A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer Proteins
Cancer hallmark genes and proteins orchestrate and drive carcinogenesis to a large extent, therefore, it is important to study these features in different cancer types to understand the process of tumorigenesis and discover measurable indicators. We performed a pan-cancer analysis to map differentia...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Journal of Personalized Medicine |
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| Online Access: | https://www.mdpi.com/2075-4426/12/11/1919 |
| _version_ | 1797464929010188288 |
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| author | Medi Kori Gullu Elif Ozdemir Kazim Yalcin Arga Raghu Sinha |
| author_facet | Medi Kori Gullu Elif Ozdemir Kazim Yalcin Arga Raghu Sinha |
| author_sort | Medi Kori |
| collection | DOAJ |
| description | Cancer hallmark genes and proteins orchestrate and drive carcinogenesis to a large extent, therefore, it is important to study these features in different cancer types to understand the process of tumorigenesis and discover measurable indicators. We performed a pan-cancer analysis to map differentially interacting hallmarks of cancer proteins (DIHCP). The TCGA transcriptome data associated with 12 common cancers were analyzed and the differential interactome algorithm was applied to determine DIHCPs and DIHCP-centric modules (i.e., DIHCPs and their interacting partners) that exhibit significant changes in their interaction patterns between the tumor and control phenotypes. The diagnostic and prognostic capabilities of the identified modules were assessed to determine the ability of the modules to function as system biomarkers. In addition, the druggability of the prognostic and diagnostic DIHCPs was investigated. As a result, we found a total of 30 DIHCP-centric modules that showed high diagnostic or prognostic performance in any of the 12 cancer types. Furthermore, from the 16 DIHCP-centric modules examined, 29% of these were druggable. Our study presents candidate systems’ biomarkers that may be valuable for understanding the process of tumorigenesis and improving personalized treatment strategies for various cancers, with a focus on their ten hallmark characteristics. |
| first_indexed | 2024-03-09T18:14:10Z |
| format | Article |
| id | doaj.art-d8b0be04843142c096fee9e455363ad5 |
| institution | Directory Open Access Journal |
| issn | 2075-4426 |
| language | English |
| last_indexed | 2024-03-09T18:14:10Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Personalized Medicine |
| spelling | doaj.art-d8b0be04843142c096fee9e455363ad52023-11-24T08:54:30ZengMDPI AGJournal of Personalized Medicine2075-44262022-11-011211191910.3390/jpm12111919A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer ProteinsMedi Kori0Gullu Elif Ozdemir1Kazim Yalcin Arga2Raghu Sinha3Department of Bioengineering, Marmara University, Istanbul 34854, TurkeyDepartment of Bioengineering, Marmara University, Istanbul 34854, TurkeyDepartment of Bioengineering, Marmara University, Istanbul 34854, TurkeyDepartment of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USACancer hallmark genes and proteins orchestrate and drive carcinogenesis to a large extent, therefore, it is important to study these features in different cancer types to understand the process of tumorigenesis and discover measurable indicators. We performed a pan-cancer analysis to map differentially interacting hallmarks of cancer proteins (DIHCP). The TCGA transcriptome data associated with 12 common cancers were analyzed and the differential interactome algorithm was applied to determine DIHCPs and DIHCP-centric modules (i.e., DIHCPs and their interacting partners) that exhibit significant changes in their interaction patterns between the tumor and control phenotypes. The diagnostic and prognostic capabilities of the identified modules were assessed to determine the ability of the modules to function as system biomarkers. In addition, the druggability of the prognostic and diagnostic DIHCPs was investigated. As a result, we found a total of 30 DIHCP-centric modules that showed high diagnostic or prognostic performance in any of the 12 cancer types. Furthermore, from the 16 DIHCP-centric modules examined, 29% of these were druggable. Our study presents candidate systems’ biomarkers that may be valuable for understanding the process of tumorigenesis and improving personalized treatment strategies for various cancers, with a focus on their ten hallmark characteristics.https://www.mdpi.com/2075-4426/12/11/1919hallmarks of cancerdifferential interactomesystem biomarkersdruggabilitypersonalized treatments |
| spellingShingle | Medi Kori Gullu Elif Ozdemir Kazim Yalcin Arga Raghu Sinha A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer Proteins Journal of Personalized Medicine hallmarks of cancer differential interactome system biomarkers druggability personalized treatments |
| title | A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer Proteins |
| title_full | A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer Proteins |
| title_fullStr | A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer Proteins |
| title_full_unstemmed | A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer Proteins |
| title_short | A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer Proteins |
| title_sort | pan cancer atlas of differentially interacting hallmarks of cancer proteins |
| topic | hallmarks of cancer differential interactome system biomarkers druggability personalized treatments |
| url | https://www.mdpi.com/2075-4426/12/11/1919 |
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