Identification of Chemokines-Related miRNAs as Potential Biomarkers in Psoriasis Based on Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35993468", "kind": "science-record", "revision": 4, "content_hash": "sha256:bac8de7ad35f8fef737ce46d9648cb2c8ee2c550816f4e1ddb95d9eb44aff620", "created_at": "2026-11-01T18:15:09Z", "updated_at": "2026-11-01T22:07:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Chemokines-Related miRNAs as Potential Biomarkers in Psoriasis Based on Integrated Bioinformatics Analysis.", "doi": "10.2174/1386207325666220819194249", "pmid": "35993468", "authors": ["Haojun Zhuang", "Xiaoming Wang", "Meiliang Guo", "Qinqin Meng", "Na Liu", "Min Wei", "Yuling Shi", "Hui Deng"], "journal": "Combinatorial chemistry & high throughput screening", "year": 2023, "abstract": "BACKGROUND: Psoriasis is an immune-mediated skin disorder caused by the proliferation of keratinocytes. Although psoriasis is generally diagnosed based on clinical manifestations, sensitive biomarkers are needed to help diagnose psoriasis early with atypical presentations. MicroRNAs play a functional role in the development of psoriasis, and they are stable and suitable as biomarkers in psoriasis.\nMATERIAL AND METHODS: The GSE50790 and GSE53552 datasets from the Gene Expression Omnibus (GEO) database were used to identify Differentially Expressed Genes (DEGs) between the control group and the lesional group. DEGs were processed for enrichment analysis to explore the functions, and a Protein-Protein Interaction (PPI) network was constructed to obtain gene clusters. The signalling pathway associated with gene cluster 1 was processed to further identify related genes. Hub genes were obtained through the intersection of cluster 1 and the related genes. Hub genes were used to predict the miRNAs through a gene-miRNA interaction network. The relative expression of miRNAs was measured by qRT-PCR to identify the suitability of miRNAs as biomarkers.\nRESULTS: Bioinformatics analysis revealed that the chemokine signalling pathway is involved in the development of psoriasis. Five related miRNAs were mined from the datasets, and qRT-PCR showed that hsa-miR-612 (p=0.0015), hsa-miR-3194-5p (p=0.0078) and hsa-miR-4316 (p<0.0001) may be potential biomarkers in psoriasis.", "claims": [{"id": "claim-method", "statement": "The obtained data were analysed by the Student’s t-test using SPSS 24.0 (Chicago, IL, USA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35993468", "locator": "sections[11] \"Statistical Analysis\" paragraph 2", "quote": "The obtained data were analysed by the Student’s t-test using SPSS 24.0 (Chicago, IL, USA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Previously reported gene expression profiles (GSE50790 and GSE53552) data were used to support this study and are available in Gene Expression Omnibus (GEO) database. All data generated from the analysis process of this study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35993468", "locator": "sections[26] \"AVAILABILITY OF DATA AND MATERIALS\" paragraph 2", "quote": "Previously reported gene expression profiles (GSE50790 and GSE53552) data were used to support this study and are available in Gene Expression Omnibus (GEO) database. All data generated from the analysis process of this study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "qRT-PCR showed that hsa-miR-612 (p=0.0015), hsa-miR-3194-5p (p=0.0078) and hsa-miR-4316 (p<0.0001) may be potential biomarkers in psoriasis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35993468", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "qRT-PCR showed that hsa-miR-612 (p=0.0015), hsa-miR-3194-5p (p=0.0078) and hsa-miR-4316 (p<0.0001) may be potential biomarkers in psoriasis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "qRT-PCR showed that hsa-miR-612 (p=0.0015), hsa-miR-3194-5p (p=0.0078) and hsa-miR-4316 (p<0.0001) may be potential biomarkers in psoriasis.", "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:35993468"], "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:GSE50790"], "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:GSE50790"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35993468", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2174/1386207325666220819194249", "sha256": "sha256:4632a94a049b779fd36f1ad1d0ae8ce912435f183def71297972e5a8f51a6811", "bytes": 25771, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2174/1386207325666220819194249", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10234082", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE50790", "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=GSE50790", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50790", "version": null, "note": "Previously reported gene expression profiles (GSE50790 and GSE53552) data were used to support this study and are available in Gene Expression Omnibus (GEO) database. All data generated from the analysis process of this study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Previously reported gene expression profiles (GSE50790 and GSE53552) data were