Choosing a pharmacogenomic strategy for targeted therapy of cystic fibrosis: the story of one patient

Introduction

Until recently, the management of cystic fibrosis (CF) was centered on supportive care, enzyme replacement therapy, and the prevention and treatment of infections. However, the recent advent of CFTR modulator therapies has revolutionized the treatment approach and, consequently, patient clinical outcomes. Targeted therapy for CF is a pathogenetic treatment that acts directly on the defective gene or the faulty CFTR protein, which is the product of this gene, thereby mitigating the cause of the disease rather than combating its consequences. Mutations causing CF are categorized into six classes, with Class II (defective CFTR protein transport) accounting for over two-thirds of all CF patients. The F508del mutation is the most prevalent variant [1].

The use of targeted therapies increases the potential for drug-drug interactions in CF. For instance, the combination drug containing elexacaftor, tezacaftor, and ivacaftor comprises three CFTR modulators and has numerous significant drug interactions. In real-world clinical practice, dose adjustments, avoidance of certain drug combinations, and safety monitoring are often required due to insufficient understanding of theoretical interactions, their clinical significance, and treatment efficacy assessment. The study of pharmacokinetic and pharmacodynamic interactions involving components of targeted therapies reveals a scarcity of existing data and a substantial need for research aimed at characterizing the probability, magnitude, and clinical impact of proposed drug interactions for both individual patients and the population at large [2].

Case Description

A 14-year-old male patient. Data from his neonatal screening for CF are unavailable. At one month of age, the child experienced bilateral polysegmental pneumonia. A sweat test was performed at three months of age, revealing sweat chloride levels of 110 mmol/L, 116 mmol/L, and 121 mmol/L, leading to a diagnosis of Cystic Fibrosis. Until the age of one, he was repeatedly hospitalized for exacerbations of the bronchopulmonary process, weight loss, and electrolyte and metabolic disturbances. Initial molecular genetic testing in 2015 (the first in his Russian region) identified a homozygous F508del mutation in the CFTR gene. In 2021, homozygosity for the F508del mutation in the CFTR gene and the absence of the complex allele c.1399C>T were confirmed at the Academician N.P. Bochkov Medical Genetic Research Center of the Russian Ministry of Health.

In July 2023, significant isolated hypogammaglobulinemia was detected. Exome sequencing performed at the Genetico Center for Genetics and Reproductive Medicine revealed a heterozygous mutation associated with Immunodeficiency Type 75, c.1232C>G (of uncertain clinical significance), and a heterozygous mutation associated with dyskeratosis congenita in the RTEL1 gene, chr20:g.62321656C>G (autosomal recessive type with uncertain clinical significance). A heterozygous increase in the number of repeats in the promoter region of the UGT1A1 gene, genotype 6TA/7TA, was also identified (a normal variant indicating no influence of Gilbert's syndrome on bilirubin metabolism). Based on the 2023 examination findings, including marked hypogammaglobulinemia and altered lymphocyte immunophenotyping, the patient with CF was diagnosed with a concomitant condition: Primary Immunodeficiency (PID), Common Variable Immunodeficiency (CVID). Regular subcutaneous human normal immunoglobulin replacement therapy was initiated.

Intervention and Impact of Targeted Therapy

In September 2023, targeted therapy with ivacaftor + lumacaftor at a daily dose of 800 mg + 500 mg was commenced. After 14 days, an isolated elevation of ALT to 142 U/L (5x the upper limit of normal, ULN) and AST to 141 U/L (5x ULN) was recorded in the absence of clinical symptoms, prompting discontinuation of the targeted therapy. By the 10th day after stopping ivacaftor + lumacaftor, ALT and AST levels decreased to within reference ranges. Due to this adverse drug reaction (ADR), a report was submitted to the Roszdravnadzor AIS with the seriousness criterion "clinically significant event." Therapy was resumed with a one-third reduction of the prescribed dose of ivacaftor + lumacaftor to 250 mg + 400 mg daily under active monitoring.

After 30 days on the reduced dose, ALT and AST levels remained within reference ranges. Subsequently, fluctuations within acceptable limits (not warranting discontinuation) were observed: after 4 months, ALT was 69.8 U/L (2x ULN) and AST was 61 U/L (2x ULN); after 5 months, ALT and AST were within normal limits. Subsequent fluctuations did not exceed 2x ULN.

