Health Characteristics of Patients with Cystic Fibrosis whose Genotype Includes a Variant of the Nucleotide Sequence c.3140-16T>A and Functional Analysis of this Variant

Abstract

Cystic fibrosis (CF) is the most common monogenic autosomal recessive disease, associated with pathogenic variants in the CFTR gene. The splicing variant c.3140-16T>A (3272-16T>A) has been described previously and, according to the Russian CF Patients Registry, occurs with a frequency of 0.34%. The phenotypic features of CF patients with the c.3140-16T>A variant were compared with those of patients with the genotype F508del/F508del. Patients with the allele c.3140-16T>A had higher average age and age at diagnosis, and the allele was present in a greater proportion of adults. Patients carrying the c.3140-16T>A allele were characterised by better physical development indicators, both in adults and in children, had preserved pancreatic function, as well as the absence of a number of complications, and required pancreatic enzyme replacement therapy less often than patients with the F508del/F508del genotype. Sweat test values also were lower in patients with the c.3140-16T>A genotype. According to the results of clinical and laboratory studies, the phenotype of patients with the genetic variant c.3140-16T>A can be considered “mild”. Functional CFTR protein activity in the presence of c.3140-16T>A was evaluated using intestinal current measurements (ICM) and the forskolin-induced swelling assay on organoids obtained from patients’ rectal biopsies. c.3140-16T>A had high residual CFTR channel activity and was amenable to effective pharmacological correction with thea VX-770 potentiator. To evaluate the effect of the variant on CFTR pre-mRNA splicing we performed a minigene assay, as well as RT-PCR analysis of RNA isolated from the nasal epithelium and rectal biopsy of patients. We showed that the c.3140-16T>A variant creates a novel acceptor AG dinucleotide within CFTR intron 19, resulting in a 14-nucleotide extension of exon 20. This frameshift produces a premature termination codon and triggers mRNA degradation by the nonsense-mediated decay (NMD) mechanism. Moreover, we observed that the c.3140-16T>A allele could produce a residual amount of normally spliced transcript, thus explaining the patient’s mild phenotype.

Clinical and Functional Characteristics of the E92K CFTR Gene Variant in the Russian and Turkish Population of People with Cystic Fibrosis

“…Patients according to their genotype were divided into groups: Group 1—E92K/E92K, Group 2—E92K/I class, Group 3—E92K/F508del, and Group 4—E92K/IV-V class. Comparison Group 5, according to European recommendations [ 18 ] included three patients with the F508del/F508del genotype, and healthy with the CFTR ( wt / wt ) functional channel in Group 6.…”

Evaluation of the Complex p.[Leu467Phe;Phe508del] CFTR Allele in the Intestinal Organoids Model: Implications for Therapy

“…The methods of obtaining stable cultures of intestinal organoids and the FIS assay were previously described in detail in studies by E. Kondratyeva (2020) and E. Kondratyeva (2021) [ 35 , 36 ]. The methods was based on protocols developed by J. M. Beekman’s guidance [ 20 , 37 , 38 ].…”

Improving Outcomes for Patients With Sickle Cell Disease in the United States

“…10 The Cystic Fibrosis Foundation Patient Registry (CFFPR) has allowed for robust quality improvement, including care guidelines with recommended nutrition and antibiotics, as well as disease-modifying therapies for the pulmonary and gastrointestinal complications of the disease. 45,46 The target population for the CFFPR is everyone with cystic fibrosis in the US; however, the registry is estimated to account for only 81% to 84% of the population of individuals with cystic fibrosis. 10 The discrepancy is because of inherent exclusion of patients not seen at least annually by an accredited cystic fibrosis care center and patients who do not consent to data collection.…”

“…The cystic fibrosis registry, which has been in place since 1986, provides detailed demographic information individuals living with cystic fibrosis to patients, clinicians, and researchers . The Cystic Fibrosis Foundation Patient Registry (CFFPR) has allowed for robust quality improvement, including care guidelines with recommended nutrition and antibiotics, as well as disease- modifying therapies for the pulmonary and gastrointestinal complications of the disease . The target population for the CFFPR is everyone with cystic fibrosis in the US; however, the registry is estimated to account for only 81% to 84% of the population of individuals with cystic fibrosis .…”