Introduction
Cystic fibrosis (CF) is the most frequent and severe rare genetic disease in Caucasian population, with a recessive modality of inheritance and an incidence observed in 1/2000–3000 newborns [
1‐
3].
More than 2000 variants of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene have been described (2114 variants, based on the CFTR1 database
http://www.genet.sickkids.on.ca/, last accessed on July 2023). Their combined inheritance gives rise to genotypes with different courses and severities of symptoms in various affected organs (
https://cftr2.org/) [
1,
2,
4‐
8].
CFTR is a transmembrane protein channel that is expressed in most epithelial tissues, regulating ion exchange [
9]. In particular, it is responsible for chloride, bicarbonate, and water efflux in the epithelia, preventing sodium-channel-driven water reabsorption, thus balancing water exchange and preserving tissue hydration and mucus fluidity and function. CFTR role is particularly relevant in respiratory, digestive and reproductive tracts, where mutated CFTR results in diseased tissues, with the most severe and life-threatening pathogenic effects occurring in the respiratory system. In fact, in the lungs of CF patients, the thick and dense mucus leads to infections, chronic inflammation, severe tissue damage, and finally, respiratory failure [
1,
2].
The most frequent pathogenic CF genotypes have been investigated and are well characterized, with effective treatments consequently made available for the corresponding patients [
10]. Therapies that are clinically approved to rescue the CFTR function comprise modulators that are used as single agents or in combinations [
11]. The potentiator Ivacaftor/VX770 has been used as a single drug (Kalydeko™) or associated with correctors Lumacaftor/VX608 (Orkambi™) or Tezacaftor/VX661 (Symdeko™) and resulted in acceptable efficacy in specific genotypes for which the drug has indications. The triple combination Trikafta™, consisting of the two Tezacaftor and Elexacaftor/VX445 correctors in addition to the Ivacaftor potentiator, was approved in 2019 by FDA and in 2020 by the European Medicines Agency (EMA)with the name Kaftrio. This drug combination proved effective in specific patient categories, resulting in unprecedented experimental and clinical success and remarkable benefit for patients’ quality of life [
12‐
15]. Currently, Trikafta™ is authorized for the treatment of homozygous F508del/F508del patients and all compound heterozygous patients carrying F508del and any other mutation on the second allele (F508del/any), representing 70–90% of the CF population according to specific geographic distribution.
On the contrary, rare variant patients remain excluded from approved modulator treatments to date [
16,
17]. Most rare mutations still have unknown impact in terms of disease symptoms and severity and underlying molecular/cellular defects (
https://www.cftr2.org). Nevertheless, due to the rarity of the specific genetic conditions, no evidence could be produced by clinical trials to support the use of Trikafta™ in the majority of rare genotypes lacking the F508del allele.
Preclinical experimentation could contribute to an increase in the functional characterization of CFTR variants and obtain information on their pharmacologic responses relative to currently approved or innovative compounds [
18‐
21]. In this context, most in vitro systems for drug testing used so far are either inefficiently obtained (primary bronchial cells) or not based on patient cells (CFTR variant overexpression on commercial cell lines) [
22]. Thus, more efficient and patient-specific in vitro approaches are required for the research of rare variants, considering the limited number of these patients and the paucity of their samples [
21].
We, and others, have implemented an innovative approach in recent years, based on the conditional reprogramming of respiratory cells, to expand pulmonary and nasal airway stem cells in vitro [
23‐
25]
. This approach generates airway epithelial stem cells from the nasal epithelia of CF patients, exhibited an unprecedented efficiency with respect to the culture establishment (100%) and remarkable cell yields (> 5 × 10
8 cell range starting from approximately 5 × 10
4 cells). These cells have proved to be capable of differentiation under appropriate conditions, generating patient-like tissues and reproducing disease models with patient-specific properties, genotypes, and pathogenic defects [
24]. These models, being obtainable virtually from each patient, were highly valuable for the assessment of drug response (theratyping) in both frequent and rare genotypes, with great implication for personalized CF therapy [
24].
