Cytotoxic CD8+ T cells persist and show transcriptional priming in lung transplantation

Allograft rejection remains a critical limitation following lung transplantation, with alloreactive CD8+ T cells serving as key effectors. We performed single-cell RNA and T cell receptor sequencing on 19 biopsies from 7 lung transplant recipients, including sequential biopsies spanning acute cellular rejection (ACR) and acute lung allograft dysfunction (ALAD). Expanded clonotypes exhibited effector/memory signatures. Following ACR resolution, persistent clonotypes displayed quiescent memory programs (KLF2, TBX21), while transitory clonotypes showed distinct activation-associated regulon activity. Pre-expansion clonotypes that later expanded exhibited transcriptional priming: a shared cytotoxic/memory program (TBX21, RUNX3, EOMES) was detectable before both events, with additional IRF9-driven interferon priming preceding fungal infection. These signatures were present in surveillance biopsies obtained before clinical disease onset. Given the role of persistent expanded T cells as a potential mechanistic link to chronic lung allograft dysfunction, these findings reveal predictive transcriptional signatures for targeting rejection-driving CD8+ T cells.