<i>NKX6.1</i> mRNA copy number is an actionable biomarker associated with islet function and clinical outcomes after islet transplantation

Islet transplantation, a validated therapy for type 1 diabetes, shows heterogeneous clinical outcomes. There is an unmet need for actionable biomarkers predicting islet graft potency before transplantation. We leveraged a comprehensive set of clinical data and islet samples to explore the relation between islet <i>NKX6.1</i> gene expression and clinical transplantation outcomes. We measured <i>NKX6.1</i> copy number with digital PCR in 114 clinical islet preparations and showed its linear correlation with islet graft function in a mouse bioassay, independently of islet mass, purity, and viability (<i>P</i> < 0.01). Analyzing the clinical outcomes of 34 patients who received two or three islet preparations, we showed the added value of total <i>NKX6.1</i> copy number to predict primary graft function, as compared with islet mass alone (Delong test, <i>P</i> < 0.001). Using a multiple regression Cox model, adjusted for islet mass, purity, and viability, a high total <i>NKX6.1</i> copy number was independently correlated with 10-year survival of islet graft success [adjusted hazard ratio (HR) [95% CI]: 0.63 [0.43; 0.92], <i>P</i> < 0.017] and insulin independence (HR [95% CI]: 0.70 [0.52; 93], <i>P</i> < 0.01). This relation was confirmed in an independent cohort of nine patients receiving a single islet transplantation in other centers. Genetic silencing with anti-<i>NKX6.1</i> shRNA or pharmacological induction of NKX6.1 with silymarin in vitro indicated a causal link between <i>NKX6.1</i> gene expression and islet graft function. These results suggest that <i>NKX6.1</i> mRNA expression can predict islet graft function and may serve as an actionable biomarker of graft potency in β cell replacement.