The L1077P (HGVS name: p.Leu1077Pro) CFTR pathogenic variant was first identified in 1994 as a transition T to C detected at nucleotide position 3362 in exon 17b of CFTR (HGVS name: c.3230T > C, exon 20). The transition causes a change from leucine (CTG) to proline (CCG) at position 1077 of the protein [
26]. This CFTR variant is relatively frequent in CF patients from specific areas, including Italy [
26‐
29]. It was first detected in a pancreatic sufficient CF patient with F508del on the other allele [
26]. In a second study, L1077P mutants were described to cause severe disease when combined with another CF-causing mutant [
30]. In our case series, it was present in 11 CF patients with pancreatic insufficiency (1 L1077P homozygote and 10 compound heterozygotes) [
28]. In the CFTR2 database (
https://cftr2.org/, last accessed July 2023), L1077P is reported as a CF-causing variant (85% of patients with pancreatic insufficiency) based on information about 93 CF patients worldwide. Further investigation is needed to better elucidate its clinical aspects, pathogenic molecular defects, and therapeutic response. The little information available, obtained in overexpression studies of the mutant L1077P variant in cell lines, shows the possibility of rescuing mutated CFTR membrane localization and function using experimental correctors that mitigate the interactions with proteostasis-involved proteins, preventing protein retention and degradation by proteasomes [
30]. However, drug-induced CFTR rescue was not remarkable in these studies. Thus, further effort is still needed to obtain data to foster biochemical and functional characterization of this mutation, identify innovative and more effective therapeutics, or determine the therapeutic response to drugs that are already approved for other variants.
Here, we characterized the L1077P pathogenic variant in highly suitable personalized experimental disease models based on CF patients' nasal epithelia-derived airway stem cells obtained using the conditionally reprogrammed cell (CRC) approach, which was previously optimized [
23,
24]. By using CRC-derived organoids and Air Liquid Interface (ALI) models, we focused on L1077P/L1077P homozygous, L1077P/W1282X and L1077P/R1066C compound heterozygous genotypes, characterizing the CFTR biochemical defects and their residual and pharmacologically rescued function in response to clinically approved CFTR modulators and their combinations, including the triple combination of Trikafta™-comprising drugs: Elexacaftor, Tezacaftor and Ivacaftor (ETI). A comparison with W1282X/W1282W and F508del/F508del homozygous genotypes was also performed. ALI-culture-based CFTR immunoblots and short-circuit current recordings in Ussing Chamber, as well as the Forskolin-induced swelling (FIS) of nasal organoids allowed the obtainment of results that support the implementation of Trikafta™-based personalized therapy for this orphan variant. The innovative methodology of CRC-based CF models proved to be powerful in vitro surrogates for patient clinical trials, and they can be considered as “in vitro clinical trials” or “patient-in-a-dish trials”, which are highly suitable approaches that can guide personalized CF therapies.
Materials and methods
Nasal brushing processing and CRC culture
Human nasal epithelial samples were provided in accordance with the consent procedures approved by the Internal Review Board of Policlinico Umberto I Hospital, Sapienza University of Rome (Ethics committee ref. 5660 prot 983/19 December 18th 2019 and ref. 6841 prot. 98/2023 February 8th 2023). Nasal epithelial cells were obtained via the cytology brushing (Doctor Brush, AIESI) of inferior turbinates from both nostrils; they were pooled into a single 15 ml conical tube filled with DMEM/F12 (Gibco, code 1320033) and 5 × antibiotics (Penicillin/Streptomycin and Amphotericin B). Samples were repeatedly washed, and the recovered cells were cultured using the Conditionally Reprogrammed Cell (CRC) methodology according to our previous protocols [
23,
24]. Briefly, epithelial cells were co‐cultivated with irradiated (30 Gy) murine J2 Swiss 3T3 fibroblasts (Kerafast, Boston, MA, USA, code EF3003) in F medium (3:1 v/v F‐12 Nutrient Mixture Ham (Gibco, code 11765054): DMEM (Gibco, code 31765-027) supplemented with 5% Fetal Bovine Serum (Euroclone, South America, code ECS01180L); 0.4 μg/ml of hydrocortisone (Sigma, code H0888); 5 μg/ml of insulin (Sigma, code 91077C); 24 μg/ml of adenine (Sigma, code A2785); 8.4 ng/ml of cholera toxin (Sigma, code C8052) in the presence of 10 μM Rock inhibitor Y‐27632 (Selleck, Munich, Germany, code S1049); and 10 ng/ml of EGF (Peprotech, code AF100-15). Fibroblasts were cultured in DMEM supplemented with 10% characterized MSC-qualified USDA-approved Fetal Bovine Serum (HyClone™,Gibco, code 12662029) and irradiated when reached 80% confluence. All cells were maintained at 37 °C in a humidified incubator with 5% CO
2.
