The laboratory mouse has long been the primary model in biomedical research. However, until now, scientists have not been able to simultaneously observe how tissues throughout the body function and which genes are activated in different cell types without disrupting their natural anatomical organization. Existing methods allowed studying either individual molecules and cells or only small tissue regions.
Researchers from the United States and Japan solved this problem by developing a method for analyzing tissues across the entire mouse body while simultaneously measuring gene activity. As a result, the scientists generated detailed spatial maps of the whole mouse body. These maps accurately reproduced the structure of 16 major organs and numerous tissues within their natural anatomical context. The method enabled visualization not only of tissue localization but also of the distribution of different cell types throughout the organism.
In addition, the researchers developed LABEL – an artificial intelligence-based model that automatically recognizes organs, tissues, and cell types in histological images. LABEL accurately identified most organs, including the brain, liver, kidneys, intestine, and lungs. The model also successfully recognized various tissues and cell types, including hepatocytes, renal epithelial cells, neurons, muscle cells, and epidermal cells.
The capabilities of the new method were demonstrated in a model of systemic inflammation – endotoxemia. The results revealed how inflammation simultaneously alters cellular states throughout the entire organism.
Cellular and Tissue Responses to Systemic Inflammation
The researchers induced systemic bacterial inflammation by administering lipopolysaccharide (LPS). The new method identified more than 5,000 genes whose activity changed across 37 tissues in 16 organs.
The results showed that the inflammatory response involved nearly the entire organism, but manifested differently across tissues. For example, genes encoding serum amyloid proteins – key inflammatory markers – were especially active in the liver, although some were additionally activated in the intestine, kidneys, and other tissues.
Levels of the chemokines Ccl5 and Cxcl9 increased simultaneously in multiple organs. Ccl12 was particularly strongly produced in the brain and thymus, whereas Cxcl13 was predominantly expressed in the spleen and skin.
The interferon-stimulated gene Irgm1 (ISG) was activated in the kidneys, liver, lungs, and heart following LPS administration, possibly reflecting its protective role during septic shock.
The researchers also identified changes in signaling pathways regulating intercellular communication. In many organs, pathways associated with inflammation, immune cell migration, vascular activation, and tissue remodeling became more active. At the same time, anti-inflammatory pathways limiting excessive immune responses were also activated.
Changes were also observed in cellular composition:
- Immune cells: macrophage numbers increased in the lungs, liver, spleen, and kidneys; neutrophils increased in the lungs and spleen; meanwhile, splenic lymphocytes and thymocytes decreased.
- Non-immune cells: proportions of endothelial cells, epithelial cells, and fibroblasts changed in the lungs, heart, liver, and kidneys, consistent with tissue injury and cell death during endotoxemia.
Systemic inflammation altered gene expression across many cell types and organs, although the greatest changes occurred in epithelial and muscle cells. The major contributors to the inflammatory response were epithelial cells of the liver, kidneys, intestines, and stomach, as well as heart and skeletal muscle cells.
Among blood and immune cells, gene activity changed most strongly in the spleen, thymus, and bone marrow, as well as in the lungs and liver.
Across different cell types in many tissues, the most pronounced alterations were observed in macrophages, endothelial cells, and fibroblasts. Moreover, macrophages not only increased in number but also altered their gene expression patterns differently across tissues.
In epithelial and immune cells, signaling pathways associated with type II interferon, IL-17A, and IL-1 became activated. At the same time, tissue-specific gene programs were activated in epithelial cells of the lungs, kidneys, colon, skin, and thymus in response to inflammation.
STAT1 and IRF1 Coordinate the Inflammatory Response Throughout the Organism
During systemic inflammation, the regulatory proteins STAT1 and IRF1 activate ISGs across multiple organs and cell types simultaneously. Activity of the Stat1 and Irf1 genes increased in nearly all hematopoietic and non-hematopoietic cells, including epithelial cells, endothelial cells, fibroblasts, muscle cells, and neurons. However, Stat1 and Irf1 activity differed between tissues. For example, Stat1 activity increased especially strongly in brain cells, whereas Irf1 did not.
Experiments in mice lacking the Stat1 or Irf1 genes demonstrated that, in their absence, the inflammatory response was markedly weakened. These mice showed significantly reduced ISG activation throughout the body, and the characteristic decrease in body temperature following LPS administration disappeared.
Conclusion
In the future, LABEL and similar models could be trained on data from different animal species, including both mammals and non-mammals, enabling automatic recognition of tissues and cells in histological images and facilitating comparisons of biological processes across organisms. Further development of LABEL may improve histological image analysis and allow adaptation of the system for use with human tissues.
The developed technology will make it possible to:
- study the effects of genetic mutations simultaneously across all organs, tissues, and cell types;
- obtain detailed information about the localization and state of cells in different organs;
- better understand how cells interact under normal conditions and how these interactions change during disease;
- evaluate drug effects across different tissues, identify both beneficial and adverse drug effects, and more precisely investigate mechanisms of action in target tissues.
Reference
Whole-body molecular and cellular mapping of the laboratory mouse
