FDA-Approved Drug Screening in Patient-Derived Organoids Demonstrates Potential of Drug Repurposing for Rare Cystic Fibrosis Genotypes

Abstract

Preclinical cell-based assays that recapitulate human disease play an important role in drug repurposing. We previously developed a functional forskolin induced swelling (FIS) assay using patient-derived intestinal organoids (PDIOs), allowing functional characterization of CFTR, the gene mutated in people with cystic fibrosis (pwCF). CFTR function-increasing pharmacotherapies have revolutionized treatment for approximately 85% of people with CF, but a large unmet need remains to identify new treatments for all pwCF. We used 76 non-homozygous F508del-CFTR PDIOs to test the efficacy of 1400 FDA-approved drugs on improving CFTR function, as measured in FIS assays. Based on the results of a secondary validation screen, we investigated CFTR elevating function of PDE4 inhibitors and currently existing CFTR modulators. We show that PDE4 inhibitors are potent CFTR function inducers in PDIOs and that CFTR modulator treatment rescues of CF genotypes that are currently not eligible for this therapy. This study exemplifies the feasibility of high-throughput compound screening using PDIOs and we show the potential of repurposing drugs for pwCF that are currently not eligible for therapies.

Redefining Hypo- and Hyper-Responding Phenotypes of CFTR Mutants for Understanding and Therapy

“…To determine why certain CFTR mutants lack a functional response to modulators, we first identified whether mutant CFTR had reached the cell surface. We focused on CFTR mutations located in different domains of CFTR (A46D, G85E, R560S, G628R, and L1335P; Figure 1 A) that are hypo-responsive to VX-809 and VX-770 in patient intestinal organoids [ 22 ], (see also Section 4 , Figure S1 ). To eliminate the effects of genetic background, we used a laboratory cell line for this study.…”

“…The conformations of G461R, G1249R, and S1251N were close to that of wild-type CFTR at early and late chase times, suggesting that the molecular defects were not causing large conformational changes in the protein. Yet, all three mutants have a functional defect [ 22 , 44 , 45 , 46 ], with impaired chloride ion conductance, implying at least subtle conformational defects. Only S1251N has been classified as class 3 [ 44 ].…”

“…The class-2 hypo-responder mutations A46D, G85E, and R560S have ≤1% residual CFTR function, and the mixed-class mutation L1335P ~2% [ 51 , 55 ]. The hyper-responder mutations either belonged to class-2 mutations with minimal function (F508del, L206W, and I336K), or class-3/4 mutations with defective channel gating or ion conductance (G461R [ 22 ], G1249R [ 46 ], and S1251N [ 44 ]). L206W and I336K have ~7% residual CFTR function [ 51 , 52 , 55 ].…”

Redefining hypo- and hyper-responding phenotypes of CFTR mutants for understanding and therapy

“…Class-2 hypo-responder mutations A46D, G85E, and R560S have ≤1% residual CFTR function, and class-4 mutation L1335P ∼2% (47, 53). The hyper-responder mutations either belonged to class-2 mutations with minimal function (F508del, L206W, and I336K), or class-3/4 mutations with defective channel gating or ion conductance (G461R (22), G1249R (54), and S1251N (54)). L206W and I336K have ∼7% residual CFTR function (47, 48, 53).…”

“…To determine why certain CFTR mutants lack a functional response to modulators, we first identified whether mutant CFTR had reached the cell surface. We focused on CFTR mutations located in different domains of CFTR (A46D, G85E, R560S, G628R, and L1335P; Figure 1A) that are hypo-responsive to VX-809 and VX-770 in patient intestinal organoids (22). To eliminate effects of genetic background we used a laboratory cell line for this study.…”