(427) Persistence of cell type-specific transcriptomic changes in the nasal epithelium in people with cystic fibrosis receiving CFTR modulators

Thursday, November 3, 2022

12:45 PM – 1:25 PM ET

Presenting Author(s)

Thaddeus Cybulski, MD, PhD

Fellow, Adult Pulmonary and Critical Care
Northwestern University
Chicago, Illinois, United States

Co-Author(s)

ZK

Zasu Klug

Northwestern University, United States
RN

Rachel Nelson

Northwestern University, United States
MS

Marc Sala, MD

Assistant Professor of Medicine
Northwestern University, United States
ED

Estefani Diaz

Northwestern University, United States
ZL

Ziyan Lu

Northwestern University, United States
AM

Alexander Misharin, MD, PhD

Assistant Professor of Medicine
Northwestern University
Chicago, Illinois, United States
MJ

Manu Jain, MD

Professor of Medicine
Northwestern University, United States

Background: Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). These mutations result in varying degrees of secretory dysfunction in multiple organ systems including the airway epithelium, resulting in bronchiectasis, chronic airway infection and progressive loss of pulmonary function. CFTR modulators have transformed approach to therapy in cystic fibrosis. However, not all people living with cystic fibrosis (PwCF) have full response to therapy. Hence, it is important to understand cellular and molecular changes that determine response or failure to respond to CFTR modulators. We thus hypothesize that single cell transcriptomic profiling (scRNA-seq) of nasal epithelial cells can reveal cellular and molecular mechanisms determining successful response to CFTR modulators and that these mechanisms can be generalized to the lower airways. To test this hypothesis we performed a pilot study in which we analyzed nasal curettage samples from healthy volunteers and PwCF using scRNA-seq.

Methods: This research was approved by the Northwestern University Institutional Review Board. All study participants or their surrogates provided informed consent. We recruited 8 healthy control subjects and 8 PwCFs, all of which had at least 1 copy of the F508del mutation and 5 of which were on CFTR modulating medications. We obtained nasal epithelial samples using nasal curettes, generated single cell suspension, and performed single cell transcriptomic profiling (RNA-seq) using the 10x Genomics platform. Data were integrated using the scVI toolkit, and resulting clusters were annotated based on expression of cell type-specific markers, followed by analysis of differential gene expression between healthy controls and PwCF within each cell type.

Results: We identify distinct populations of cells, including secretory, ciliated, lymphoid, and myeloid cell types, as well as rare cell types such as ionocytes. We found no difference in the cell type composition of the nasal epithelium between healthy controls and PwCF. Ionocytes had higher expression of CFTR than secretory cells; however, secretory cells were far more abundant than ionocytes. While most PwCF were on CFTR modulators, analysis of differential gene expression between healthy volunteers and PwCF identified persistent cell type-specific changes. Specifically, we found transcriptomic evidence of altered fluid transport in secretory cells (AQP3, AQP5) and increased activation of immune cells in PwCF.

Conclusions: We found that collecting NC samples for sc-RNAseq is feasible in PwCF. We are able to reconstitute known elements of the upper-airway epithelium and inflammatory milieu as well as identify rare cell types that have been previously described. In doing so, we demonstrate scRNA-seq of nasal curettage samples as a reliable method for obtaining detailed transcriptomic data in patients with cystic fibrosis. Further analysis accounting for a number of clinical covariates e.g. therapeutics, pulmonary function, and clinical outcomes, will allow for a richer understanding of this transcriptomic data.

Acknowledgements: This work was supported by the Cystic Fibrosis Foundation: JAIN19K0

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