Multi-scale geometric network analysis identifies melanoma immunotherapy response gene modules Journal Article
| Authors: | Murgas, K. A.; Elkin, R.; Riaz, N.; Saucan, E.; Deasy, J. O.; Tannenbaum, A. R. |
| Article Title: | Multi-scale geometric network analysis identifies melanoma immunotherapy response gene modules |
| Abstract: | Melanoma response to immune-modulating therapy remains incompletely characterized at the molecular level. In this study, we assess melanoma immunotherapy response using a multi-scale network approach to identify gene modules with coordinated gene expression in response to treatment. Using gene expression data of melanoma before and after treatment with nivolumab, we modeled gene expression changes in a correlation network and measured a key network geometric property, dynamic Ollivier-Ricci curvature, to distinguish critical edges within the network and reveal multi-scale treatment-response gene communities. Analysis identified six distinct gene modules corresponding to sets of genes interacting in response to immunotherapy. One module alone, overlapping with the nuclear factor kappa-B pathway (NFkB), was associated with improved patient survival and a positive clinical response to immunotherapy. This analysis demonstrates the usefulness of dynamic Ollivier-Ricci curvature as a general method for identifying information-sharing gene modules in cancer. © The Author(s) 2024. |
| Keywords: | genetics; melanoma; immunotherapy; gene regulatory network; gene regulatory networks; humans; human |
| Journal Title: | Scientific Reports |
| Volume: | 14 |
| ISSN: | 2045-2322 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2024-01-01 |
| Start Page: | 6082 |
| Language: | English |
| DOI: | 10.1038/s41598-024-56459-7 |
| PUBMED: | 38480759 |
| PROVIDER: | scopus |
| PMCID: | PMC10937921 |
| DOI/URL: | |
| Notes: | The MSK Cancer Center Support Grant (P30 CA008748) is acknowledged in the PubMed record and PDF. Corresponding MSK author is Joseph O. Deasy -- Source: Scopus |
Altmetric
Citation Impact
BMJ Impact Analytics
Related MSK Work