Differentiation of CRC in air–liquid interface (ALI) culture conditions
To induce differentiation, 1.1 × 105 cells were plated in transwell inserts (Corning, code 3460) and cultured in CRC complete medium in both basal and apical chambers until confluence was reached (5–7 days); afterwards, the medium was replaced with PneumaCult-ALI Medium (Stem Cell Technologies, Cambridge, UK 05001) in the basal chamber, leaving the apical chamber empty for 4–6 weeks with medium replacement every other day. These cultures were used for immunoblotting assays. Alternatively, for their subsequent use in Ussing Chamber assays, smaller-size transwell Corning inserts (Corning, 3470) were used, and 5 × 104 cells were plated for ALI-culture differentiation.
CFTR mutational analysis
Genomic DNA was extracted from the CF-CRC cells using the QIAamp DNA Blood midi kit (Qiagen, Hilden, Germany 51183), and fluorimetric quantification was performed (Qubit, Invitrogen, CA, USA). Proximal 5’-flanking, all exons and adjacent intronic zones, and the 3′-UTR of the CFTR gene (RefSeq NM_000492.4, NG_016465.4) were sequenced using the Sanger cycle sequencing protocol (ThermoFisher Scientific, Waltham, MA, USA), as previously described [
31‐
33] and a genetic analyzer (ABI PRISM 3130
xl; Applied Biosystems, Foster City, CA, USA). Genotype analysis was completed using multiplex ligation-dependent probe amplification (SALSA MLPA probemix P091 CFTR, MRC Holland, Amsterdam, the Netherlands, EKI-FAM, P091-100).
CFTR expression analysis
RNA was extracted from CF-CRC cells using the RNeasy mini kit (Qiagen, Hilden, Germany, 74104). It was reverse transcribed by the iScript cDNA Synthesis kit (Bio-Rad, Hercules, CA, USA, 170–8891). Retrotranscription was performed using 1 μg of total RNA in 5.5 μl, 4 μl of 5 × iScript reaction mix, 1 U of iScript reverse transcriptase in 1 μl, and 9.5 μl of H2O in a final volume of 20 μl, according to the manufacturer’s instructions. The reactions were incubated in a PTC 100 thermocycler (Bio-Rad) according to the following program: 5′ 25 °C, 30′ 42 °C, and 5′ 85 °C.
For qualitative CFTR expression analyses, the amplification of the CFTR cDNA using an RT-PCR procedure was performed according to our protocol [
34]
. Briefly, a PCR mix was prepared in a final volume of 15 µl containing the following: 2.5 µl of cDNA mix, 175 µM of each dNTP (Fermentas, Waltham, MA, USA, FL-50R0181), 1.5 mM of MgCl
2, 6 pmol of each primer, and 0.5 U GoTaq hot start polymerase with 1× manufacturer’s buffer (Promega, Madison, Wisconsin, USA, M5006). A PTC100 thermocycler (Bio-Rad, Hercules, CA, USA) was used with the following PCR cycle: 2′ 95 °C; 35 cycles of 45″ 94 °C, 1′ 30″ 60 °C, 2′ 30″ 72 °C, followed by 7′ 72 °C. The amplicons were subsequently analyzed using electrophoresis on a 3% agarose gel. The cDNA amplicons of interest were extracted from agarose and individually sequenced as described above.
For quantitative CFTR expression analysis, droplet digital PCR (ddPCR) was performed starting from the cDNA mix described above, and a TaqMan gene expression assay (code 4331182, ID Hs00357011_m1; ThermoFisher Scientific, Waltham, MA, USA) with a dye-labeled TaqMan probe FAM, according to the manufacturer’s instructions. The aqueous final reaction volume was 20 μL using 1 μL of cDNA mix, 10 μl of 2 × ddPCR Supermix for probes (no dUTP) (Bio-Rad, Hercules, CA, USA, 1863024), 1 μl of specific TaqMan probe assay, and 8 μl of H2O. According to manufacturer instructions, 70 μl of droplet generation oil for probes was added. The water-in-oil droplet emulsion was prepared using a QX200 Droplet Generator (Bio-Rad). The amplification step was performed using 40 μl of emulsion in a C1000 thermal cycler (Bio-Rad) using the following protocol: 10′ 95 °C; 45 cycles of 30″ 94 °C, 1′ 60 °C, followed by 10′ 98 °C. The ddPCR reactions were analyzed using the QX200 Droplet Reader and QuantaSoft software version 1.7.4 (both from Bio-Rad).
