Dynamic network curvature analysis of gene expression reveals novel potential therapeutic targets in sarcoma Journal Article
| Authors: | Elkin, R.; Oh, J. H.; Dela Cruz, F.; Norton, L.; Deasy, J. O.; Kung, A. L.; Tannenbaum, A. R. |
| Article Title: | Dynamic network curvature analysis of gene expression reveals novel potential therapeutic targets in sarcoma |
| Abstract: | Network properties account for the complex relationship between genes, making it easier to identify complex patterns in their interactions. In this work, we leveraged these network properties for dual purposes. First, we clustered pediatric sarcoma tumors using network information flow as a similarity metric, computed by the Wasserstein distance. We demonstrate that this approach yields the best concordance with histological subtypes, validated against three state-of-the-art methods. Second, to identify molecular targets that would be missed by more conventional methods of analysis, we applied a novel unsupervised method to cluster gene interactomes represented as networks in pediatric sarcoma. RNA-Seq data were mapped to protein-level interactomes to construct weighted networks that were then subjected to a non-Euclidean, multi-scale geometric approach centered on a discrete notion of curvature. This provides a measure of the functional association among genes in the context of their connectivity. In confirmation of the validity of this method, hierarchical clustering revealed the characteristic EWSR1-FLI1 fusion in Ewing sarcoma. Furthermore, assessing the effects of in silico edge perturbations and simulated gene knockouts as quantified by changes in curvature, we found non-trivial gene associations not previously identified. © 2024, The Author(s). |
| Keywords: | child; genetics; metabolism; gene expression; pathology; cell line, tumor; ewing sarcoma; sarcoma; gene expression regulation; gene expression regulation, neoplastic; tumor cell line; oncogene proteins, fusion; rna binding protein ews; transcription factor fli 1; soft tissue neoplasms; soft tissue tumor; proto-oncogene protein c-fli-1; rna-binding protein ews; sarcoma, ewing; humans; human; oncogene fusion protein |
| Journal Title: | Scientific Reports |
| Volume: | 14 |
| ISSN: | 2045-2322 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2024-01-01 |
| Start Page: | 488 |
| Language: | English |
| DOI: | 10.1038/s41598-023-49930-4 |
| PUBMED: | 38177639 |
| PROVIDER: | scopus |
| PMCID: | PMC10766622 |
| DOI/URL: | |
| Notes: | The MSK Cancer Center Support Grant (P30 CA008748) is acknowledged in the PDF. Corresponding MSK author is Rena Elkin -- Source: Scopus |
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