The Genetic Cross-Talk between Periodontitis and Chronic Kidney Failure Revealed by Transcriptomic Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37510279", "kind": "science-record", "revision": 4, "content_hash": "sha256:89bb0f7c13a9ceb12395a3f153814ba59cbc7c03c3a30f4c6cb4ca78b1280658", "created_at": "2026-11-01T19:02:16Z", "updated_at": "2026-11-01T22:52:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Genetic Cross-Talk between Periodontitis and Chronic Kidney Failure Revealed by Transcriptomic Analysis.", "doi": "10.3390/genes14071374", "pmid": "37510279", "authors": ["Dandan Ren", "Thomas Ebert", "Deborah Kreher", "Bero Luke Vincent Ernst", "Jonathan de Fallois", "Gerhard Schmalz"], "journal": "Genes", "year": 2023, "abstract": "Periodontitis and chronic kidney failure (CKF) are potentially related to each other. This bioinformatics analysis aimed at the identification of potential cross-talk genes and related pathways between periodontitis and CKF. Based on NCBI Gene Expression Omnibus (GEO), datasets GSE10334, GSE16134, and GSE23586 were extracted for periodontitis. A differential expression analysis (p < 0.05, |log2(FC)| > 0.5) was performed to assess deregulated genes (DEGs). CKF-related genes were extracted from DisGeNET and examined regarding their overlap with periodontitis-related DEGs. Cytoscape was used to construct and analyze a protein-protein interaction (PPI) network. Based on Cytoscape plugin MCODE and a LASSO regression analysis, the potential hub cross-talk genes were identified. Finally, a complex PPI of the hub genes was constructed. A total of 489 DEGs for periodontitis were revealed. With the 805 CKF-related genes, an overlap of 47 cross-talk genes was found. The PPI network of the potential cross-talk genes was composed of 1081 nodes and 1191 edges. The analysis with MCODE resulted in 10 potential hub genes, while the LASSO regression resulted in 22. Finally, five hub cross-talk genes, CCL5, FCGR3B, MMP-9, SAA1, and SELL, were identified. Those genes were significantly upregulated in diseased samples compared to controls (p ≤ 0.01). Furthermore, ROC analysis showed a high predictive value of those genes (AUC ≥ 73.44%). Potentially relevant processes and pathways were primarily related to inflammation, metabolism, and cardiovascular issues. In conclusion, five hub cross-talk genes, i.e., CCL5, FCGR3B, MMP-9, SAA1, and SELL, could be involved in the interplay between periodontitis and CKF, whereby primarily inflammation, metabolic, and vascular issues appear to be of relevance.", "claims": [{"id": "claim-method", "statement": "Under application of the “limma” package of the R language, differential expression analysis was performed for each of the three PD-related expression matrices.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37510279", "locator": "sections[5] \"2.3. Genes Differentially Expressed in PD (DEGs)\" paragraph 2", "quote": "Under application of the “limma” package of the R language, differential expression analysis was performed for each of the three PD-related expression matrices."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Periodontitis data can be assessed from http://www.ncbi.nlm.nih.gov/database (assessed on 2 November 2022; GSE10334, GSE16134, GSE23586). Data for chronic kidney failure (CKF)-related genes were searched from DisGeNET https://www.disgenet.org/home/ (assessed on 4 November 2022).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37510279", "locator": "sections[28] \"Data Availability Statement\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Periodontitis data can be assessed from http://www.ncbi.nlm.nih.gov/database (assessed on 2 November 2022; GSE10334, GSE16134, GSE23586). Data for chronic kidney failure (CKF)-related genes were searched from DisGeNET https://www.disgenet.org/home/ (assessed on 4 November 2022)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified five hub cross-talk genes—CCL5, FCGR3B, MMP-9, SAA1, and SELL—as potentially involved in the interplay between periodontitis and chronic kidney failure.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37510279", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Finally, five hub cross-talk genes, CCL5, FCGR3B, MMP-9, SAA1, and SELL, were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified five hub cross-talk genes—CCL5, FCGR3B, MMP-9, SAA1, and SELL—as potentially involved in the interplay between periodontitis and chronic kidney failure.", "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:37510279"], "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:GSE10334"], "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:GSE10334"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37510279", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/genes14071374", "sha256": "sha256:ec0336865acd2c5f725e71eb39823faf4072583f6a9a7deda3bad5c11c8910ac", "bytes": 55423, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/genes14071374", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10379591", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10334", "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=GSE10334", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10334", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Periodontitis data can be assessed from http://www.ncbi.nlm.nih.gov/database (assessed on 2 November 2022; GSE10334, GSE16134, GSE23586). Data for chronic kidney failure (CKF)-related genes were searched from DisGeNET https://www.disgenet.org/home/ (assessed on 4 November 2022).", "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 on reasonable request. Periodontitis data can be assessed from http://www.ncbi.nlm.nih.gov/database (assessed on 2 November 2022; GSE10334, GSE16134, GSE23586). 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Periodontitis data can be assessed from http://www.ncbi.nlm.nih.gov/database (assessed on 2 November 2022; GSE10334, GSE16134, GSE23586). Data for chronic kidney failure (CKF)-related genes were searched from DisGeNET https://www.disgenet.org/home/ (assessed on 4 November 2022).", "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 on reasonable request. Periodontitis data can be assessed from http://www.ncbi.nlm.nih.gov/database (assessed on 2 November 2022; GSE10334, GSE16134, GSE23586). 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Periodontitis data can be assessed from http://www.ncbi.nlm.nih.gov/database (assessed on 2 November 2022; GSE10334, GSE16134, GSE23586). Data for chronic kidney failure (CKF)-related genes were searched from DisGeNET https://www.disgenet.org/home/ (assessed on 4 November 2022).", "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 on reasonable request. Periodontitis data can be assessed from http://www.ncbi.nlm.nih.gov/database (assessed on 2 November 2022; GSE10334, GSE16134, GSE23586). 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