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Letter to the Editor
Open Access
Available online 24 October 2021
Impact of CFTR large deletions and insertions on the clinical and laboratory severity of cystic fibrosis: a serial case report
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L.R. Pereiraa,b,1, T.M. Limaa,b,1, V.F. Melania,b,1, M.F. Mendesa,b,1, S.V. Pereirac, C.S. Bertuzzoc, F.A.L. Marsona,b,c,1,
Corresponding author
fernando.marson@usf.edu.br

Corresponding author at: University of São Francisco; Postgraduate Program in Health Science; Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds and Laboratory of Human and Medical Genetics. Avenida São Francisco de Assis, 218. Jardim São José, Bragança Paulista, São Paulo, Brasil, 12916-900.
a Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, University of São Francisco, Bragança Paulista, São Paulo, Brazil
b Laboratory of Human and Medical Genetics, University of São Francisco, Bragança Paulista, São Paulo, Brazil
c Laboratory of Human and Medical Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
Received 26 July 2021. Accepted 25 September 2021
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Table 1. Description of genotype, race, and diagnostic tests results in cystic fibrosis patients in the presence of CFTR large deletions or insertions.
Table 2. Comorbidities, Shwachman-Kulczycki score and medications in cystic fibrosis patients in the presence of CFTR large deletions or insertions.
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Dear editor,

Cystic fibrosis (CF OMIM: #219700) is an autosomal recessive disorder caused by pathogenic variants in the CFTR (Cystic Fibrosis Transmembrane Conductance Regulator).1 Among the 2,106 variants described in CFTR, large deletions or insertions are considered rare [59 (2.80%)].2 The identification of large alterations in the CFTR is challenging and might result in wrong diagnosis, indicating false-negative in carriers of rare variants that are potentially severe.3,4 Thus, the implementation of additional techniques in the CF diagnosis workflow becomes necessary, which includes the use of Multiplex Ligation Probe Amplification (MLPA) to identify chromosome rearrangements, deletions, and insertions.3 So we aimed to describe the genetic profile of large deletions or insertions in CFTR identified using MLPA and to describe its influence on CF patients’ phenotype in a referral center.

Five CF patients (chloride over 60 mEq/L in two sweat tests) presenting at least one pathogenic variant in the CFTR characterized as a large deletion or insertion were included after the study approval by the Ethics Committee (#78192216.2.0000.5404). The caregivers of the CF patients who participated in our study signed the consent to publish patients’ data. The screening of the pathogenic variants in the CFTR was carried out as previously desbribed.5 The following markers were described: patients’ age at diagnosis; ethnic group; spirometry, classified according to the forced expiratory volume (FEV1) at different levels of obstruction: mild (≥70%), moderate (60-69%), moderately severe (50-59%), severe (35-49%), and very severe (<35%); Shwachman-Kulczycki score graded as excellent (86-100), good (71-85), mild (56-70), moderate (41-55), and severe (≤40)6; immunoreactive trypsinogen; and sweat test results. The microbiological evaluation was carried out for the colonization by 11 microorganisms. In addition, the comorbidities and medication used by the patients were described.

All the patients had one identified variant, c.1521_1523delCTT (F508del; p.Phe508del). The MLPA technique also identified four variants considered large deletions or insertions, namely, CFTRdele7-18, CFTRdup6b-16, CFTRdele14b+CFTRdup9, and CFTRdele16-20. The variant CFTRdele16-20 was identified in two patients. The CFTR genotype, race, and diagnostic tests were described (Table 1), as well as the comorbidities, Shwachman-Kulczycki score, microorganism profile, and medication used by the patients (Table 2).

Table 1.

Description of genotype, race, and diagnostic tests results in cystic fibrosis patients in the presence of CFTR large deletions or insertions.

Marker    BSD  JDQS  EVFM  JVQS  ECM 
CFTR GenotypeAllele 1  F508del  F508del  F508del  F508del  F508del 
Allele 2  CFTRdele7-18  CFTRdele16-20  CFTRdup6b-16  CFTRdele16-20  CFTRdele14b and CFTRdup9 
Race    Caucasian  Caucasian  Caucasian  Mixed race  Caucasian 
IRT (ng/mL)*    204/131  86/138  262/354  159/147  260/410 
Sweat chloride ion (mEq/L)*    89/92  95/92  95/90  110/106  116/128 

F508del; p.Phe508del = c.1521_1523delCTT; IRT: immunoreactive trypsinogen; CFTR: Cystic Fibrosis Transmembrane Regulator.

, first and second dosages were demonstrated.

Table 2.

Comorbidities, Shwachman-Kulczycki score and medications in cystic fibrosis patients in the presence of CFTR large deletions or insertions.

