Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis
Abstract The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis. Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammatio...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-025-86455-4 |
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| author | Pradeep K. Yadalam Prabhu Manickam Natarajan Carlos M. Ardila |
| author_facet | Pradeep K. Yadalam Prabhu Manickam Natarajan Carlos M. Ardila |
| author_sort | Pradeep K. Yadalam |
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| description | Abstract The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis. Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage. This study evaluates the efficacy of Variational Graph Autoencoders (VGAEs) in reconstructing gene data related to NLRP3-mediated pyroptosis in periodontitis. The NCBI GEO dataset GSE262663, containing three samples with and without hypoxia exposure, was analyzed using unsupervised K-means clustering. This method identifies natural groupings within biological data without prior labels. VGAE, a deep learning model, captures complex graph relationships for tasks like link prediction and edge detection. The VGAE model demonstrated exceptional performance with an accuracy of 99.42% and perfect precision. While it identified 5,820 false negatives, indicating a conservative approach, it accurately predicted 4,080 out of 9,900 positive samples. The model’s latent space distribution differed significantly from the original data, suggesting a tightly clustered representation of the gene expression patterns. K-means clustering and VGAE show promise in gene expression analysis and graph structure reconstruction for periodontitis research. |
| format | Article |
| id | doaj-art-733fe6400aec4dbc999961462d4021f7 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-733fe6400aec4dbc999961462d4021f72025-01-19T12:19:09ZengNature PortfolioScientific Reports2045-23222025-01-0115111110.1038/s41598-025-86455-4Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitisPradeep K. Yadalam0Prabhu Manickam Natarajan1Carlos M. Ardila2Department of Periodontics, Saveetha Dental College, Saveetha Institute of Medical and Technology Sciences, SIMATS, Saveetha UniversityDepartment of Clinical Sciences, Center of Medical and Bio-allied Health Sciences and Research, College of Dentistry, Ajman UniversityDepartment of Basic Sciences, Faculty of Dentistry, Universidad de Antioquia U de AAbstract The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis. Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage. This study evaluates the efficacy of Variational Graph Autoencoders (VGAEs) in reconstructing gene data related to NLRP3-mediated pyroptosis in periodontitis. The NCBI GEO dataset GSE262663, containing three samples with and without hypoxia exposure, was analyzed using unsupervised K-means clustering. This method identifies natural groupings within biological data without prior labels. VGAE, a deep learning model, captures complex graph relationships for tasks like link prediction and edge detection. The VGAE model demonstrated exceptional performance with an accuracy of 99.42% and perfect precision. While it identified 5,820 false negatives, indicating a conservative approach, it accurately predicted 4,080 out of 9,900 positive samples. The model’s latent space distribution differed significantly from the original data, suggesting a tightly clustered representation of the gene expression patterns. K-means clustering and VGAE show promise in gene expression analysis and graph structure reconstruction for periodontitis research.https://doi.org/10.1038/s41598-025-86455-4PeriodontitisVariational autoencodersInflammasomeK means clustering |
| spellingShingle | Pradeep K. Yadalam Prabhu Manickam Natarajan Carlos M. Ardila Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis Scientific Reports Periodontitis Variational autoencoders Inflammasome K means clustering |
| title | Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis |
| title_full | Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis |
| title_fullStr | Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis |
| title_full_unstemmed | Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis |
| title_short | Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis |
| title_sort | variational graph autoencoder for reconstructed transcriptomic data associated with nlrp3 mediated pyroptosis in periodontitis |
| topic | Periodontitis Variational autoencoders Inflammasome K means clustering |
| url | https://doi.org/10.1038/s41598-025-86455-4 |
| work_keys_str_mv | AT pradeepkyadalam variationalgraphautoencoderforreconstructedtranscriptomicdataassociatedwithnlrp3mediatedpyroptosisinperiodontitis AT prabhumanickamnatarajan variationalgraphautoencoderforreconstructedtranscriptomicdataassociatedwithnlrp3mediatedpyroptosisinperiodontitis AT carlosmardila variationalgraphautoencoderforreconstructedtranscriptomicdataassociatedwithnlrp3mediatedpyroptosisinperiodontitis |