Detection of reproducible liver cancer specific ligand-receptor signaling in blood
Cell-cell communication mediated by ligand-receptor interactions (LRI) is critical to coordinating diverse biological processes in homeostasis and disease. Lately, our understanding of these processes has greatly expanded through the inference of cellular communication, utilizing RNA extracted from...
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| Format: | Article |
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2024.1332782/full |
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| author | Aram Safrastyan Aram Safrastyan Damian Wollny Damian Wollny Damian Wollny |
| author_facet | Aram Safrastyan Aram Safrastyan Damian Wollny Damian Wollny Damian Wollny |
| author_sort | Aram Safrastyan |
| collection | DOAJ |
| description | Cell-cell communication mediated by ligand-receptor interactions (LRI) is critical to coordinating diverse biological processes in homeostasis and disease. Lately, our understanding of these processes has greatly expanded through the inference of cellular communication, utilizing RNA extracted from bulk tissue or individual cells. Considering the challenge of obtaining tissue biopsies for these approaches, we considered the potential of studying cell-free RNA obtained from blood. To test the feasibility of this approach, we used the BulkSignalR algorithm across 295 cell-free RNA samples and compared the LRI profiles across multiple cancer types and healthy donors. Interestingly, we detected specific and reproducible LRIs particularly in the blood of liver cancer patients compared to healthy donors. We found an increase in the magnitude of hepatocyte interactions, notably hepatocyte autocrine interactions in liver cancer patients. Additionally, a robust panel of 30 liver cancer-specific LRIs presents a bridge linking liver cancer pathogenesis to discernible blood markers. In summary, our approach shows the plausibility of detecting liver LRIs in blood and builds upon the biological understanding of cell-free transcriptomes. |
| format | Article |
| id | doaj-art-0e5cc25b26ce4af5a0b8cf7a7bff6f8d |
| institution | Kabale University |
| issn | 2673-7647 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj-art-0e5cc25b26ce4af5a0b8cf7a7bff6f8d2025-01-09T06:10:28ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472025-01-01410.3389/fbinf.2024.13327821332782Detection of reproducible liver cancer specific ligand-receptor signaling in bloodAram Safrastyan0Aram Safrastyan1Damian Wollny2Damian Wollny3Damian Wollny4RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, GermanyGenetics and Epigenetics of Aging, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, GermanyRNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, GermanyGenetics and Epigenetics of Aging, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, GermanyDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyCell-cell communication mediated by ligand-receptor interactions (LRI) is critical to coordinating diverse biological processes in homeostasis and disease. Lately, our understanding of these processes has greatly expanded through the inference of cellular communication, utilizing RNA extracted from bulk tissue or individual cells. Considering the challenge of obtaining tissue biopsies for these approaches, we considered the potential of studying cell-free RNA obtained from blood. To test the feasibility of this approach, we used the BulkSignalR algorithm across 295 cell-free RNA samples and compared the LRI profiles across multiple cancer types and healthy donors. Interestingly, we detected specific and reproducible LRIs particularly in the blood of liver cancer patients compared to healthy donors. We found an increase in the magnitude of hepatocyte interactions, notably hepatocyte autocrine interactions in liver cancer patients. Additionally, a robust panel of 30 liver cancer-specific LRIs presents a bridge linking liver cancer pathogenesis to discernible blood markers. In summary, our approach shows the plausibility of detecting liver LRIs in blood and builds upon the biological understanding of cell-free transcriptomes.https://www.frontiersin.org/articles/10.3389/fbinf.2024.1332782/fullliquid biopsyliver cancercell-cell interactionsingle-cell RNA sequencingcell-free RNAbioinformatics |
| spellingShingle | Aram Safrastyan Aram Safrastyan Damian Wollny Damian Wollny Damian Wollny Detection of reproducible liver cancer specific ligand-receptor signaling in blood Frontiers in Bioinformatics liquid biopsy liver cancer cell-cell interaction single-cell RNA sequencing cell-free RNA bioinformatics |
| title | Detection of reproducible liver cancer specific ligand-receptor signaling in blood |
| title_full | Detection of reproducible liver cancer specific ligand-receptor signaling in blood |
| title_fullStr | Detection of reproducible liver cancer specific ligand-receptor signaling in blood |
| title_full_unstemmed | Detection of reproducible liver cancer specific ligand-receptor signaling in blood |
| title_short | Detection of reproducible liver cancer specific ligand-receptor signaling in blood |
| title_sort | detection of reproducible liver cancer specific ligand receptor signaling in blood |
| topic | liquid biopsy liver cancer cell-cell interaction single-cell RNA sequencing cell-free RNA bioinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2024.1332782/full |
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