Immunoblot and analysis of pharmacologic rescue of mature CFTR protein
For immunoblotting studies, 20 μg of total lysate proteins from each sample were resolved on 3–8% polyacrylamide gel electrophoresis NuPAGE Tris–Acetate (Invitrogen, Carlsbad, CA, USA, EA03752BOX) and transferred to nitrocellulose membranes (GGE Healthcare Life Science, AmershamTM ProtranTM, 10600018). The following primary antibodies were used: mouse monoclonal CFTR-596 (CFTR Antibody Distribution Program Cystic Fibrosis Foundation, UNC-Chapel Hill, dilution 1:2500), mouse monoclonal DM1A alpha Tubulin (Novus Biologicals NB-100–690, dilution 1:1000), and mouse monoclonal β-actin (Sigma-Aldrich A5441, dilution 1:10,000). Peroxidase-conjugated secondary antibodies were purchased from Amersham™ (NA931V, NA934V, dilution 1:4000).
For the evaluation of the ability of drugs to rescue CFTR protein maturation, CF-CRC cells differentiated in ALI cultures for 4–6 weeks were exposed to the following drugs for 48 h: 5 µM of VX809/Lumacaftor (Selleck Chemicals S1565), 10 µM of VX661/Tezacaftor (Selleck Chemicals, S7059), and 3 µM of VX445/Elexacaftor (Selleck Chemicals, S7059) or their combinations before cell lysis and lysates were processed as described above. The quantification of immunoblot band intensity was performed using Image lab software (Chemidoc XRS + , Biorad). To quantify CFTR maturation, the relative amount of the CFTR band-C protein was normalized to actin or tubulin measured in the same protein sample, and these levels were used for subsequent calculations.
CRC-derived organoid generation and forskolin-induced swelling assay
Cells were suspended at 30,000 cells/100 µl in growth-factor-reduced matrigel (Corning 354,230) using vigorous but careful pipetting to generate a single-cell suspension while avoiding the generation of air bubbles. This mixture was seeded in 100 µl aliquots into 24-well plates, creating a spherical “drop” of matrigel. The plates were incubated at 37 °C and 5% CO2 for 30 min to allow the setting of matrigel. CRC medium was added to the wells to cover the matrigel drop. After 5–7 days, cells were shifted in PneumaCult–ALI Medium until mature 3D structure was formed (typically after 21 days, with the presence of a lumen and a slightly thickened spheroid wall, suggesting a pseudostratified epithelium with motile cilia visible under high-magnification microscope), and the medium was replaced every other day. After 21 days, for the FIS assay, organoids were pre-treated with Lumacaftor, Tezacaftor and Elexacaftor or their combinations for 48 h, at the same doses as described above, based on our previous results and in line with therapeutically effective doses. Then, spheroid images were captured (10X magnification) at time 0 (48 h after corrector treatment), using a time-lapse imaging station (Olympus, Tokyo, Japan). Each organoid was monitored, and after 2 days of subsequent stimulation with the same correctors and 5 µM of Ivacaftor VX770 (Selleck Chemicals, code S1144) and 10 µM of Forskolin (Selleck Chemicals, code S2449), new images were taken (indicated as T1 in figures) to monitor and assess spheroid swelling. N = 10 spheroids in each experimental condition for a total of 3 experiments were analyzed. Images were analyzed by manually delineating the outer area of each spheroid using ImageJ software before and after the second treatment in order to avoid potential bias due to organoid size heterogeneity. Spheroid outer area data (basal and after stimulation) were imported into Microsoft Excel, and the fold change was calculated for each individual spheroid with respect to non-treated organoids.
