FANCI serve as a prognostic biomarker correlated with immune infiltrates in skin cutaneous melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38077326", "kind": "science-record", "revision": 3, "content_hash": "sha256:73ad1c1e87a8a08e14dcf7b3a2f7b49946f3059afbef000b6e024e2e2418c4eb", "created_at": "2026-11-01T19:03:01Z", "updated_at": "2026-11-01T22:10:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "FANCI serve as a prognostic biomarker correlated with immune infiltrates in skin cutaneous melanoma.", "doi": "10.3389/fimmu.2023.1295831", "pmid": "38077326", "authors": ["Zhenguo Cai", "Yanjuan Duan", "Wen Li", "Zhuohang Liu", "Zijun Gong", "Sheng Hong", "Xu He", "Xinyang Xuanyuan", "Youdong Chen", "Xinling Bi", "Wuqing Wang"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "Background: As a member of tumor, Skin cutaneous melanoma (SKCM) poses a serious threat to people's health because of its strong malignancy. Unfortunately, effective treatment methods for SKCM remain lacking. FANCI plays a vital role in the occurrence and metastasis of various tumor types. However, its regulatory role in SKCM is unclear. The purpose of this study was to explore the association of FANCI with SKCM.\nMethods: This study investigated the expression of FANCI in GSE46517, GSE15605, and GSE114445 from the Gene Expression Omnibus database and The Cancer Genome Atlas (TCGA)-SKCM datasets using the package \"limma\" or \"DESeq2\" in R environment and also investigated the prognostic significance of FANCI by utilizing the GEPIA database. Additionally, our research made use of real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining to verify FANCI expression between SKCM and normal tissues and developed the knockdown of FANCI in A375 and A875 cells to further analyze the function of FANCI. Finally, this study analyzed the correlation of FANCI and tumor-infiltrating immune cells by CIBERSORT, ESTIMATE, and ssGSEA algorithms.\nResults: The FANCI level was increasing in SKCM tissues from GSE46517, GSE15605, GSE114445, and TCGA-SKCM. However, high FANCI expression correlated with poor overall survival. The RT-qPCR and IHC confirmed the accuracy of bioinformatics. Knocking down FANCI suppresses A375 and A875 cell proliferation, migration, and invasion. FANCI could be involved in the immunological milieu of SKCM by regulating immune responses and infiltrating numerous immune cells, particularly neutrophils, CD8+ T cells, and B cells. Furthermore, patients with SKCM who have a high FANCI expression level are reported to exhibit immunosuppression, whereas those with a low FANCI expression level are more likely to experience positive outcomes from immunotherapy.\nConclusions: The increased FANCI expression in SKCM can be a prognostic biomarker. Knockdown FANCI can reduce the occurrence and progression of SKCM. The FANCI expression provides a foundation for predicting the immune status and treatment of SKCM.", "claims": [{"id": "claim-method", "statement": "We generated Kaplan–Meier curves using the TIMER database to display immune cell infiltration and FANCI expression in SKCM.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38077326", "locator": "sections[22] \"FANCI may regulate immune microenvironment of SKCM\" paragraph 2", "quote": "We generated Kaplan–Meier curves using the TIMER database to display immune cell infiltration and FANCI expression in SKCM."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38077326", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:38077326"], "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:GSE114445"], "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:GSE114445"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38077326", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2023.1295831", "sha256": "sha256:69bc0a1132f0cb9aabc7a49445b7959b70bd1655496919e13b22045b42e444c7", "bytes": 46896, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2023.1295831", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10703153", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE114445", "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=GSE114445", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE114445", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3141811", "GSM3141812", "GSM3141813", "GSM3141814", "GSM3141815", "GSM3141816", "GSM3141817", "GSM3141818", "GSM3141819", "GSM3141820", "GSM3141821", "GSM3141822", "GSM3141823", "GSM3141824", "GSM3141825", "GSM3141826", "GSM3141827", "GSM3141828", "GSM3141862", "GSM3141863", "GSM3141864", "GSM3141865", "GSM3141866", "GSM3141867", "GSM3141868", "GSM3141869", "GSM3141870", "GSM3141871", "GSM3141872", "GSM3141873", "GSM3141874", "GSM3141875", "GSM3141876", "GSM3141877"], "sample_count": 34, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Progressive immune activation and negative immunoregulation from common melanocytic nevi to dysplastic nevi to melanoma", "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:GSE15605", "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=GSE15605", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15605", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE46517", "GSE15605", "GSE114445"], "resolved_accessions": ["GSE46517", "GSE15605", "GSE114445"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."], "basis": "The paper names GSE46517, GSE15605, GSE114445 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:38077326", "data:geo:GSE114445"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE114445"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:02:25Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13940, "completion_tokens": 3075, "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:38077326", "type": "paper", "label": "pmid:38077326"}, {"id": "source:pmid:38077326", "type": "manuscript", "label": "PMID 38077326 full text"}, {"id": "data:geo:GSE114445", "type": "dataset", "label": "GEO GSE114445"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38077326", "type": "paper", "label": "pmid:38077326"}, {"id": "source:pmid:38077326", "type": "manuscript", "label": "PMID 38077326 full text"}, {"id": "data:geo:GSE114445", "type": "dataset", "label": "GEO GSE114445"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38077326", "type": "extraction", "used": ["source:pmid:38077326"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE114445", "type": "accession_resolution", "used": ["data:geo:GSE114445"], "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:38077326", "parent_hash": "sha256:b02fc09c917be867c9a6f639aec3b5dd958f1378e41cad25e26a99d3892e5e04", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE114445 licence not read", "asset:data:geo:GSE114445 not downloaded", "asset:data:geo:GSE15605 licence not read", "asset:data:geo:GSE15605 not downloaded", "asset:data:geo:GSE46517 licence not read", "asset:data:geo:GSE46517 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining to v", "n correlated with poor overall survival. The RT-qPCR and IHC confirmed the accuracy of bioinforma", "e quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining to v", "orrelated with poor overall survival. The RT-qPCR and IHC confirmed the accuracy of bioinforma"], "order_basis": "paper_text_order:894", "id": "assay:1"}, {"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": ["tive polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining to verify FANCI expression be", "reaction (RT-qPCR) and immunohistochemical (IHC) staining to verify FANCI expression between", "with poor overall survival. The RT-qPCR and IHC confirmed the accuracy of bioinformatics. Kn"], "order_basis": "paper_text_order:907", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["en SKCM and normal tissues and developed the knockdown of FANCI in A375 and A875 cells to further a", "ssion in SKCM can be a prognostic biomarker. Knockdown FANCI can reduce the occurrence and progress"], "order_basis": "paper_text_order:1019", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["Materials and methods Cell culture We cultured A375 and A875 cells in Dulbecco’s Modified E"], "order_basis": "paper_text_order:2277", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["DESeq2"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}