A Proteomic Survey of the Cystic Fibrosis Transmembrane Conductance Regulator Surfaceome

Abstract

The aim of this review article is to collate recent contributions of proteomic studies to cystic fibrosis transmembrane conductance regulator (CFTR) biology. We summarize advances from these studies and create an accessible resource for future CFTR proteomic efforts. We focus our attention on the CFTR interaction network at the cell surface, thus generating a CFTR 'surfaceome'. We review the main findings about CFTR interactions and highlight several functional categories amongst these that could lead to the discovery of potential biomarkers and drug targets for CF.

Keywords: BioID; CFTR interactions; CFTR modulators; PDZ domain; clathrin-mediated endocytosis; cystic fibrosis; interactome; peripheral quality control; surfaceome.

Figure 1

Schematic of different proteomic approaches used to investigate the CFTR interactome. Schematic for the workflow of the different proteomic approaches discussed in this review: Co-PIT, MaMTH-HTS, and proximity-dependent biotinylation methods (BioID and TurboID). Co-purifying Protein Identification Technology (Co-PIT).

Figure 2

Summary of findings of different proteomic approaches used to investigate the CFTR interactome. Key details and findings for each of the five proteomic studies profiled in this review [11,25,27,28,29]. Arrows indicate an increase (↑) or decrease (↓) in WT or ∆F508-CFTR activity and/or trafficking. Check mark indicates the confirmed finding of each candidate interactor in the different studies. Created using BioRender.com.

Figure 3

WT-CFTR Surfaceome. Depiction of CFTR protein structure consisting of two nucleotide binding domains (NBD1/2), membrane spanning domains (MSD21/2), and regulatory domain (R) inserted in the PM. Interactors generated from the different proteomic approaches that are associated with the PM according to Gene Ontology (Supplementary Dataset S5), arranged according to their predicted (if known) site of binding to CFTR. Degree of overlap of interactors between different approaches is represented by colour: purple (6), red (5), orange (4), and yellow (3). Created using BioRender.com.

Figure 4

WT-CFTR surfaceome includes set of PDZ-domain-containing proteins. Candidate interactors that contain PDZ-domains. Created using BioRender.com.

Figure 5

WT-CFTR surfaceome includes a diverse set of membrane transport interactors. Candidate interactors derived from different proteomic approaches that correspond to ion channel proteins or previously reported solute carrier transporter proteins [11,25]. Created using BioRender.com.

Figure 6

∆F508-CFTR interactome. Overlapping interactors derived from different ∆F508-CFTR interactomes that are associated with (1) cellular response to stress; (2) endoplasmic reticulum; (3) protein folding; and (4) proteosome degradation. Created using BioRender.com.

Figure 7

WT-CFTR surfaceome reveals subunits of the clathrin-mediated endocytic pathway. Depiction of steps involved in clathrin-mediated endocytosis from clathrin-coated pit assembly to clathrin-coated vesicle scission, overlaid with candidate interactors generated from the different proteomic approaches. Locations are approximated based on where these proteins are predicted to be involved in clathrin-coated vesicle formation. Created using BioRender.com.