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pmid:40980067

Prognostic significance and pathogenesis of RFC3 gene expression in diffuse large B-cell lymphoma.

PeerJ · 2025 doi:10.7717/peerj.20001

Paper

partial

Experiment

partial

Data

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Analysis

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Execution

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:40980067
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Prognostic significance and pathogenesis of RFC3 gene expression in diffuse large B-cell lymphoma.
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10.7717/peerj.20001
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40980067
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null
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2025
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Data included in present analysis.
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Correlation between RFC3 expression and clinicopathological features in DLBCL.
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Elevated RFC3 expression correlates with aggressive clinical features in DLBCL
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Correlation between RFC3 expression and clinicopathological features in DLBCL.
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Results of the enrichment analysis of RFC3 expression in DLBCL.
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RFC3 plays a role in various tumor-related signaling pathways in DLBCL
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Results of the enrichment analysis of RFC3 expression in DLBCL.
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[2]
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4.09E−05
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[3]
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[2]
1.89
[3]
9.78E−06
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1.58E−05
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4.12E−05
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[2]
1.48
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0.007781
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[2]
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0.000245
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[2]
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0.000102
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0.000123
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135
[2]
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0.000233
[4]
0.000257
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187
[2]
−2.36
[3]
1.00E−10
[4]
2.42E−10
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{ "target_result": "The headline finding is that RFC3 expression was significantly upregulated in DLBCL and that high RFC3 expression was associated with poor prognosis; no numerical effect size or numerical prognostic result is reported in the supplied text.", "work_type": "analysis_plus_physical_validation", "physical_methods": [ "Immunohistochemistry (IHC) validation of RFC3 expression in DLBCL samples" ], "analysis_methods": [ "Multi-omics analysis", "Kaplan–Meier survival analysis", "Chi-square test", "Gene Set Enrichment Analysis (GSEA)", "Immune infiltration analysis using the IOBR package", "Single-sample gene set enrichment analysis (ssGSEA)", "Spearman correlation analysis", "IMvigor210 immunotherapy-response prediction using the IMvigor210CoreBiologics R package", "Drug-susceptibility analysis using oncoPredict", "Pan-cancer analysis using easyTCGA and TCGAplot", "Cox proportional hazards model" ], "statistical_method": "Kaplan–Meier method", "method_evidence": "Survival analysis was conducted using the Kaplan–Meier method.", "repositories": [ { "repository": "Gene Expression Omnibus (GEO)", "accession": "GSE181063", "data_description": "Multi-omics data used for the RFC3 analyses; GSE181063 was specifically used for immune infiltration analyses based on the tumor immune microenvironment.", "evidence": "Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA). The relationship between RFC3 expression and the tumor immune microenvironment (TIME) in DLBCL was investigated using immune infiltration analyses based on the GSE181063 dataset.", "publicly_downloadable": false }, { "repository": "Gene Expression Omnibus (GEO)", "accession": "GSE10846", "data_description": "Multi-omics data used for the RFC3 analyses.", "evidence": "Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).", "publicly_downloadable": false }, { "repository": "Gene Expression Omnibus (GEO)", "accession": "GSE32918", "data_description": "Multi-omics data used for the RFC3 analyses.", "evidence": "Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).", "publicly_downloadable": false }, { "repository": "Gene Expression Omnibus (GEO)", "accession": "GSE31312", "data_description": "Multi-omics data used for the RFC3 analyses.", "evidence": "Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).", "publicly_downloadable": false }, { "repository": "Gene Expression Omnibus (GEO)", "accession": "GSE32018", "data_description": "Multi-omics data used for the RFC3 analyses.", "evidence": "Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).", "publicly_downloadable": false }, { "repository": "Gene Expression Omnibus (GEO)", "accession": "GSE12453", "data_description": "Multi-omics data used for the RFC3 analyses.", "evidence": "Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).", "publicly_downloadable": false }, { "repository": "The Cancer Genome Atlas (TCGA)", "accession": "unknown", "data_description": "Multi-omics data used for the RFC3 analyses, including