After 15 months of targeted therapy with ivacaftor + lumacaftor at the reduced dose, clinical efficacy was deemed insufficient: a decrease in sweat electrolyte levels from 128 to 88 mmol/L was recorded, along with modest positive dynamics in weight-height indices (BMI increased from 15 to 16) and stabilization of lung function parameters. However, there was no reduction in the number of days on antibiotic therapy for bronchopulmonary exacerbations, and imaging revealed negative dynamics of polypous pansinusitis.

In April 2024, the targeted therapy was switched to ivacaftor + tezacaftor + elexacaftor at a dose of 150 mg + 100 mg + 200 mg, plus ivacaftor 300 mg daily. Over 6 months of the new regimen, the previously noted fluctuations in ALT and AST (within 2x ULN) persisted. Furthermore, after 2 months, alterations in bilirubin levels and fractions emerged. As shown in Figure 1, a slight two-fold increase in total bilirubin was noted in the third month, predominantly in the indirect fraction, with the direct bilirubin fraction constituting up to 23% of the total.

Further investigation confirmed the heterozygous UGT1A1 promoter genotype 6TA/7TA, described as a normal variant, indicating that Gilbert's syndrome was not contributing to the elevated indirect bilirubin.

After 12 months on ivacaftor + tezacaftor + elexacaftor + ivacaftor, therapy was temporarily halted at the legal representative's request from February 19 to 21, 2025. Unfortunately, during this period and after therapy resumption, a four-fold increase in total bilirubin was observed, driven by a rise in the direct fraction to 45% of the total. This was followed by a two-fold decrease in total bilirubin, with the direct bilirubin level falling from 56.3 µmol/L to 15 µmol/L. Observation and assessment are ongoing. The observed biochemical abnormalities were not accompanied by clinical manifestations.

Fig. 1. Safety monitoring of targeted therapy for cystic fibrosis based on the dynamics of liver biochemical parameters over a period of 15 months in a patient with cystic fibrosis F508del in the CFTR gene, combined with PID CVID, and carrier of CYP3A5 *3/*3 and SLCO1B1 *1/*5.
Notes: * — switch from one brand of targeted therapy (ivacaftor + tezacaftor + elexacaftor 150 mg + 100 mg + 200 mg and ivacaftor 300 mg daily) "Trikafta" to "Trilexa" (after a therapy break); ALT — alanine aminotransferase; GGT — gamma-glutamyltransferase; ALP — alkaline phosphatase; ULN — upper limit of normal.

Indications for Personalization

The necessity for genetic testing of cytochrome P450 gene polymorphisms to determine a personalized dosage and/or regimen for ivacaftor + tezacaftor + elexacaftor + ivacaftor arose from the following data:

1. A history of ADR to ivacaftor + lumacaftor at a daily dose of 800 mg + 500 mg, which resolved upon re-initiation at a one-third reduced dose.

2. Isolated fluctuations in biochemical markers (ALT within 2x ULN) accompanied by changes in total bilirubin and its fractions upon switching to ivacaftor + tezacaftor + elexacaftor + ivacaftor, in the absence of Gilbert's syndrome.

Type of Personalization

DNA was analyzed using the iPLEX Pro PGx panel (Agena Bioscience) in the "VeriDose® Core Panel" modification, which detects the most relevant variants in key genes involved in the metabolism of antimicrobials and commonly used concomitant therapies (ABCB1, APOE, CYP1A2, CYP2B6, CYP2C19, CYP2D6, CYP3A4, CYP3A5, DRD2, F2, F5, GLP1R, MTHFR, OPRM1, PNPLA5, SLCO1B1, SULT4A1, VKORC1).

Patient Results: Pg-s gene ABCB1 (rs1045642) G/G, APOE E2/E3, CYP1A2*1A/*1F, CYP2B6*1/*1, CYP2C19*1/*1, CYP3A4*1/*1, CYP3A5*3/*3, PNPLA5 (rs5764010) C/C, and SLCO1B1*1/*5.
Description: A potentially unfavorable combination for liver metabolism—CYP3A5*3/*3 and SLCO1B1*1/*5—was identified, indicating a need for personalization and monitoring of CF targeted therapy.

Changes Following Personalization

Genetic testing confirmed the hereditary origin of the liver biochemistry deviations in this patient, a carrier of the "problematic" genotype variants CYP3A5*3/*3 and SLCO1B1*1/*5, which are involved in the metabolism of the CFTR modulators ivacaftor, tezacaftor, elexacaftor, and lumacaftor.

