Identification of miRNA-mRNA Pairs in Relation to TNF-α/IL-1β Induced Inflammatory Response in Intervertebral Disc Degeneration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35990856", "kind": "science-record", "revision": 3, "content_hash": "sha256:6ed72c6fdc05ccab402979d7223cbff06f80cf556999f9f2b9e383390b94f16f", "created_at": "2026-11-01T18:15:07Z", "updated_at": "2026-11-01T21:28:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of miRNA-mRNA Pairs in Relation to TNF-α/IL-1β Induced Inflammatory Response in Intervertebral Disc Degeneration.", "doi": "10.1155/2022/3374091", "pmid": "35990856", "authors": ["Ye Wei", "Yulin Chen", "Han Su", "Chunyan Ling", "Guangtian Huang", "Dongling Wang", "Guanghui Chen"], "journal": "Evidence-based complementary and alternative medicine : eCAM", "year": 2022, "abstract": "Objective: The determination of miRNA-mRNA pairs for intervertebral disc degeneration (IVDD) regulated by pro-inflammatory cytokines were investigated.\nMethods: Two dataset (accession number GSE27494 and GSE41883 from platform GPL1352) of expression profiling was downloaded from Gene Expression Omnibus (GEO). The annulus cells were isolated from annulus fibrosus in patients with degenerative disc disease. The cells were then cultured in a three-dimensional (3D) collagen containing with/without proinflammatory cytokines (tumor necrosis factor alpha (TNF-α) or interleukin beta (IL-1β)). After being cultured for 14 days, the isolated total RNA was analyzed via microarray, and the expression array data were obtained using BRB-Array Tools followed by analyzing the differentially expressed genes (DEGs) and the prediction of potential miRNA targets of hub genes through online database.\nResults: Firstly, 52 and 296 DEGs were found in IL-1β- and TNF-α-induced annulus cells, respectively, of these there had 42 common DEGs (co-DEGs) with 34 increased transcripts and 8 reduced ones. Based on the GO and KEGG software, these co-DEGs were mainly enriched in the response to lipopolysaccharide (LPS) and molecule of bacterial origin, the regulation of receptor ligand activity and signaling receptor activator activity, as well as the following signaling pathways, including TNF signaling pathway, IL-17 signaling pathway, and NF-κB signaling pathway. Top hub genes (CXCL1, CXCL2, CXCL8, IL1Β and PTGS2) regulated by several potential microRNAs were involved in TNF-α/IL-1β treated annulus cells.\nConclusions: Several candidate genes regulated by miRNAs caused by TNF-α/IL-1β in the annulus cells were found, which will guide diagnosis and treatment for degenerative disc disease.", "claims": [{"id": "claim-method", "statement": "Using the unpaired t-test with statistical significance as the threshold of adjusted P value < 0.05 and log fold change (Log2FC) ≥ 1.5, the DEGs were screened, followed by generating a volcano plot of DEGs with statistical significance using BRB Array Tools (version 3.7) strictly according to the user's manual.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35990856", "locator": "sections[5] \"2.3. Identification of Differentially Expressed Genes (DEGs) Analysis\" paragraph 2", "quote": "Using the unpaired t-test with statistical significance as the threshold of adjusted P value < 0.05 and log fold change (Log2FC) ≥ 1.5, the DEGs were screened, followed by generating a volcano plot of DEGs with statistical significance using BRB Array Tools (version 3.7) strictly according to the user's manual."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data supporting the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35990856", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The data supporting the findings of this study are included within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "IL-1β treatment produced 52 DEGs, TNF-α treatment produced 296 DEGs, and the treatments shared 42 co-DEGs, including 34 upregulated and 8 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35990856", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Firstly, 52 and 296 DEGs were found in IL-1β- and TNF-α-induced annulus cells, respectively, of these there had 42 common DEGs (co-DEGs) with 34 increased transcripts and 8 reduced ones."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "IL-1β treatment produced 52 DEGs, TNF-α treatment produced 296 DEGs, and the treatments shared 42 co-DEGs, including 34 upregulated and 8 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:35990856"], "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:GSE27494"], "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:GSE27494"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35990856", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/3374091", "sha256": "sha256:58684d102201ca326b3c264ab3151493c6887a2086e7cd43a179443f14b305e5", "bytes": 32557, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/3374091", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9391105", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE27494", "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=GSE27494", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27494", "version": null, "note": "The data supporting the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM679415", "GSM679416", "GSM679417", "GSM679418", "GSM679419", "GSM679420", "GSM679421", "GSM679422"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "1352", "taxon": "Homo sapiens", "title": "IL-1 Exposure Significantly increases gene expression of BDNF, NTF3 and NRP2 as well as NGF Production in Human Annulus Cells", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE41883", "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=GSE41883", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41883", "version": null, "note": "The data supporting the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1026926", "GSM1026927", "GSM1026928", "GSM1026929", "GSM1026930", "GSM1026931", "GSM1026932", "GSM1026933"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "1352", "taxon": "Homo sapiens", "title": "Human annulus disc cells grown in a 3D collagen sponge and exposed to TNF-a", "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:GSE27494 not downloaded", "asset:data:geo:GSE27494 licence not read", "asset:data:geo:GSE41883 not downloaded", "asset:data:geo:GSE41883 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Unpaired t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using the unpaired t-test with statistical significance as the threshold of adjusted P value < 0.05 and log fold change (Log2FC) ≥ 1.5, the DEGs were screened, followed by generating a volcano plot of DEGs with statistical significance using BRB Array Tools (version 3.7) strictly according to the user's manual."}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Unpaired t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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