SUMMARY A growing number of serious disorders ranging from syndromic autism and intellectual disability to cancers of the brain and gut have been linked to intracellular members of a family of electroneutral Na+/H+ exchangers, including endosomal isoforms NHE6 and NHE9 (eNHE), that regulate pH and Na+ within the compartments of the endo-lysosomal pathway. Plasma membrane NHE isoforms have been thoroughly characterized and pharmaceutically targeted. In contrast, intracellular NHE remain poorly studied due to limitations and challenges in sensing organelle-specific lumenal ions. Furthermore, overlapping distributions of eNHE isoforms and contradictory reports on the direction of sodium and proton transport within organelles has hindered a mechanistic understanding of transporter function and physiology. Case reports linking disease to eNHE genetic variants are sporadic and genotype-phenotype correlations are incomplete. This proposal brings together three research groups with unique and complementary expertise, together with powerful tools and resources to tackle these problems. To overcome the technical challenges in measuring the activity of these transporters, we have developed a multi-functional fluorescent reporter for both Na+ and H+ to precisely assay intracellular Na+/H+ exchange. This reporter can be targeted to specific organelles to simultaneously read out Na+ and H+ levels therein using an imaging method called two-ion measurement. In Aim 1, we will deploy this reporter to specific compartments along the endo-lysosomal pathway to quantify [Na+] and [H+] in both healthy and disease states. We will determine the functional contribution and mode of transport of individual eNHE isoforms in key organelles. This aim will lay the groundwork for functional analysis of clinically impactful gene variants in eNHE. To capture the disease landscape for eNHE, in Aim 2 we will evaluate the clinical significance of rare and common gene variants in SLC9A6 and SLC9A9. For these analyses, we will leverage large-scale exome sequencing of a clinical cohort, paired with their de-identified electronic health records. Combining genetic associations, gene expression and functional analysis will provide mechanistic insight on the biological basis of disease associated with eNHE. In summary, our comprehensive biochemical mapping of the endo-lysosomal pathway and disease-agnostic approach to link gene variants and expression to phenotypes will capture a broad range of cellular and clinical correlates that will pave the way to successful therapeutic targeting of these transporters in disease.