Single-cell RNAseq identifies persistent epithelial and immune dysfunction in PwCF by mitigating inter-individual...

Nasal epithelium (NE) is used as a surrogate for lower airway epithelium in cystic fibrosis (CF). However, NE is composed of diverse cell types with unique functions; changes to this heterogeneous tissue in disease can be cell-type specific. To explore the impact of tissue heterogeneity, we examine NE gene expression and cell-type heterogeneity using single-cell transcriptomics of people with CF (PwCF) and healthy volunteers (HV). We also compare cell-type abundance in paired single-cell and bulk transcriptomic samples.

Single-cell RNAseq (scRNAseq) was performed on nasal curettage samples from 9 PwCF and 7 HVs. Differential gene expression, gene set expression, and cell-type abundance were estimated. Cell-type abundance was estimated for paired bulk RNAseq data from 5 PwCF and 5 HVs using deconvolution and compared to scRNAseq data.

We find cell-type-specific differentially expressed genes in CF NE, including genes involved in ubiquitination and inflammation. We find downregulation of chaperome expression in epithelial cells and macrophages, broadly observed in prior bulk transcriptomic studies. We find no significant differences in cell-type abundance between PwCF and HVs and observe considerable inter-individual heterogeneity. We find variable correlation between bulk- and scRNAseq cell-type abundance.

Cell-type heterogeneity in HVs and PwCF and variable correlation between cell-type abundances in bulk and single-cell RNAseq confirm substantial NE tissue heterogeneity. This strengthens the rationale for single-cell transcriptomics as an informative complement to bulk RNAseq in NE. Chaperome downregulation in cell-types with relatively low CFTR expression suggests endogenous and exogenous factors regulate chaperome expression in CF.