Spatial Cellular Networks from omics data with SpaCeNet
Advances in omics technologies have allowed spatially resolved molecular profiling of single cells, providing a window not only into the diversity and distribution of cell types within a tissue, but also into the effects of interactions between cells in shaping the transcriptional landscape. Cells send chemical and mechanical signals which are received by other cells, where they can subsequently initiate context-specific gene regulatory responses. These interactions and their responses shape the individual molecular phenotype of a cell in a given microenvironment. RNAs or proteins measured in individual cells, together with the cells' spatial distribution, provide invaluable information about these mechanisms and the regulation of genes beyond processes occurring independently in each individual cell. "SpaCeNet" is a method designed to elucidate both the intracellular molecular networks (how molecular variables affect each other within the cell) and the intercellular molecular networks (how cells affect molecular variables in their neighbors). This is achieved by estimating conditional independence (CI) relations between captured variables within individual cells and by disentangling these from CI relations between variables of different cells.
Authors
- Robert Lohmayer (ORCID: https://orcid.org/0000-0001-6207-4695)
- Tim Beißbarth (ORCID: https://orcid.org/0000-0001-6509-2143)
- Stefan Schrod (ORCID: https://orcid.org/0000-0001-9936-3984)
- Tina Wipfler
- Michael Altenbuchinger (ORCID: https://orcid.org/0000-0003-1102-6532)
- Katherine H. Shutta (ORCID: https://orcid.org/0000-0003-0402-3771)
- Stefan Solbrig (ORCID: https://orcid.org/0009-0002-0338-3142)
- Peter Josef Oefner (ORCID: https://orcid.org/0000-0002-1499-3977)
- John Quackenbush (ORCID: https://orcid.org/0000-0002-2702-5879)
- Marouen Ben Guebila (ORCID: https://orcid.org/0000-0001-5934-966X)
- Helena U. Zacharias (ORCID: https://orcid.org/0000-0003-3633-1330)
- Dennis Völkl
- Niklas Lück
- Andreas Schäfer (ORCID: https://orcid.org/0000-0003-1171-0078)
Institutions
- Brigham and Women's Hospital (US)
- Harvard University (US)
- Leibniz Association (DE)
- Medizinische Hochschule Hannover (DE)
- Universitätsmedizin Göttingen (DE)
- Leibniz Institute for Immunotherapy
- University of Regensburg (DE)
- University of Göttingen (DE)
Publication Details
- Journal
- Genome Research
- Published
- 2024-09-01
- DOI
- https://doi.org/10.1101/gr.279125.124
- Citations
- 5
- Primary Topic
- Opportunistic and Delay-Tolerant Networks
- Type
- article
Funders
- Wilhelm Sander-Stiftung
- Deutsche Forschungsgemeinschaft
- Bundesministerium für Bildung und Forschung
- National Institutes of Health
- National Heart, Lung, and Blood Institute
- National Human Genome Research Institute
- National Cancer Institute