Metabolic alterations in cystic fibrosis lymphocyte memory accompany restoration of CFTR function

Abstract Rationale Elexacaftor/tezacaftor/ivacaftor (ETI) broadly improves outcomes in cystic fibrosis (CF). Cystic fibrosis transmembrane conductance regulator (CFTR) correction by ETI is incomplete, and patients with established disease continue to experience infection. We hypothesized that CFTR restoration by ETI would modify T-cell memory, providing a basis for improved infectious outcomes after treatment. Objectives To evaluate ETI modification of lymphocyte signatures using transcriptomics and metabolomics in blood samples taken from adults with CF (awCF). Methods and Main Results Circulating CD3+ T cells from awCF (n = 18) before and after ETI initiation were evaluated by cellular indexing of transcriptomes and epitopes by sequencing. Single-cell data profiled multiple T-cell populations, including naive, memory, and effector states, with the most extensive changes occurring in CD4+ T-cell populations. Simultaneous plasma metabolomic measurements were analyzed in association with CD4+ T-cell metabolic gene signatures. The relationships between clinical outcomes, cell-specific gene expression, and metabolomics were evaluated using generalized linear mixed models. The effect of reduced CFTR in lymphocytes was evaluated in vitro using CRISPR/Cas9-mediated CFTR knockdown in primary human lymphocyte cultures, as well as in splenocytes harvested from CFTR knockout mice. Conclusions We reveal that altered metabolism occurs within the CD4+ T memory compartment following CFTR modulation, identifying multiple previously unrecognized changes in memory functions. Memory T-cell metabolic switches are highly related to a reduction in hospitalizations after treatment. Adaptive immune memory in awCF after modulator therapy is highly associated with improved outcomes from CF pulmonary infections, with variation seen in individuals experiencing lesser benefit after modulators.