The patient was advised to avoid foods and beverages containing grapefruit and green tea.
Concomitant use of the following drugs should be avoided: apalutamide, carbamazepine, enzalutamide, fosphenytoin, mitotane, pentobarbital, phenobarbital, phenytoin, primidone, rifampicin, St. John's wort, bexarotene, bosentan, dexamethasone, efavirenz, etravirine, rifabutin.

If concomitant use with the following drugs is necessary (atazanavir, clarithromycin, idelalisib, indinavir, itraconazole, ketoconazole, nelfinavir, posaconazole, ritonavir, saquinavir, telithromycin, voriconazole, aprepitant, ceritinib, crizotinib, cyclosporine, diltiazem, erythromycin, fluconazole, fluvoxamine, imatinib, netupitant-palonosetron, tucatinib, verapamil), a dose reduction of the targeted therapy will be required, necessitating consultation with the treating physician for regimen adjustment.

Increased concentration/efficacy of CFTR modulators is expected when co-administered with amiodarone, azithromycin, carvedilol, ciprofloxacin, dipyridamole, doxazosin, felodipine, gemfibrozil, grapefruit, propafenone, propranolol, quinidine, atorvastatin, cannabis, celecoxib, dabigatran, diclofenac, digoxin, docetaxel, enalapril, everolimus, fexofenadine, fluvastatin, glimepiride, glipizide, glyburide, lesinurad, meloxicam, midazolam, paclitaxel, pravastatin, repaglinide, rosuvastatin, simvastatin, sirolimus, tacrolimus, valsartan, warfarin. This requires monitoring by the treating physician and a clinical pharmacologist for potential regimen correction.

Conclusion

The CFTR modulators ivacaftor, tezacaftor, and elexacaftor are susceptible to drug-drug interactions mediated by cytochrome P450 enzymes and transporter proteins. All three modulators are substrates of CYP3A, with ivacaftor being a sensitive substrate. This means their metabolism and subsequent serum concentrations (particularly of ivacaftor) are altered by concomitant use of other drugs that inhibit (e.g., itraconazole) or induce (e.g., rifampin) CYP3A enzyme activity. While tezacaftor and elexacaftor have a low potential to induce or inhibit the metabolism of other drugs via CYP enzymes, ivacaftor can also inhibit CYP2C9 metabolism, for which warfarin is a common substrate.

Tezacaftor is a substrate for the transporter proteins OATP1B1 and P-gp. OATP1B1, located on the sinusoidal membrane of hepatocytes, facilitates the uptake of drugs (in this case, tezacaftor) into hepatocytes for metabolism [3]. Inhibition of OATP1B1 increases serum tezacaftor concentrations, while induction decreases them. P-gp, an efflux transporter on the luminal membrane of enterocytes, promotes drug secretion into the intestinal lumen, thereby limiting the bioavailability of orally administered drugs (e.g., tezacaftor) [3]. Both tezacaftor and ivacaftor are weak inhibitors of P-gp, potentially increasing the bioavailability of its sensitive substrates. Elexacaftor is known to inhibit both OATP1B1 and OATP1B3. OATP1B3, like OATP1B1, is a transporter that facilitates the movement of substances from the blood into hepatocytes [3]. Inhibition of these transporters by elexacaftor increases serum concentrations of substrates by reducing their availability for hepatic metabolism.

Previous research has demonstrated the impact of the homozygous CYP3A5*3/*3 polymorphism on reducing the liver's capacity for the oxidative metabolism of xenobiotics in oncology patients. For instance, children with neuroblastoma who were homozygous for CYP3A5*3/*3 had a 4.3-fold increased risk of death compared to heterozygous or wild-type carriers, suggesting serious limitations in drug inactivation as a cause of increased adverse outcome risks [4].

It has also been shown that children heterozygous for the SLCO1B1*1/*5 genotype have alterations in the OATP1B1 protein structure, which mediates the uptake and excretion of conjugated bilirubin across the hepatic sinusoidal membranes into bile, potentially influencing the development of liver dysfunction [5]. Furthermore, an increased likelihood of liver function impairment has been described with the combination of CYP3A5*3/*3 and SLCO1B1*1/*5 genotypes, associated with antiretroviral drugs in HIV-infected patients [6].

Contemporary pharmacogenetic testing capabilities identified a potentially "problematic" genotype combination (CYP3A5*3/*3 and SLCO1B1*1/*5) in this patient, associated with altered drug metabolism in the liver. Therefore, the use of pharmacogenetic testing in patients with genetic diseases opens prospects for therapy personalization and enhanced pharmacotherapy safety, potentially preventing or delaying organ dysfunction to improve quality of life and tolerance to regular medication.