh", "Mohammad Reza Asadi", "Mirmohsen Sharifi-Bonab", "Bashdar Mahmud Hussen", "Mohammad Taheri", "Seyed Abdulmajid Ayatollahi", "Maryam Rezazadeh"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Slow-burning inflammation at the lesion rim is connected to the expansion of chronic multiple sclerosis (MS) lesions. However, the underlying processes causing expansion are not clearly realized. In this context, the current study used a bioinformatics approach to identify the expression profiles and related lncRNA-associated ceRNA regulatory axes in the periplaque region in MS patients. Expression data (GSE52139) from periplaque regions in the secondary progressive MS spinal cord and controls were downloaded from the Gene Expression Omnibus database (GEO), which has details on mRNAs and lncRNAs. Using the R software's limma package, the differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were found. The RNA interactions were also found using the DIANA-LncBase, miRTarBase, and HMDD databases. The Pearson correlation coefficient was used to determine whether there were any positive correlations between DEmRNAs and DElncRNAs in the ceRNA network. Finally, lncRNA-associated ceRNA axes were created based on co-expression and connections between DElncRNA, miRNA, and DEmRNA. We used the Enrichr tool to enrich the biological process, molecular function, and pathways for DEmRNAs and DElncRNAs. A network of DEmRNAs' protein-protein interactions was developed, and the top five hub genes were found using Cytoscape and STRING. The current study indicates that 15 DEmRNAs, including FOS, GJA1, NTRK2, CTNND1, and SP3, are connected to the MS ceRNA network. Additionally, four DElncRNAs (such as TUG1, ASB16-AS1, and LINC01094) that regulated the aforementioned mRNAs by sponging 14 MS-related miRNAs (e.g., hsa-miR-145-5p, hsa-miR-200a-3p, hsa-miR-20a-5p, hsa-miR-22-3p, hsa-miR-23a-3p, hsa-miR-27a-3p, hsa-miR-29b-3p, hsa-miR-29c-3p, hsa-miR-34a-5p) were found. In addition, the analysis of pathway enrichment revealed that DEmRNAs were enriched in the pathways for the \"MAPK signaling pathway\", \"Kaposi sarcoma-associated herpesvirus infection\", \"Human immunodeficiency virus one infection\", \"Lipid and atherosclerosis\", and \"Amphetamine addiction\". Even though the function of these ceRNA axes needs to be investigated further, this study provides research targets for studying ceRNA-mediated molecular mechanisms related to periplaque demyelination in MS.", "claims": [{"id": "claim-method", "statement": "The Pearson correlation analysis was done to study the positive correlations in the regulatory axes of ceRNA among DEmRNAs and DElncRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36324503", "locator": "sections[6] \"Analysis of correlation between DEmRNAs and DElncRNAs, and lncRNA-associated ceRNA axes construction\" paragraph 2", "quote": "The Pearson correlation analysis was done to study the positive correlations in the regulatory axes of ceRNA among DEmRNAs and DElncRNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52139).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36324503", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52139)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The current study indicates that 15 DEmRNAs, including FOS, GJA1, NTRK2, CTNND1, and SP3, are connected to the MS ceRNA network.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36324503", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The current study indicates that 15 DEmRNAs, including FOS, GJA1, NTRK2, CTNND1, and SP3, are connected to the MS ceRNA network."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The current study indicates that 15 DEmRNAs, including FOS, GJA1, NTRK2, CTNND1, and SP3, are connected to the MS ceRNA network.", "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:36324503"], "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:GSE52139"], "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:GSE52139"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36324503", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.1011350", "sha256": "sha256:7c6afe714d146f081587a2514411daa209573e450adaba2500cd031643896c10", "bytes": 59670, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2022.1011350", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9619104", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE52139", "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=GSE52139", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE52139", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52139).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52139).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1260234", "GSM1260235", "GSM1260236", "GSM1260237", "GSM1260238", "GSM1260239", "GSM1260240", "GSM1260241", "GSM1260242", "GSM1260243", "GSM1260244", "GSM1260245", "GSM1260246", "GSM1260247", "GSM1260248", "GSM1260249"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from periplaque regions in multiple sclerosis spinal cord", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE52139 not downloaded", "asset:data:geo:GSE52139 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Pearson correlation analysis was done to study the positive correlations in the regulatory axes of ceRNA among DEmRNAs and DElncRNAs."}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE52139"], "resolved_accessions": ["GSE52139"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52139)."], "basis": "The paper names GSE52139 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pearson_r"], "assets": ["source:pmid:36324503", "data:geo:GSE52139"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE52139"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:14:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 18291, "completion_tokens": 1729, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36324503", "type": "paper", "label": "pmid:36324503"}, {"id": "source:pmid:36324503", "type": "manuscript", "label": "PMID 36324503 full text"}, {"id": "data:geo:GSE52139", "type": "dataset", "label": "GEO GSE52139"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36324503", "type": "paper", "label": "pmid:36324503"}, {"id": "source:pmid:36324503", "type": "manuscript", "label": "PMID 36324503 full text"}, {"id": "data:geo:GSE52139", "type": "dataset", "label": "GEO GSE52139"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36324503", "type": "extraction", "used": ["source:pmid:36324503"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE52139", "type": "accession_resolution", "used": ["data:geo:GSE52139"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:36324503", "parent_hash": "sha256:108141bb8b410be399e500439918d508c42ec10759d7b147bd8087e770b85bba", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE52139 licence not read", "asset:data:geo:GSE52139 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Pearson correlation analysis was done to study the positive correlations in the regulatory axes of ceRNA among DEmRNAs and DElncRNAs."], "order_basis": "analysis_only", "id": "assay:1"}]}