pan-cancer expression and prognostic analyses.", "evidence": "Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).", "publicly_downloadable": false }, { "repository": "IMvigor210 dataset", "accession": "unknown", "data_description": "Transcriptomic and clinical data from patients with urothelial carcinoma treated with anti–PD-L1 therapy, used to assess associations between RFC3 expression and immunotherapy outcomes.", "evidence": "The immunotherapy response was predicted using the IMvigor210 cohort through the IMvigor210CoreBiologics R package (Nickles & Bourgon, 2019). This dataset includes transcriptomic and clinical data from patients with urothelial carcinoma treated with anti–PD-L1 therapy, allowing us to assess potential associations between RFC3 expression and immunotherapy outcomes.", "publicly_downloadable": false }, { "repository": "Genomics of Drug Sensitivity in Cancer (GDSC)", "accession": "version 1 and version 2", "data_description": "Pharmacogenomic profiles of cancer cell lines exposed to therapeutic agents, used to analyze the relationship between RFC3 expression and drug sensitivity.", "evidence": "For this analysis, we obtained drug response data from the Genomics of Drug Sensitivity in Cancer (GDSC) data version 1 and 2 and the Cancer Therapeutics Response Portal, version 2 (CTRP2). These datasets include pharmacogenomic profiles of cancer cell lines exposed to a range of therapeutic agents for different RFC3 expression levels.", "publicly_downloadable": false }, { "repository": "Cancer Therapeutics Response Portal", "accession": "CTRP2", "data_description": "Pharmacogenomic profiles of cancer cell lines exposed to a range of therapeutic agents, used to analyze the relationship between RFC3 expression and drug sensitivity.", "evidence": "For this analysis, we obtained drug response data from the Genomics of Drug Sensitivity in Cancer (GDSC) data version 1 and 2 and the Cancer Therapeutics Response Portal, version 2 (CTRP2). These datasets include pharmacogenomic profiles of cancer cell lines exposed to a range of therapeutic agents for different RFC3 expression levels.", "publicly_downloadable": false }, { "repository": "Supplemental Files", "accession": "unknown", "data_description": "Raw data underlying the study.", "evidence": "The raw data is available in the Supplemental Files.", "publicly_downloadable": false } ], "availability_statement": "The raw data is available in the Supplemental Files.", "data_on_request": false, "source_claims": [ "RFC3 expression was significantly upregulated in DLBCL.", "High RFC3 expression was closely associated with poor prognosis, adverse clinical features, and adverse tumor microenvironment characteristics in DLBCL patients.", "RFC3 expression was validated via immunohistochemistry (IHC) in DLBCL samples.", "Survival analysis was conducted using the Kaplan–Meier method.", "The chi-square test was used to assess the association between RFC3 expression and clinical characteristics of DLBCL.", "Gene Set Enrichment Analysis (GSEA) was employed to identify tumor signaling pathways associated with RFC3.", "Elevated RFC3 expression is a negative prognostic indicator in DLBCL.", "The raw data is available in the Supplemental Files." ], "missing_information": [ "The supplied text does not report a numerical value for the headline RFC3 result, such as expression fold change, hazard ratio, log-rank P value, or survival difference.", "The TCGA accession is not provided.", "The IMvigor210 accession is not provided.", "The paper does not explicitly state that the repositories or Supplemental Files can be downloaded without an application, embargo, or request." ], "evidence_spans": [ "Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).", "RFC3 expression was validated via immunohistochemistry (IHC) in DLBCL samples.", "Survival analysis was conducted using the Kaplan–Meier method.", "The chi-square test was used to assess the association between RFC3 expression and clinical characteristics of DLBCL.", "Gene Set Enrichment Analysis (GSEA) was employed to identify tumor signaling pathways associated with RFC3.", "RFC3 expression was significantly upregulated in DLBCL.", "High RFC3 expression was closely associated with poor prognosis, adverse clinical features, and adverse tumor microenvironment characteristics in DLBCL patients.", "The immunotherapy response was predicted using the IMvigor210 cohort through the IMvigor210CoreBiologics R package (Nickles & Bourgon, 2019).", "For this analysis, we obtained drug response data from the Genomics of Drug Sensitivity in Cancer (GDSC) data version 1 and 2 and the Cancer Therapeutics Response Portal, version 2 (CTRP2).", "The raw data is available in the Supplemental Files." ] }
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The relationship between RFC3 expression and the tumor immune microenvironment (TIME) in DLBCL was investigated using immune infiltration analyses based on the GSE181063 dataset.\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"Gene Expression Omnibus (GEO)\",\n      \"accession\": \"GSE10846\",\n      \"data_description\": \"Multi-omics data used for the RFC3 analyses.\",\n      \"evidence\": \"Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"Gene Expression Omnibus (GEO)\",\n      \"accession\": \"GSE32918\",\n      \"data_description\": \"Multi-omics data used for the RFC3 analyses.\",\n      \"evidence\": \"Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"Gene Expression Omnibus (GEO)\",\n      \"accession\": \"GSE31312\",\n      \"data_description\": \"Multi-omics data used for the RFC3 analyses.\",\n      \"evidence\": \"Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"Gene Expression Omnibus (GEO)\",\n      \"accession\": \"GSE32018\",\n      \"data_description\": \"Multi-omics data used for the RFC3 analyses.