Short circuit currents recordings in Ussing Chamber assay
ALI-culture differentiated cells grown for at least 4 weeks in Corning 3470 insert transwells were left untreated (control) or pre-treated with the correctors Lumacaftor, Tezacaftor, Elexacaftor and the potentiator Ivacaftor for 2 days.Transwell membranes were mounted on a slider (P2302T; 0.33 cm
2 aperture) in an Ussing chamber (P2300, PI). The transepithelial voltage was short-circuited with a voltage clamp (VCC MC8 Multichannel Voltage/Current Clamp, Physiologic Instruments). The offset between voltage electrodes and fluid resistance was cancelled before experiments. Recordings were performed filling both apical and basolateral hemi-chambers with 5 ml of a solution containing the following: 126 mM of NaCl, 0.38 mM of KH
2PO
4, 2.13 mM of K
2HPO
4, 1 mM of MgSO
4, 1 mM of CaCl
2, 24 mM of NaHCO
3, and 10 mM of glucose, with a final pH of 7–7.3. Both sides were continuously bubbled with a gas mixture containing 5% CO
2 and 95% 0
2, and the temperature of the solution was maintained at 37 °C. Subsequently, the ENaC blocker Amiloride (100 µM), the cAMP agonist forskolin (FSK; 10 µM), and at the end of the test, the CFTR inhibitor CFTR 172inh 10 µM were added both to the apical and basolateral sides. The short-circuit current was acquired and analyzed using Acquire & Analyze software Version 2.3.8 (Physiologic Instruments). Raw tracings were processed using GraphPad Prism Version 8.0.0 for Windows as we previously reported [
35]. We calculated the Isc changes (ΔIsc) by taking the difference in the Isc recorded after adding Forskolin or CFTR 172 inh.
Discussion
Trikafta™ is the third drug (after Symdeko™ and Orkambi™) approved by the FDA that rescues defects caused by the most frequent pathogenic variant: F508del. It is a triple combination of the correctors Elexacaftor and Tezacaftor in addition to the potentiator Ivacaftor and is superior to previous treatments. It improved respiratory function (FEV1), decreased exacerbations to a greater extent, and was highly effective also in CF patients who harbor only one copy of this mutation [
42]. Therefore, the majority of CF patients have access to this therapy (representing 70–90% of the cystic fibrosis population according to specific geographic distribution). Nevertheless, the majority of genotypes lacking the F508del allele are ineligible for Trikafta™ or other treatments and currently remain orphans of modulator therapies. Among these rare genotypes, the L1077P CFTR pathogenic variant causes severe disease when combined with another CF-causing variant. Patients with the L1077P variant in their genotype undergo recurrent respiratory infections, chronic bronchial/lung inflammation and pancreatic insufficiency and intestinal problems, requiring oral supplements to help absorb the nutrients and vitamins, as well as oral pancreatic supplements to improve digestion.
Here, we used patient-specific in vitro disease models that we previously developed based on patient-derived nasal epithelial conditionally reprogrammed cells (CRCs): the 3D organoids and the ALI culture models [
24,
24]. Here, we exploited these nasal CRC-derived in vitro models of CF for the characterization of the L1077P CFTR variant and the evaluation of its response to the ETI combination to obtain important inferences for future personalized patient therapy. Firstly, cells derived from two different patients carrying the homozygous L1077P/L1077P genotype and the compound heterozygous L1077P/W1282X genotype have been the object of this study, together with W1282X/W1282X and F508del/F508del genotypes used for comparison.
