IL-17 signaling pathway plays a key role in laryngeal squamous cell carcinoma with ethnic specificity.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34249422", "kind": "science-record", "revision": 3, "content_hash": "sha256:14a660cc9c085f90bacf6a1e492d95f873f386c6f7a87a5936014ca5586c9034", "created_at": "2026-11-01T17:35:37Z", "updated_at": "2026-11-01T21:25:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "IL-17 signaling pathway plays a key role in laryngeal squamous cell carcinoma with ethnic specificity.", "doi": null, "pmid": "34249422", "authors": ["Li Qi", "Wenzhao Bao", "Wei Li", "Xiaoxu Ding", "Aihui Yan"], "journal": "American journal of cancer research", "year": 2021, "abstract": "Laryngeal squamous cell carcinoma (LSCC) is a common aggressive head and neck squamous cell carcinoma (HNSCC) and racial disparities have been reported to exist in it. However, its molecular mechanism and associated ethnic specificity are still unclear. Here, we leveraged mRNA expression data from 2 gene expression omnibus datasets (GSE142083 & GSE117005) of Chinese samples and the cancer genome atlas (TCGA) datasets of Caucasian samples to demonstrate the expression signature of LSCC. The GSE142083 dataset was used as the discovery set since it had 53 pairs of LSCC tissues and matched adjacent normal tissues, and the GSE117005 dataset was treated as the validation set with 5 pairs of tissues. Differential gene expression analysis and enrichment pathway analysis were performed. Besides, we employed weighted gene co-expression network analysis to identify hub genes in validated pathways. The TCGA datasets were used to evaluate ethnic specificity. Immunohistochemistry (IHC) was employed to further validate the hub gene. Overall, the IL-17 signaling pathway was significantly enriched for upregulated genes in two Chinese datasets while not in TCGA datasets; and IL17RC, MAPK3, S100A8, MMP3, CXCL8, and TNFA1P3 were hub genes regulating such pathway. Therein, IL17RC might be the most important one and the IHC results displayed that the IL17RC gene upregulated in the LSCC tissue. IL-17 signaling pathway has an ethnicity-specific effect in LSCC where it is upregulated in the Chinese while not in the Caucasians and IL17RC might play a key role. Targeting genes located in the IL-17 signaling pathway may be beneficial for Chinese LSCC patients.", "claims": [{"id": "claim-method", "statement": "Differential gene expression analysis and enrichment pathway analysis were performed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34249422", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Differential gene expression analysis and enrichment pathway analysis were performed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Here, we leveraged mRNA expression data from 2 gene expression omnibus datasets (GSE142083 & GSE117005) of Chinese samples and the cancer genome atlas (TCGA) datasets of Caucasian samples to demonstrate the expression signature of LSCC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34249422", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we leveraged mRNA expression data from 2 gene expression omnibus datasets (GSE142083 & GSE117005) of Chinese samples and the cancer genome atlas (TCGA) datasets of Caucasian samples to demonstrate the expression signature of LSCC."}], "state": "complete"}, {"id": "claim-target-result", "statement": "IL-17 signaling pathway has an ethnicity-specific effect in LSCC where it is upregulated in the Chinese while not in the Caucasians and IL17RC might play a key role.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34249422", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "IL-17 signaling pathway has an ethnicity-specific effect in LSCC where it is upregulated in the Chinese while not in the Caucasians and IL17RC might play a key role."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "complete", "objective": "IL-17 signaling pathway has an ethnicity-specific effect in LSCC where it is upregulated in the Chinese while not in the Caucasians and IL17RC might play a key role.", "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:34249422"], "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:GSE117005"], "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:GSE117005"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34249422", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:d0ebb4c8f0d4d9d0cb42e90186e69f7aeedadab5d552365e90527a832a7025d3", "bytes": 1673, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "34249422", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8263688", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE117005", "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=GSE117005", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE117005", "version": null, "note": "Here, we leveraged mRNA expression data from 2 gene expression omnibus datasets (GSE142083 & GSE117005) of Chinese samples and the cancer genome atlas (TCGA) datasets of Caucasian samples to demonstrate the expression signature of LSCC.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Here, we leveraged mRNA expression data from 2 gene expression omnibus datasets (GSE142083 & GSE117005) of Chinese samples and the cancer genome atlas (TCGA) datasets of Caucasian samples to demonstrate the expression signature of LSCC.