\",\n      \"evidence\": \"Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"Gene Expression Omnibus (GEO)\",\n      \"accession\": \"GSE12453\",\n      \"data_description\": \"Multi-omics data used for the RFC3 analyses.\",\n      \"evidence\": \"Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"The Cancer Genome Atlas (TCGA)\",\n      \"accession\": \"unknown\",\n      \"data_description\": \"Multi-omics data used for the RFC3 analyses, including pan-cancer expression and prognostic analyses.\",\n      \"evidence\": \"Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"IMvigor210 dataset\",\n      \"accession\": \"unknown\",\n      \"data_description\": \"Transcriptomic and clinical data from patients with urothelial carcinoma treated with anti–PD-L1 therapy, used to assess associations between RFC3 expression and immunotherapy outcomes.\",\n      \"evidence\": \"The immunotherapy response was predicted using the IMvigor210 cohort through the IMvigor210CoreBiologics R package (Nickles & Bourgon, 2019). This dataset includes transcriptomic and clinical data from patients with urothelial carcinoma treated with anti–PD-L1 therapy, allowing us to assess potential associations between RFC3 expression and immunotherapy outcomes.\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"Genomics of Drug Sensitivity in Cancer (GDSC)\",\n      \"accession\": \"version 1 and version 2\",\n      \"data_description\": \"Pharmacogenomic profiles of cancer cell lines exposed to therapeutic agents, used to analyze the relationship between RFC3 expression and drug sensitivity.\",\n      \"evidence\": \"For this analysis, we obtained drug response data from the Genomics of Drug Sensitivity in Cancer (GDSC) data version 1 and 2 and the Cancer Therapeutics Response Portal, version 2 (CTRP2). These datasets include pharmacogenomic profiles of cancer cell lines exposed to a range of therapeutic agents for different RFC3 expression levels.\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"Cancer Therapeutics Response Portal\",\n      \"accession\": \"CTRP2\",\n      \"data_description\": \"Pharmacogenomic profiles of cancer cell lines exposed to a range of therapeutic agents, used to analyze the relationship between RFC3 expression and drug sensitivity.\",\n      \"evidence\": \"For this analysis, we obtained drug response data from the Genomics of Drug Sensitivity in Cancer (GDSC) data version 1 and 2 and the Cancer Therapeutics Response Portal, version 2 (CTRP2). These datasets include pharmacogenomic profiles of cancer cell lines exposed to a range of therapeutic agents for different RFC3 expression levels.\",\n      \"publicly_downloadable\": false\n    },\n    {\n      \"repository\": \"Supplemental Files\",\n      \"accession\": \"unknown\",\n      \"data_description\": \"Raw data underlying the study.\",\n      \"evidence\": \"The raw data is available in the Supplemental Files.\",\n      \"publicly_downloadable\": false\n    }\n  ],\n  \"availability_statement\": \"The raw data is available in the Supplemental Files.\",\n  \"data_on_request\": false,\n  \"source_claims\": [\n    \"RFC3 expression was significantly upregulated in DLBCL.\",\n    \"High RFC3 expression was closely associated with poor prognosis, adverse clinical features, and adverse tumor microenvironment characteristics in DLBCL patients.\",\n    \"RFC3 expression was validated via immunohistochemistry (IHC) in DLBCL samples.\",\n    \"Survival analysis was conducted using the Kaplan–Meier method.\",\n    \"The chi-square test was used to assess the association between RFC3 expression and clinical characteristics of DLBCL.\",\n    \"Gene Set Enrichment Analysis (GSEA) was employed to identify tumor signaling pathways associated with RFC3.\",\n    \"Elevated RFC3 expression is a negative prognostic indicator in DLBCL.\",\n    \"The raw data is available in the Supplemental Files.\"\n  ],\n  \"missing_information\": [\n    \"The supplied text does not report a numerical value for the headline RFC3 result, such as expression fold change, hazard ratio, log-rank P value, or survival difference.\",\n    \"The TCGA accession is not provided.\",\n    \"The IMvigor210 accession is not provided.\",\n    \"The paper does not explicitly state that the repositories or Supplemental Files can be downloaded without an application, embargo, or request.\"\n  ],\n  \"evidence_spans\": [\n    \"Multi-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA).\",\n    \"RFC3 expression was validated via immunohistochemistry (IHC) in DLBCL samples.\",\n    \"Survival analysis was conducted using the Kaplan–Meier method.\",\n    \"The chi-square test was used to assess the association between RFC3 expression and clinical characteristics of DLBCL.\",\n    \"Gene Set Enrichment Analysis (GSEA) was employed to identify tumor signaling pathways associated with RFC3.\",\n    \"RFC3 expression was significantly upregulated in DLBCL.\",\n    \"High RFC3 expression was closely associated with poor prognosis, adverse clinical features, and adverse tumor microenvironment characteristics in DLBCL patients.\",\n    \"The immunotherapy response was predicted using the IMvigor210 cohort through the IMvigor210CoreBiologics R package (Nickles & Bourgon, 2019).\",\n    \"For this analysis, we obtained drug response data from the Genomics of Drug Sensitivity in Cancer (GDSC) data version 1 and 2 and the Cancer Therapeutics Response Portal, version 2 (CTRP2).\",\n    \"The raw data is available in the Supplemental Files.\"\n  ]\n}"}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": 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