Unravelling the mechanisms of clozapine-induced neutropenia in treatment-resistant schizophrenia using cellular genomics

Background: About one-third of individuals with schizophrenia do not respond to first-line antipsychotics. Clozapine has superior efficacy for treatment-resistant schizophrenia (TRS), yet remains underutilised partly due to a 1% risk of potentially fatal clozapine-induced neutropenia (CIN). However, the biological mechanisms underlying CIN remain poorly understood. Methods: We recruited six individuals with TRS who had previously received clozapine: three who ceased clozapine following CIN and three who stopped for reasons unrelated to CIN. Peripheral blood mononuclear cells were collected and cultured in vitro under three conditions: untreated, clozapine alone, or clozapine with its two major metabolites. Single nucleus RNA sequencing was performed to profile the cellular transcriptomic landscape following exposure to clozapine and its metabolites. Results: After quality control, 59,313 cells spanning 26 distinct clusters were retained. Multiple cell type-specific genes were differentially expressed in TRS with CIN, or in response to clozapine exposure in TRS donors with CIN (but not in those without CIN), after adjusting for age, sex and smoking status. We also identified a CIN-associated co-expression module in naive CD4 T cells that was driven by the transcription factor SREBF1, and robust evidence for differential cell-cell communication involving seven intercellular ligand-receptor pairs. There was limited evidence that clozapine-related metabolites contributed to these transcriptional changes. Conclusions: Our findings provide novel insights into cell type-specific transcriptional changes associated with CIN status and/or clozapine exposure in TRS with CIN. With replication in larger, independent cohorts, this work may contribute to the future development of predictive biomarkers for CIN and safer therapeutic strategies for TRS.