CLARITY analysis of the Cl/pH sensor expression in the brain of transgenic mice

Genetically encoded biosensors are widely used in cell biology for the non-invasive imaging of concentrations of ions or the activity of enzymes, to evaluate the distribution of small molecules, proteins and organelles, and to image protein interactions in living cells. These fluorescent molecules can be used either by transient expression in cultured cells or in entire organisms or through stable expression by producing transgenic animals characterized by genetically encoded and heritable biosensors. Using the mouse Thy1 mini-promoter, we generated a line of transgenic mice expressing a genetically encoded sensor for the simultaneous measurements of intracellular Cl − and pH. This construct, called ClopHensor, consists of a H + - and Cl − -sensitive variant of the enhanced green fluorescent protein (E 2 GFP) fused with a red fluorescent protein (DsRedm). Stimulation of hippocampal Schaffer collaterals proved that the sensor is functionally active. To reveal the expression pattern of ClopHensor across the brain of Thy1 ::ClopHensor mice, we obtained transparent brain samples using the CLARITY method and imaged them with confocal and light-sheet microscopy. We then developed a semi-quantitative approach to identify brain structures with high intrinsic sensor fluorescence. This approach allowed us to assess cell morphology and track axonal projection, as well as to confirm E 2 GFP and DsRedm fluorescence colocalization. This analysis also provides a map of the brain areas suitable for non-invasive monitoring of intracellular Cl − /pH in normal and pathological conditions. This article is part of a Special Issue entitled: Honoring Ricardo Miledi - outstanding neuroscientist of XX-XXI centuries. • Generated transgenic mice expressing a genetically encoded sensor of ions • Neuron-specific Thy1 ::ClopHensor allows simultaneous measurements of Cl − and pH • Obtained transparent brain samples using the CLARITY method • Identified brain structures with high intrinsic sensor fluorescence • Analysis provides a detailed map of the brain areas expressing ClopHensor