Identification of the Subtypes of Renal Ischemia-Reperfusion Injury Based on Pyroptosis-Related Genes
Ischemia-reperfusion injury (IRI) often occurs in the process of kidney transplantation, which significantly impacts the subsequent treatment and prognosis of patients. The prognosis of patients with different subtypes of IRI is quite different. Therefore, in this paper, the gene expression data of...
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MDPI AG
2023-02-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/13/2/275 |
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| author | Xinhao Niu Yin Celeste Cheuk Xiao Li Ruiming Rong Xiaoqing Xu Cuidi Xu Yongsheng Luo Pingbao Zhang Jingjing Guo |
| author_facet | Xinhao Niu Yin Celeste Cheuk Xiao Li Ruiming Rong Xiaoqing Xu Cuidi Xu Yongsheng Luo Pingbao Zhang Jingjing Guo |
| author_sort | Xinhao Niu |
| collection | DOAJ |
| description | Ischemia-reperfusion injury (IRI) often occurs in the process of kidney transplantation, which significantly impacts the subsequent treatment and prognosis of patients. The prognosis of patients with different subtypes of IRI is quite different. Therefore, in this paper, the gene expression data of multiple IRI samples were downloaded from the GEO database, and a double Laplacian orthogonal non-negative matrix factorization (DL-ONMF) algorithm was proposed to classify them. In this algorithm, various regularization constraints are added based on the non-negative matrix factorization algorithm, and the prior information is fused into the algorithm from different perspectives. The connectivity information between different samples and features is added to the algorithm by Laplacian regularization constraints on samples and features. In addition, orthogonality constraints on the basis matrix and coefficient matrix obtained by the algorithm decomposition are added to reduce the influence of redundant samples and redundant features on the results. Based on the DL-ONMF algorithm for clustering, two PRGs-related IRI isoforms were obtained in this paper. The results of immunoassays showed that the immune microenvironment was different among PRGS-related IRI types. Based on the differentially expressed PRGs between subtypes, we used LASSO and SVM-RFE algorithms to construct a diagnostic model related to renal transplantation. ROC analysis showed that the diagnostic model could predict the outcome of renal transplant patients with high accuracy. In conclusion, this paper presents an algorithm, DL-ONMF, which can identify subtypes with different disease characteristics. Comprehensive bioinformatic analysis showed that pyroptosis might affect the outcome of kidney transplantation by participating in the immune response of IRI. |
| first_indexed | 2024-03-11T09:06:10Z |
| format | Article |
| id | doaj.art-a0c3479cdfeb45d0b6dec666636bc8a9 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-11T09:06:10Z |
| publishDate | 2023-02-01 |
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| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-a0c3479cdfeb45d0b6dec666636bc8a92023-11-16T19:22:51ZengMDPI AGBiomolecules2218-273X2023-02-0113227510.3390/biom13020275Identification of the Subtypes of Renal Ischemia-Reperfusion Injury Based on Pyroptosis-Related GenesXinhao Niu0Yin Celeste Cheuk1Xiao Li2Ruiming Rong3Xiaoqing Xu4Cuidi Xu5Yongsheng Luo6Pingbao Zhang7Jingjing Guo8Shanghai Key Laboratory of Organ Transplantation, Shanghai 200032, ChinaShanghai Key Laboratory of Organ Transplantation, Shanghai 200032, ChinaDepartment of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaShanghai Key Laboratory of Organ Transplantation, Shanghai 200032, ChinaShanghai Key Laboratory of Organ Transplantation, Shanghai 200032, ChinaShanghai Key Laboratory of Organ Transplantation, Shanghai 200032, ChinaShanghai Key Laboratory of Organ Transplantation, Shanghai 200032, ChinaShanghai Key Laboratory of Organ Transplantation, Shanghai 200032, ChinaShanghai Key Laboratory of Organ Transplantation, Shanghai 200032, ChinaIschemia-reperfusion injury (IRI) often occurs in the process of kidney transplantation, which significantly impacts the subsequent treatment and prognosis of patients. The prognosis of patients with different subtypes of IRI is quite different. Therefore, in this paper, the gene expression data of multiple IRI samples were downloaded from the GEO database, and a double Laplacian orthogonal non-negative matrix factorization (DL-ONMF) algorithm was proposed to classify them. In this algorithm, various regularization constraints are added based on the non-negative matrix factorization algorithm, and the prior information is fused into the algorithm from different perspectives. The connectivity information between different samples and features is added to the algorithm by Laplacian regularization constraints on samples and features. In addition, orthogonality constraints on the basis matrix and coefficient matrix obtained by the algorithm decomposition are added to reduce the influence of redundant samples and redundant features on the results. Based on the DL-ONMF algorithm for clustering, two PRGs-related IRI isoforms were obtained in this paper. The results of immunoassays showed that the immune microenvironment was different among PRGS-related IRI types. Based on the differentially expressed PRGs between subtypes, we used LASSO and SVM-RFE algorithms to construct a diagnostic model related to renal transplantation. ROC analysis showed that the diagnostic model could predict the outcome of renal transplant patients with high accuracy. In conclusion, this paper presents an algorithm, DL-ONMF, which can identify subtypes with different disease characteristics. Comprehensive bioinformatic analysis showed that pyroptosis might affect the outcome of kidney transplantation by participating in the immune response of IRI.https://www.mdpi.com/2218-273X/13/2/275renal ischemia-reperfusion injuryrenal transplantpyroptosisimmune microenvironmentdiagnostic modelnon-negative matrix factorization |
| spellingShingle | Xinhao Niu Yin Celeste Cheuk Xiao Li Ruiming Rong Xiaoqing Xu Cuidi Xu Yongsheng Luo Pingbao Zhang Jingjing Guo Identification of the Subtypes of Renal Ischemia-Reperfusion Injury Based on Pyroptosis-Related Genes Biomolecules renal ischemia-reperfusion injury renal transplant pyroptosis immune microenvironment diagnostic model non-negative matrix factorization |
| title | Identification of the Subtypes of Renal Ischemia-Reperfusion Injury Based on Pyroptosis-Related Genes |
| title_full | Identification of the Subtypes of Renal Ischemia-Reperfusion Injury Based on Pyroptosis-Related Genes |
| title_fullStr | Identification of the Subtypes of Renal Ischemia-Reperfusion Injury Based on Pyroptosis-Related Genes |
| title_full_unstemmed | Identification of the Subtypes of Renal Ischemia-Reperfusion Injury Based on Pyroptosis-Related Genes |
| title_short | Identification of the Subtypes of Renal Ischemia-Reperfusion Injury Based on Pyroptosis-Related Genes |
| title_sort | identification of the subtypes of renal ischemia reperfusion injury based on pyroptosis related genes |
| topic | renal ischemia-reperfusion injury renal transplant pyroptosis immune microenvironment diagnostic model non-negative matrix factorization |
| url | https://www.mdpi.com/2218-273X/13/2/275 |
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