MicroRNA-Based Markers of Oral Tongue Squamous Cell Carcinoma and Buccal Squamous Cell Carcinoma: A Systems Biology Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37143570", "kind": "science-record", "revision": 2, "content_hash": "sha256:02a9ab33da7523f63bfdec26780eaf550b6571d946df5a1e0bcf74c0868680e9", "created_at": "2026-11-01T19:01:48Z", "updated_at": "2026-11-01T21:30:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MicroRNA-Based Markers of Oral Tongue Squamous Cell Carcinoma and Buccal Squamous Cell Carcinoma: A Systems Biology Approach.", "doi": "10.1155/2023/5512894", "pmid": "37143570", "authors": ["Setareh Shojaei", "Pouya Menbari", "Shokoofeh Jamshidi", "Amir Taherkhani"], "journal": "Biochemistry research international", "year": 2023, "abstract": "Objective: Oral tongue squamous cell carcinoma (OTSCC) and buccal squamous cell carcinoma (BSCC) are the first and second leading causes of oral cancer, respectively. OTSCC and BSCC are associated with poor prognosis in patients with oral cancer. Thus, we aimed to indicate signaling pathways, Gene Ontology terms, and prognostic markers mediating the malignant transformation of the normal oral tissue to OTSCC and BSCC.\nMethods: The dataset GSE168227 was downloaded and reanalyzed from the GEO database. Orthogonal partial least square (OPLS) analysis identified common differentially expressed miRNAs (DEMs) in OTSCC and BSCC compared to their adjacent normal mucosa. Next, validated targets of DEMs were identified using the TarBase web server. With the use of the STRING database, a protein interaction map (PIM) was created. Using the Cytoscape program, hub genes and clusters within the PIM were shown. Next, gene-set enrichment analysis was carried out using the g:Profiler tool. Using the GEPIA2 web tool, analyses of gene expression and survival analysis were also performed.\nResults: Two DEMs, including has-miR-136 and has-miR-377, were common in OTSCC and BSCC (p value <0.01; |Log2 FC| > 1). A total of 976 targets were indicated for common DEMs. PIM included 96 hubs, and the upregulation of EIF2S1, CAV1, RAN, ANXA5, CYCS, CFL1, MYC, HSP90AA1, PKM, and HSPA5 was significantly associated with a poor prognosis in the head and neck squamous cell carcinoma (HNSCC), while NTRK2, HNRNPH1, DDX17, and WDR82 overexpression was significantly linked to favorable prognosis in the patients with HNSCC. \"Clathrin-mediated endocytosis\" was considerably dysregulated in OTSCC and BSCC.\nConclusion: The present study suggests that has-miR-136 and has-miR-377 are underexpressed in OTSCC and BSCC than in normal oral mucosa. Moreover, EIF2S1, CAV1, RAN, ANXA5, CYCS, CFL1, MYC, HSP90AA1, PKM, HSPA5, NTRK2, HNRNPH1, DDX17, and WDR82 demonstrated prognostic markers in HNSCC. These findings may benefit the prognosis and management of individuals with OTSCC/BSCC. However, additional experimental verification is required.", "claims": [{"id": "claim-method", "statement": "DEMs in OTSCC and BSCC were found using OPLSs in comparison to the comparable normal tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37143570", "locator": "sections[3] \"2.1. Dataset Recovery and Statistical Analysis\" paragraph 2", "quote": "DEMs in OTSCC and BSCC were found using OPLSs in comparison to the comparable normal tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37143570", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The common differentially expressed miRNAs were has-miR-136 and has-miR-377, and 14 hub genes were identified as prognostic markers in HNSCC.", "kind": "quantitative", "target": {"value": 0.01, "unit": "p-value", "tolerance": null, "source": "Two DEMs, including has-miR-136 and has-miR-377, were common in OTSCC and BSCC (p value <0.01; |Log2 FC| > 1)."}, "evidence": [{"asset": "source:pmid:37143570", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Two DEMs, including has-miR-136 and has-miR-377, were common in OTSCC and BSCC (p value <0.01; |Log2 FC| > 1)."}, {"asset": "source:pmid:37143570", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The present study suggests that has-miR-136 and has-miR-377 are underexpressed in OTSCC and BSCC than in normal oral mucosa. Moreover, EIF2S1, CAV1, RAN, ANXA5, CYCS, CFL1, MYC, HSP90AA1, PKM, HSPA5, NTRK2, HNRNPH1, DDX17, and WDR82 demonstrated prognostic markers in HNSCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The common differentially expressed miRNAs were has-miR-136 and has-miR-377, and 14 hub genes were identified as prognostic markers in HNSCC.", "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:37143570"], "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:GSE168227"], "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:GSE168227"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37143570", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2023/5512894", "sha256": "sha256:c50407342bc633968537c9978523929508bf8a43127d62638e3133e7d7473eac", "bytes": 42129, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2023/5512894", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10151719", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE168227", "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=GSE168227", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE168227", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5134247", "GSM5134248", "GSM5134249", "GSM5134250", "GSM5134251", "GSM5134252", "GSM5134253", "GSM5134254", "GSM5134255", "GSM5134256", "GSM5134257", "GSM5134258", "GSM5134259", "GSM5134260", "GSM5134261", "GSM5134262", "GSM5134263", "GSM5134264", "GSM5134265", "GSM5134266", "GSM5134267", "GSM5134268", "GSM5134269", "GSM5134270", "GSM5134271", "GSM5134272", "GSM5134273", "GSM5134274", "GSM5134275", "GSM5134276", "GSM5134277", "GSM5134278", "GSM5134279", "GSM5134280", "GSM5134281", "GSM5134282", "GSM5134283", "GSM5134284", "GSM5134285", "GSM5134286", "GSM5134287", "GSM5134288", "GSM5134289", "GSM5134290", "GSM5134291", "GSM5134292", "GSM5134293", "GSM5134294"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "8227", "taxon": "Homo sapiens", "title": "MiRNA SIGNATURE FOR ORAL SQUAMOUS CELL CARCINOMA", "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:GSE168227 not downloaded", "asset:data:geo:GSE168227 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "DEMs in OTSCC and BSCC were found using OPLSs in comparison to the comparable normal tissues."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.01, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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