C95-09 Transcriptomic Endotypes in Cystic Fibrosis and Response to Triple-modulator Therapy

Rationale While cystic fibrosis (CF) is a monogenic disorder, there is substantial variability in disease severity and outcomes, even among individuals with the same CFTR genotype. Triple modulator therapy with elexacaftor/tezacaftor/ivacaftor (ETI) has markedly improved outcomes for people with CF (pwCF), but responses may vary. We hypothesized that endotypes defined by T-helper (Th) immune pathways (Th1, Th2, Th17) may underlie variability in lung function responses to ETI. Methods PwCF ≥6 years old were recruited at the University of Pittsburgh CF Center, Nov 2019-Oct 2021. RNAseq was performed on nasal epithelial samples collected before (n = 41) and after (n = 28) ETI initiation. We evaluated transcriptomic profiles associated with ETI response, defined as a 5% or greater increase in year’s-best FEV1 (ΔybFEV1 ≥5%). Expression of 13 “signature” genes (Th1: STAT1, IFNG, CD8A, CD8B, CXCL10; Th2: POSTN, CLCA1, SERPINB2; Th17: CXCL1, CXCL2, CXCL3, IL8, CSF3) was normalized and used for k-means clustering to define transcriptomic endotypes: Th1-high, Th17-high, Th1+Th17-high, Th2-high, and Th-low (Th1/Th2/Th17-low). Differential expression was analyzed in DESeq2, with DEGs defined at FDR-P <0.01. Results We analyzed 69 nasal samples from 41 pwCF. Endotypes were as follows: Th1-high n = 14 (20%), Th17-high n = 17 (25%), Th1+Th17-high n = 7 (10%), Th2-high n = 8 (12%), and Th-low n = 23 (33%) (Figure 1A). Baseline Th1-high profiles were over-represented among those who responded to ETI, independent of Th17 levels (Fig.1B). Mean expression of the Th1 5-gene signature was positively correlated with ΔybFEV1 (Fig.1C, r = 0.4, p = 0.012); pwCF who had Th1-high profiles at baseline were significantly more likely to respond to ETI compared with other profiles. Differential expression analysis identified 727 upregulated genes in Th1-high versus Th1-low profiles, including HLA genes, CTSW, CD8A, CD3E, CCL5, IRF1, IL2RB, etc (Fig.1D). It also included 12 of 30 (40%) of genes in the transcriptomic risk score we previously reported to predict ETI response (Yue et al AJRCMB 2024). Enriched pathways included regulation of T-cell activation, lymphocyte-mediated immunity, and interferon signaling. Conclusions We identified T-helper transcriptomic endotypes in nasal respiratory epithelium samples from pwCF. A Th1-high endotype was strongly associated with improved lung function response to ETI and enriched for relevant biologic pathways. Our findings suggest that immune-driven transcriptomic endotypes may help explain variability in CFTR modulator response and highlight potential biomarkers for precision medicine in CF.