used to support this study and are available in Gene Expression Omnibus (GEO) database. All data generated from the analysis process of this study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1229341", "GSM1229342", "GSM1229343", "GSM1229344", "GSM1229345", "GSM1229346", "GSM1229347", "GSM1229348"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression in psoriasis lesions and uninvolved skin", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE53552", "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=GSE53552", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53552", "version": null, "note": "Previously reported gene expression profiles (GSE50790 and GSE53552) data were used to support this study and are available in Gene Expression Omnibus (GEO) database. All data generated from the analysis process of this study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Previously reported gene expression profiles (GSE50790 and GSE53552) data were used to support this study and are available in Gene Expression Omnibus (GEO) database. All data generated from the analysis process of this study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1296024", "GSM1296025", "GSM1296026", "GSM1296027", "GSM1296028", "GSM1296029", "GSM1296030", "GSM1296031", "GSM1296032", "GSM1296033", "GSM1296034", "GSM1296035", "GSM1296036", "GSM1296037", "GSM1296038", "GSM1296039", "GSM1296040", "GSM1296041", "GSM1296042", "GSM1296043", "GSM1296044", "GSM1296045", "GSM1296046", "GSM1296047", "GSM1296048", "GSM1296049", "GSM1296050", "GSM1296051", "GSM1296052", "GSM1296053", "GSM1296054", "GSM1296055", "GSM1296056", "GSM1296057", "GSM1296058", "GSM1296059", "GSM1296060", "GSM1296061", "GSM1296062", "GSM1296063", "GSM1296064", "GSM1296065", "GSM1296066", "GSM1296067", "GSM1296068", "GSM1296069", "GSM1296070", "GSM1296071", "GSM1296072", "GSM1296073", "GSM1296074", "GSM1296075", "GSM1296076", "GSM1296077", "GSM1296078", "GSM1296079", "GSM1296080", "GSM1296081", "GSM1296082", "GSM1296083", "GSM1296084", "GSM1296085", "GSM1296086", "GSM1296087", "GSM1296088", "GSM1296089", "GSM1296090", "GSM1296091", "GSM1296092", "GSM1296093", "GSM1296094", "GSM1296095", "GSM1296096", "GSM1296097", "GSM1296098", "GSM1296099", "GSM1296100", "GSM1296101", "GSM1296102", "GSM1296103", "GSM1296104", "GSM1296105", "GSM1296106", "GSM1296107", "GSM1296108", "GSM1296109", "GSM1296110", "GSM1296111", "GSM1296112", "GSM1296113", "GSM1296114", "GSM1296115", "GSM1296116", "GSM1296117", "GSM1296118", "GSM1296119", "GSM1296120", "GSM1296121", "GSM1296122"], "sample_count": 99, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling in psoriatic lesional and non-lesional skin [brodalumab treatment]", "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:GSE50790 not downloaded", "asset:data:geo:GSE50790 licence not read", "asset:data:geo:GSE53552 not downloaded", "asset:data:geo:GSE53552 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": "Student’s t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The obtained data were analysed by the Student’s t-test using SPSS 24.0 (Chicago, IL, USA)."}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE50790", "GSE53552"], "resolved_accessions": ["GSE50790", "GSE53552"], "statements": ["Previously reported gene expression profiles (GSE50790 and GSE53552) data were used to support this study and are available in Gene Expression Omnibus (GEO) database. All data generated from the analysis process of this study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE50790, GSE53552 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:35993468", "data:geo:GSE50790"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE50790"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:01:22Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7647, "completion_tokens": 1411, "cached_tokens": 0}}, "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:35993468", "type": "paper", "label": "pmid:35993468"}, {"id": "source:pmid:35993468", "type": "manuscript", "label": "PMID 35993468 full text"}, {"id": "data:geo:GSE50790", "type": "dataset", "label": "GEO GSE50790"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35993468", "type": "paper", "label": "pmid:35993468"}, {"id": "source:pmid:35993468", "type": "manuscript", "label": "PMID 35993468 full text"}, {"id": "data:geo:GSE50790", "type": "dataset", "label": "GEO GSE50790"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35993468", "type": "extraction", "used": ["source:pmid:35993468"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE50790", "type": "accession_resolution", "used": ["data:geo:GSE50790"], "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:35993468", "parent_hash": "sha256:b7cebccf1e4f48b8d2751ed53bbc49d9fc758ada3320de8eaad30866e7698854", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE50790 licence not read", "asset:data:geo:GSE50790 not downloaded", "asset:data:geo:GSE53552 licence not read", "asset:data:geo:GSE53552 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Protein-Protein Interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}