Proteomic analysis reveals some common proteins in the kidney stone matrix
Background Proteins are the most abundant component of kidney stone matrices and their presence may reflect the process of the stone’s formation. Many studies have explored the proteomics of urinary stones and crystals. We sought to comprehensively identify the proteins found in kidney stones and to...
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PeerJ Inc.
2021-07-01
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| author | Yuanyuan Yang Senyuan Hong Cong Li Jiaqiao Zhang Henglong Hu Xiaolong Chen Kehua Jiang Fa Sun Qing Wang Shaogang Wang |
| author_facet | Yuanyuan Yang Senyuan Hong Cong Li Jiaqiao Zhang Henglong Hu Xiaolong Chen Kehua Jiang Fa Sun Qing Wang Shaogang Wang |
| author_sort | Yuanyuan Yang |
| collection | DOAJ |
| description | Background Proteins are the most abundant component of kidney stone matrices and their presence may reflect the process of the stone’s formation. Many studies have explored the proteomics of urinary stones and crystals. We sought to comprehensively identify the proteins found in kidney stones and to identify new, reliable biomolecules for use in nephrolithiasis research. Methods We conducted bioinformatics research in November 2020 on the proteomics of urinary stones and crystals. We used the ClusterProfiler R package to transform proteins into their corresponding genes and Ensembl IDs. In each study we located where proteomic results intersected to determine the 20 most frequently identified stone matrix proteins. We used the Human Protein Atlas to obtain the biological information of the 20 proteins and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis to explore their biological functions. We also performed immunohistochemistry to detect the expression of the top five stone matrix proteins in renal tissue. Results We included 19 relevant studies for analysis. We then identified 1,409 proteins in the stone matrix after the duplicates were removed. The 20 most-commonly identified stone matrix proteins were: S100A8, S100A9, uromodulin, albumin, osteopontin, lactotransferrin, vitamin K-dependent protein Z, prothrombin, hemoglobin subunit beta, myeloperoxidase, mannan-binding lectin serine protease 2, lysozyme C, complement C3, serum amyloid P-component, cathepsin G, vitronectin, apolipoprotein A-1, eosinophil cationic protein, fibrinogen alpha chain, and apolipoprotein D. GO and KEGG analysis revealed that these proteins were typically engaged in inflammation and immune response.Immunohistochemistry of the top five stone matrix proteins in renal tissue showed that the expression of S100A8, S100A9, and osteopontin increased, while uromodulin decreased in kidney stone patients. Albumin was rarely expressed in the kidney with no significant difference between healthy controls and kidney stone patients. Conclusion Proteomic analysis revealed some common inflammation-related proteins in the kidney stone matrix. The role of these proteins in stone formation should be explored for their potential use as diagnostic biomarkers and therapeutic targets for urolithiasis. |
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| last_indexed | 2024-03-09T07:02:14Z |
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| spelling | doaj.art-67924df043824e5390be8f1f240795162023-12-03T09:49:23ZengPeerJ Inc.PeerJ2167-83592021-07-019e1187210.7717/peerj.11872Proteomic analysis reveals some common proteins in the kidney stone matrixYuanyuan Yang0Senyuan Hong1Cong Li2Jiaqiao Zhang3Henglong Hu4Xiaolong Chen5Kehua Jiang6Fa Sun7Qing Wang8Shaogang Wang9Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, ChinaDepartment of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, ChinaDepartment of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, ChinaDepartment of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, ChinaDepartment of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, ChinaDepartment of Urology, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, ChinaDepartment of Urology, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, ChinaDepartment of Urology, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, ChinaDepartment of Urology, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, ChinaDepartment of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, ChinaBackground Proteins are the most abundant component of kidney stone matrices and their presence may reflect the process of the stone’s formation. Many studies have explored the proteomics of urinary stones and crystals. We sought to comprehensively identify the proteins found in kidney stones and to identify new, reliable biomolecules for use in nephrolithiasis research. Methods We conducted bioinformatics research in November 2020 on the proteomics of urinary stones and crystals. We used the ClusterProfiler R package to transform proteins into their corresponding genes and Ensembl IDs. In each study we located where proteomic results intersected to determine the 20 most frequently identified stone matrix proteins. We used the Human Protein Atlas to obtain the biological information of the 20 proteins and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis to explore their biological functions. We also performed immunohistochemistry to detect the expression of the top five stone matrix proteins in renal tissue. Results We included 19 relevant studies for analysis. We then identified 1,409 proteins in the stone matrix after the duplicates were removed. The 20 most-commonly identified stone matrix proteins were: S100A8, S100A9, uromodulin, albumin, osteopontin, lactotransferrin, vitamin K-dependent protein Z, prothrombin, hemoglobin subunit beta, myeloperoxidase, mannan-binding lectin serine protease 2, lysozyme C, complement C3, serum amyloid P-component, cathepsin G, vitronectin, apolipoprotein A-1, eosinophil cationic protein, fibrinogen alpha chain, and apolipoprotein D. GO and KEGG analysis revealed that these proteins were typically engaged in inflammation and immune response.Immunohistochemistry of the top five stone matrix proteins in renal tissue showed that the expression of S100A8, S100A9, and osteopontin increased, while uromodulin decreased in kidney stone patients. Albumin was rarely expressed in the kidney with no significant difference between healthy controls and kidney stone patients. Conclusion Proteomic analysis revealed some common inflammation-related proteins in the kidney stone matrix. The role of these proteins in stone formation should be explored for their potential use as diagnostic biomarkers and therapeutic targets for urolithiasis.https://peerj.com/articles/11872.pdfBioinformaticNephrolithiasisProteomicsStone matrixBiomarker |
| spellingShingle | Yuanyuan Yang Senyuan Hong Cong Li Jiaqiao Zhang Henglong Hu Xiaolong Chen Kehua Jiang Fa Sun Qing Wang Shaogang Wang Proteomic analysis reveals some common proteins in the kidney stone matrix PeerJ Bioinformatic Nephrolithiasis Proteomics Stone matrix Biomarker |
| title | Proteomic analysis reveals some common proteins in the kidney stone matrix |
| title_full | Proteomic analysis reveals some common proteins in the kidney stone matrix |
| title_fullStr | Proteomic analysis reveals some common proteins in the kidney stone matrix |
| title_full_unstemmed | Proteomic analysis reveals some common proteins in the kidney stone matrix |
| title_short | Proteomic analysis reveals some common proteins in the kidney stone matrix |
| title_sort | proteomic analysis reveals some common proteins in the kidney stone matrix |
| topic | Bioinformatic Nephrolithiasis Proteomics Stone matrix Biomarker |
| url | https://peerj.com/articles/11872.pdf |
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