Biochemical and functional studies demonstrated a strong ability of ETI (and the experimental drug combination Lumacaftor + Elexacaftor + Ivacaftor) to rescue the CFTR L1077P variant in immunoblot, in the FIS assay of organoids, and in short-circuit recordings in Ussing chamber assay in both homozygous and compound heterozygous genotypes. These results, coupled with the observed dramatically reduced W1282X CFTR mRNA (compatible with NMD of PTC RNA, as described by others for this variant), showed that ETI induced a strong rescue of the L1077P variant even when present in single copy, displaying similar behavior with the F508del mutation. Thus, in line with what was already observed for F508del-bearing genotypes, our findings could open the way to the global approval of Trikafta not only for L1077P homozygous genotypes but also for genotypes that carry one copy of the responsive L1077P allele associated with any other variant on the second allele. This is also particularly relevant for genotypes carrying the other CFTR variant that is not correctable or not expressed, as in the case of nonsense mutations, expanding the cohort of patients that are eligible for modulator therapy. Thus, our studies may generate therapeutic opportunities for a reasonable number of patients that are currently not eligible for modulator therapy due to the assessment of a CFTR modulator response in a patient-personalized manner. Nevertheless, if the same theratyping results of ETI response obtained for these specific patients with the L1077P allele are reproduced in cells derived from different patients bearing the same allele, they might acquire increased reliability and be translated to other individuals with the same CF-causing mutation even though their cells are not specifically tested. For instance, patients that are too young or are unwilling or unable, for various reasons, to undergo nasal brushing and drug-testing experiments could benefit from the extrapolation of these results. Thus, we assessed CFTR expression and modulator response in a third genotypebearing L1077P allele, specifically the compound heterozygous L1077P/R1066C genotype (Patient 4 in Table
1). Our results showed the marked ability of ETI to rescue CFTR function in all CRC-based in vitro models, confirming the results obtained for other L1077P-bearing genotypes (Patient 1 and Patient 2) and suggesting that other genotypes that bear the L1077P allele may be responding to the triple drug combination independently of the type of CFTR mutation that is present on the second allele. Functional rescue by the triple combination of L1077P-containing genotypes was comparable to the F508del/F508del genotype rescue both in the FIS of organoids and Ussing chamber assay (Figs.
4B,
5C), further encouraging future Trikafta™ label expansion for the L1077P variant even if present in single-copy form, analogously with its indication for the F508del variant.
We also demonstrated in CRC-derived models with W1282X homozygous genotype, that this variant cannot be rescued by ETI, as a consequence of heavily compromised CFTR protein expression. In this genotype, undetectable levels of truncated protein in the immunoblot are likely to result from two combined mechanisms. The most significant quantitative effect seems to be due to the degradation of the PTC-mutated RNA (Figs.
3,
6D), with the consequence of a significantly reduced availability of mRNA for protein translation. Nevertheless, a reduced amount of PTC-mutated RNA seems to escape degradation, as revealed by a very sensitive ddPCR expression assay (Fig.
6D). However, this reduced quote of W1282X-mutated mRNA appears not to be properly translated/processed or the CFTR protein might be degraded as a consequence of its abnormal conformation in untreated cells. Consequently, the W1282X protein function cannot be rescued by correctors (Fig.
6A–C. These results are in line with the multiple mutational classes proposed for the W1282X variant [
11]. Therefore, the basal and induced amount of CFTR protein present in L1077P/W1282X cells is likely to originate from the translation of the L1077P transcript. Additionally, the transcription of the L1077P allele in this compound heterozygote appears to be enhanced, possibly for the compensation of the compromised missense allele. In fact, by the ddPCR expression assay (Fig.
6D), only a limited reduction in CFTR mRNA is shown in the compound heterozygote with respect to the L1077P homozygote, in line with the limited reduction in protein (Fig.
2B). Importantly, these data indicate that the strong CFTR protein correction observed after treatment with Tezacaftor + Elexacaftor or Lumacaftor + Elexacaftor also in the compound heterozygous genotype is likely to depend on the activity of drugs on the L1077P protein produced by the single allele (Fig.
2).
These results highlight that a single L1077P allele may be sufficient to confer marked and satisfactory response to ETI in patient-derived CF cells. Therefore, the concept of an in vitro guided personalized therapy of non-F508del patients is strengthened and additionally extended to patients with a single targetable non-F508del allele. In addition, our results suggest that besides targeting two non-F508del alleles, the expression modulation of a single non-F508del allele also contributes to functional recovery. In this regard, an intriguing mechanism of single-allele expression enhancement, and consequently more effective therapeutic modulation, could be proposed. Due to its potential impact on the therapy of rare genotypes with only one non-F508del targetable allele, further studies appear mandatory.
Importantly, for the first time, CRC-derived ALI cultures were used in the Ussing chamber assay, extending its valuable predictive use for personalized medicine [
43,
44]. Ussing chamber results confirmed the robust L1077P variant response to ETI, with great implications for therapeutic intervention.
Moreover, the obtainment of comparative results in the Ussing chamber assay and organoid FIS confers further reliability to the FIS assay of CRC-derived nasal organoids as a powerful and highly valuable ex vivo model of CF.
