Preclinical Studies of a Rare CF-Causing Mutation in the Second Nucleotide Binding Domain (c.3700A>G) Show Robust Functional Rescue in Primary Nasal Cultures by Novel CFTR Modulators

Abstract

The combination therapies ORKAMBITM and TRIKAFTATM are approved for people who have the F508del mutation on at least one allele. In this study we examine the effects of potentiator and corrector combinations on the rare mutation c.3700A>G. This mutation produces a cryptic splice site that deletes six amino acids in NBD2 (I1234-R1239del). Like F508del it causes protein misprocessing and reduced chloride channel function. We show that a novel cystic fibrosis transmembrane conductance regulator CFTR modulator triple combination (AC1, corrector, AC2-2, co-potentiator and AP2, potentiator), rescued I1234-R1239del-CFTR activity to WT-CFTR level in HEK293 cells. Moreover, we show that although the response to ORKAMBI was modest in nasal epithelial cells from two individuals homozygous for I1234-R1239del-CFTR, a substantial functional rescue was achieved with the novel triple combination. Interestingly, while both the novel CFTR triple combination and TRIKAFTATM treatment showed functional rescue in gene-edited I1234-R1239del-CFTR-expressing HBE cells and in nasal cells from two CF patients heterozygous for I1234-R1239del/W1282X, nasal cells homozygous for I1234-R1239del-CFTR showed no significant response to the TRIKAFTATM combination. These data suggest a potential benefit of CFTR modulators on the functional rescue of I1234-R1239del -CFTR, which arises from the rare CF-causing mutation c.3700A>G, and highlight that patient tissues are crucial to our full understanding of functional rescue in rare CFTR mutations.

Personalized Medicine Based on Nasal Epithelial Cells: Comparative Studies with Rectal Biopsies and Intestinal Organoids

“…This finding highlights that both cellular models can be used to predict the clinical benefit of a single drug or combination of drugs for a certain individual, despite the fact that CFTR function in pHNEs was measured by an Ussing chamber, whereas in intestinal organoids, it was indirectly measured by organoid swelling. Several groups already use either of these two models to predict responses to CFTR modulator drugs [ 16 , 17 , 18 , 20 , 39 , 40 , 46 , 47 , 48 , 49 ], but here, we show that the establishment of a responder or non-responder was the same in both models ( Figure 3 ), using both types of samples from the same individual. The only exception was the individual with the D614G/F508del genotype who was considered a non-responder through pHNE analysis but appeared as a responder from intestinal organoid data.…”

“…Our results show a significant and high correlation (95%) between CFTR basal function measured in pHNEs and rectal biopsies ( Figure 2 ). This was somewhat expected since measurements of CFTR-mediated Cl − secretion in both pHNEs and rectal biopsies have already been published by several independent groups and show good correlations with clinical data [ 16 , 20 , 31 , 33 , 40 ]. Additionally, CFTR activation in these two models has some practical similarities since CFTR is activated by the same concentration of Fsk and IBMX (2 µM and 100 µM, respectively) and CFTR activity is measured by the same electrophysiological technique, i.e., in the Ussing chamber.…”

“…As highly effective CFTR modulator therapies (HEMT) emerge, there is an unmet need to find effective drugs for individuals with CF with ultra-rare mutations, for whom there are no dedicated drug discovery programs [ 3 , 40 , 41 , 42 , 43 , 44 ]. Therefore, the development of techniques and models that reliably predict the clinical benefit from CFTR modulator therapies are required for these individuals through personalized approaches termed theranostics [ 41 ].…”

Phenotyping Rare CFTR Mutations Reveal Functional Expression Defects Restored by TRIKAFTATM

“…On the other hand, the clinical response size is highly variable even in patients homozygous for F508del [ 7 ]. Therefore, we and others are examining the utility of modulator testing on patient-derived nasal cultures or rectal organoids to predict clinical response size [ 18 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ].…”

Potential of Intestinal Current Measurement for Personalized Treatment of Patients with Cystic Fibrosis

“…However, in addition to ICM, rectal biopsies can also be used to generate patient-derived intestinal organoids as a versatile model system for preclinical testing of investigational compounds targeting rare CFTR mutations that are not eligible for treatment with an approved CFTR modulator [ 59 , 60 ]. In addition, nasal or bronchial epithelial cells collected by brushings can be expanded and differentiated under air-liquid interface conditions to enable testing of multiple drug candidates in primary airway epithelial cultures derived from individual patients harboring specific CFTR mutations [ 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 ]. Several preclinical studies in these patient-derived model systems showed that the triple combination of elexacaftor–tezacaftor–ivacaftor, as well as several novel modulator combinations improve CFTR function in class II mutations other than F508del , as well as other rare CFTR mutations [ 68 , 69 , 70 , 71 , 72 , 73 , 74 ].…”