Methods for relating spatial patterns of microenvironmental pH and oxygen levels with gene expression of single cells

Local pH and oxygen (O2) levels are key to physiological homeostasis in organs of any species. While the effect of O2 and, to some degree, pH, are well-studied in isolated cell models, their spatial and temporal dynamics and their impact on gene expression in individual cells within organs remain unexplored. Spatial transcriptomics methods can measure gene expression of cells within tissues, but methods to simultaneously map the effects of pH and O2 microenvironments to single cell gene expression are lacking. To this end, this project will develop methods to measure pH and O₂ levels within tissues, integrating these readouts with spatially resolved single-cell gene expression data. By applying these methods to liver tissue, we will generate models of how local O₂ and pH environments shape cellular gene expression and function. This represents a key step toward quantitative molecular physiology of organ microenvironment