Organoids FIS assay proved to be suitable in providing the predictive indication of patient response to specific drugs, and these are helpful for guiding therapeutic choices for personalized patient therapy. Although all functional tests applied provided a similar indication of drug response, a standardization effort is needed to integrate their quantitative outcome in order to define the overall extent of in vitro response that need to be aligned with the parameters of clinical response.
Theratyping is routinely undertaken in CF care centers across the United States in order to guide patient therapy, while in Europe, CF patient response to modulators assessed in vitro cannot be formally exploited for clinical therapeutic indication. In fact, EMA and the Italian Medicines Agency (AIFA) regulation require patient enrollment in clinical trials for the subsequent label extension approval of modulators relative to specific genotypes. Based on the promising results of the patient-derived cell models described here, the hope is that the FIS assay performed in CRC-derived nasal organoids and assays based on ALI cultures may represent formally recognized in vitro tools for theratyping worldwide in the near future, with the acceptance of in vitro assay results as a valuable guide for the therapeutic management of rare patients.
Indeed, the high efficiency of the CRC-based model approach may satisfy several important needs. The first is that patient-derived models may be generated from any genotype in a personalized manner, allowing any in vitro drug testing in the cultures of a specific patient within his genetic background, known to modulate drug response in patients. Second, patient-specific cultures more faithfully reproduce the proper CFTR variant characteristics in terms of protein defects and expression. For instance, in some classes of mutations, such as nonsense mutations or splicing mutations, CFTR expression is also altered at the mRNA level (mRNA degradation due to NMD in the case of nonsense mutations, lack or very low amounts of wild-type mature mRNA expression in the case of abnormal splicing), affecting the levels of produced CFTR protein. In these contexts, CFTR variant overexpression in commercial cell lines or even in commercially available bronchial primary cells, which are often used, may be not optimal for theratyping and might provide incomplete or even biased results. Another important significant benefit of the CRC-based approach would be the ability to expand and preserve epithelial cells that retain their CF-causing genotype for future expansion and testing as new therapies develop.
Concerning the limits of theratyping approaches, it is worth mentioning that although several interconnected strategies are emerging for nasal cell expansion or for generation of nasal or rectal organoids, a common standardized approach of model generation and CFTR assay execution, shared by all laboratories, is still missing, calling for the need to develop common Standard Operating Procedures (SOPs) [
45‐
47]. In this context, the unification into standard procedures, collecting the strengths of each methodology, might promote the prompt acceptance of in vitro theratyping as a powerful clinical therapeutic tool.
Moreover, the relevance of CFTR and other chloride channels that are expressed in organoid models has been reported and shed further light on their relevance in FIS assays [
45]. Organoid generation has been further optimized to achieve higher CFTR expression and a more homogeneous degree of organoid differentiation [
45]. Further investigation will be necessary to clarify the specific contribution of CFTR and other chloride channels in FIS assays in the models used in this study, although the use of modulators specific for CFTR should bypass this limit.
Another possible limitation of this studies, based on patient-derived models is that they imply the evaluation of the drug response of specific genotypes while not discriminating the contribution of the single pathogenic variants to genotype response.
However, as a point of strength, the theratyping of properly selected genotypes allowed the extrapolation of the contribution of each allele present in the studied genotypes to the modulator response. Of note, the use of patient-derived models is of higher value with respect to the heterotopic expression of variant CFTR cDNA, as in these models the endogenous expression of CFTR is not modified as by the overexpression and remains under the patient genetic background. Additionally, these models more faithfully mimic the patient tissue.
Finally, the comparison of drug response among uncharacterized and control genotypes with known clinical response (i.e., F508del) may provide information on the therapeutic relevance of preclinical findings. What would be useful is a direct comparison of these in vitro data with the clinical response to Kaftrio of the corresponding patients. Hopefully, this study will contribute to hastening the indication extension of Kaftrio by European and Italian regulatory agencies relative to L1077P-bearing patients, and this will in turn allow retrospective studies to assess the correspondence between in vitro drug testing and clinical response.
As a final conclusion, CRC-based models may be valuable tools that can guide personalized therapy, representing a non-invasive, rapid, suitable and valuable surrogate for clinical trials with great benefit for those rare patients who are still excluded from approved modulator therapies and do not have access to clinical studies.