SPATIAL BIOLOGY APPROACHES TO EXPLORE NOVEL BIOMARKERS AND THERAPEUTIC TARGETS FOR CYSTIC FIBROSIS

Cystic fibrosis (CF) is a life-threatening genetic disorder caused by mutations in the CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene leading to defective chloride and bicarbonate transport in epithelial tissues. While CFTR modulators have revolutionized treatment for patients with responsive mutations, diagnostic challenges persist in CF screenpositive, inconclusive diagnosis (CFSPID) cases and effective therapies remain unavailable for individuals with minimal function (MF) or nonsense mutations. This study employs spatial biology approaches to characterize CFTR protein expression at the single-cell level, identify novel biomarkers, and explore alternative therapeutic targets for patients which do not respond to CFTR modulators. Using Ionocyte CFTR Content (ICC) as a biomarker, we assessed CFTR protein restoration in different CF genotypes following treatment with elexacaftor/tezacaftor/ivacaftor (ETI). ICC provided a quantitative measure of CFTR correction, correlating with functional outcomes and demonstrating its potential as a diagnostic and prognostic tool in CFSPID. Notably, ICC allowed us to detect CFTR expression defects in patients with inconclusive sweat chloride and genetic test results, suggesting its utility for early CF risk stratification. Beyond CFTR, we investigated SLC26A9, a chloride/bicarbonate transporter co-expressed in airway epithelial cells, particularly in pulmonary neuroendocrine cells (PNECs). Our findings revealed that SLC26A9 expression is highly compartmentalized, with potential functional relevance in airway ion transport. Using CRISPR activation, we successfully increased SLC26A9 expression, supporting its potential as an alternative therapeutic target for CF patients who are not eligible for CFTR modulators. Overall, this study highlights the transformative potential of spatial biology in CF research, providing novel insights into CFTR modulation, early CF diagnosis in CFSPID, and alternative therapeutic strategies. ICC emerges as a robust biomarker for CFTR function, while SLC26A9 represents a promising alternative target for CF patients lacking effective treatments. Future research should focus on validating ICC in clinical practice, optimizing SLC26A9-targeted therapies, and integrating spatial multi-omics approaches to advance precision medicine in CF.