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3267245", "GSM3267246", "GSM3267247", "GSM3267248", "GSM3267249", "GSM3267250", "GSM3267251", "GSM3267252", "GSM3267253", "GSM3267254"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "20115", "taxon": "Homo sapiens", "title": "Comprehensive analysis of the whole coding and noncoding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma [lncRNA-mRNA]", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE142083", "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=GSE142083", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE142083", "version": null, "note": "Here, we leveraged mRNA expression data from 2 gene expression omnibus datasets (GSE142083 & GSE117005) of Chinese samples and the cancer genome atlas (TCGA) datasets of Caucasian samples to demonstrate the expression signature of LSCC.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Here, we leveraged mRNA expression data from 2 gene expression omnibus datasets (GSE142083 & GSE117005) of Chinese samples and the cancer genome atlas (TCGA) datasets of Caucasian samples to demonstrate the expression signature of LSCC.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4219666", "GSM4219667", "GSM4219668", "GSM4219669", "GSM4219670", "GSM4219671", "GSM4219672", "GSM4219673", "GSM4219674", "GSM4219675", "GSM4219676", "GSM4219677", "GSM4219678", "GSM4219679", "GSM4219680", "GSM4219681", "GSM4219682", "GSM4219683", "GSM4219684", "GSM4219685", "GSM4219686", "GSM4219687", "GSM4219688", "GSM4219689", "GSM4219690", "GSM4219691", "GSM4219692", "GSM4219693", "GSM4219694", "GSM4219695", "GSM4219696", "GSM4219697", "GSM4219698", "GSM4219699", "GSM4219700", "GSM4219701", "GSM4219702", "GSM4219703", "GSM4219704", "GSM4219705", "GSM4219706", "GSM4219707", "GSM4219708", "GSM4219709", "GSM4219710", "GSM4219711", "GSM4219712", "GSM4219713", "GSM4219714", "GSM4219715", "GSM4219716", "GSM4219717", "GSM4219718", "GSM4219719", "GSM4219720", "GSM4219721", "GSM4219722", "GSM4219723", "GSM4219724", "GSM4219725", "GSM4219726", "GSM4219727", "GSM4219728", "GSM4219729", "GSM4219730", "GSM4219731", "GSM4219732", "GSM4219733", "GSM4219734", "GSM4219735", "GSM4219736", "GSM4219737", "GSM4219738", "GSM4219739", "GSM4219740", "GSM4219741", "GSM4219742", "GSM4219743", "GSM4219744", "GSM4219745", "GSM4219746", "GSM4219747", "GSM4219748", "GSM4219749", "GSM4219750", "GSM4219751", "GSM4219752", "GSM4219753", "GSM4219754", "GSM4219755", "GSM4219756", "GSM4219757", "GSM4219758", "GSM4219759", "GSM4219760", "GSM4219761", "GSM4219762", "GSM4219763", "GSM4219764", "GSM4219765", "GSM4219766", "GSM4219767", "GSM4219768", "GSM4219769", "GSM4219770", "GSM4219771"], "sample_count": 106, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Transcriptome sequencing of laryngeal squamous cell carcinoma and paired adjacent normal mucosa tissues", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE117005 not downloaded", "asset:data:geo:GSE117005 licence not read", "asset:data:geo:GSE142083 not downloaded", "asset:data:geo:GSE142083 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Differential gene expression analysis and enrichment pathway analysis were performed.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differential gene expression analysis and enrichment pathway analysis were performed."}}], "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 (Differential gene expression analysis and enrichment pathway analysis were performed.), 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE142083", "GSE117005"], "resolved_accessions": ["GSE142083", "GSE117005"], "statements": ["Here, we leveraged mRNA expression data from 2 gene expression omnibus datasets (GSE142083 & GSE117005) of Chinese samples and the cancer genome atlas (TCGA) datasets of Caucasian samples to demonstrate the expression signature of LSCC."], "basis": "The paper names GSE142083, GSE117005 in gene expression omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:34249422", "data:geo:GSE117005"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE117005"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:02:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 1987, "completion_tokens": 1095, "cached_tokens": 188}}, "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:34249422", "type": "paper", "label": "pmid:34249422"}, {"id": "source:pmid:34249422", "type": "manuscript", "label": "PMID 34249422 full text"}, {"id": "data:geo:GSE117005", "type": "dataset", "label": "GEO GSE117005"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34249422", "type": "paper", "label": "pmid:34249422"}, {"id": "source:pmid:34249422", "type": "manuscript", "label": "PMID 34249422 full text"}, {"id": "data:geo:GSE117005", "type": "dataset", "label": "GEO GSE117005"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34249422", "type": "extraction", "used": ["source:pmid:34249422"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE117005", "type": "accession_resolution", "used": ["data:geo:GSE117005"], "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:34249422", "parent_hash": "sha256:fb82e6ae5fdc5e5768852f693103e5fa592c0821b1f57f4f3c9a62af70641675", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE117005 licence not read", "asset:data:geo:GSE117005 not downloaded", "asset:data:geo:GSE142083 licence not read", "asset:data:geo:GSE142083 not downloaded", "doi", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ts were used to evaluate ethnic specificity. Immunohistochemistry (IHC) was employed to further validate the h", "te ethnic specificity. Immunohistochemistry (IHC) was employed to further validate the hub ge", "17RC might be the most important one and the IHC results displayed that the IL17RC gene upreg"], "order_basis": "paper_text_order:1018", "id": "assay:1"}]}