Marker  BSD  JDQS  EVFM  JVQS  ECM 
Comorbidities           
Nasal polyposis  Yes  No  No  No  No 
Meconium ileus  No  No  No  No  Yes 
Pancreatic insufficiency  Yes  Yes  Yes  Yes  Yes 
Liver involvement  No  No  Yes  No  Yes 
Growth deficit  No  Yes  No  Yes  Yes 
Persistent respiratory symptom  No  No  No  No  Yes 
Metabolic disorder  No  No  Yes  No  No 
Shwachman-Kulczycki score (age, months)  54  18  71  104  138 
General activity  20  25  25  20  25 
Physical examination  20  25  25  20  25 
Nutrition  25  25  20  15  25 
Thorax X-ray  10  20  20  20  25 
Total score  75  95  90  75  25 
Score classification  Good  Excellent  Excellent  Good  Excellent 
Bacteria           
Pseudomonas aeruginosa  Yes  Yes  Yes  Yes  Yes 
mucoid Pseudomonas aeruginosa  No  Yes  No  No  No 
Staphylococcus aureus  Yes  Yes  Yes  Yes  Yes 
Streptococcus pneumoniae  No  Yes  No  No  No 
Stenotrophomonas maltophilia  No  Yes  No  No  Yes 
Haemophilus influenzae  No  No  Yes  Yes  No 
Klebsiella pneumoniae  No  No  Yes  No  No 
Escherichia coli  No  No  Yes  No  No 
Moraxella catarrhalis  No  No  No  Yes  Yes 
Acinetobacter baumannii  No  No  No  No  Yes 
Burkholderia cepacia complex  No  No  No  No  No 
Bronchodilator           
Short-acting β2-agonist  No  No  No  Yes  Yes 
Long-acting β2-agonist  Yes  No  No  Yes  Yes 
Anticholinergic  Yes  Yes  No  No  No 
Inhaled corticosteroid  No  No  No  No  Yes 
Inhaled antibiotic           
Colomycin  No  No  Yes  No  Yes 
Tobramycin  Yes  Yes  Yes  Yes  Yes 
Mucolytic           
Dornase alfa  Yes  Yes  Yes  Yes  Yes 
N-Acetylcysteine  Yes  No  No  No  No 
Saline solutions           
0.9%  Yes  No  No  Yes  Yes 
3%  Yes  No  No  Yes  No 
Oral medication           
Azithromycin  No  Yes  Yes  Yes  Yes 
Ibuprofen  No  No  No  Yes  No 
Corticosteroid  No  No  No  No  Yes 
Proton pump inhibitors  No  No  Yes  No  No 
H2 Blockers  Yes  Yes  Yes  No  No 
Ursodeoxycholic acid  Yes  No  No  No  Yes 
Pancreatic enzymes  Yes  Yes  Yes  Yes  Yes 
Nutritional supplement  Yes  Yes  Yes  Yes  Yes 
P. aeruginosa eradication treatment  Yes  Yes  No  Yes  No 

In our cohort, four patients were self-declared Caucasians, and one was of mixed race; four of them were female. Two patients were diagnosed when they were five months old; two were two months old; and one was one month old. The Shwachman-Kulczycki score varied distinctly for each participant. All participants were colonized by Pseudomonas aeruginosa and Staphylococcus aureus, while unequal colonization by other microorganisms was observed in the patients. All participants used inhaled antibiotics, mucolytic agents, nutritional supplements, and pancreatic enzymes; four patients used bronchodilator and one used inhaled corticosteroid. In addition, all patients in our study cohort had pancreatic insufficiency (Table 2).

Since the CFTR pathogenic variants present different effects on the phenotype, it seems relevant to optimize the detection method to avoid inaccurate and/or delayed diagnosis.7,8 In such contexts, the MLPA technique implementation in the CF diagnosis should be optimized.7 For instance, Atag et al. (2019) evaluated 250 CF patients that presented 80 genetic distinct variants in the CFTR and, out of those, five (CFTRdele2, CFTRdele4-11, CFTRdele5-10, CFTRdele12, and CFTRdele19-21) were characterized as large deletions and occurred in 16 CF patients. Large deletions were associated to the worst pulmonary phenotype, pancreatic insufficiency and liver involvement.8 The same findings were reported by Martins et al. (2019) who reported the presence of a severe phenotype with pancreatic insufficiency and infection by P. aeruginosa9 in five patients with large deletions or insertions in the CFTR.

The identification of all types of CFTR variants, including large deletions and insertions, should be one of the main points to be considered in the patients’ differential diagnosis.4 For example, in a study carried out in Serbia, twenty-two different CFTR variants were identified in the population studied, evidence of high heterogeneity. Most of these variants had not been reported in neighboring countries, possibly due to the use of commercial tests for CF diagnosis in those places, which did not include the MLPA technique. Due to the use of different molecular analysis techniques, an increase from 54.45% to 72.8% was observed in the effectiveness rate to identify the CFTR genotype.10

The description of clinical manifestations along with the identification of large deletions or insertions in the CFTR pointed out a more severe phenotype of these patients in our serial case report. And, although younger patients do not present some symptoms, there is still great potential for developing them in the future. Currently, there is no corrective therapy for CFTR large deletions or insertions, due to the difficulties of modulating the impact of these large deletions and insertions in the gene expression mechanisms.11

In conclusion, our study identified four genetic variants of the type CFTR large deletions and insertions, which were characterized by their low genotypic and diagnostic frequency. Two participants presented the same variant, while the variants identified in the other three participants were unique. The identification of large deletions and insertions through a broader genetic analysis is very important for CF diagnosis, since those variants, despite being rare, might be associated with the disease higher severity phenotypes.

Author contribution

All authors approved the manuscript and agreed with its submission to the journal. Also, all authors wrote and revised the manuscript.

Acknowledgments

The pediatrics outpatient service of the University Hospital for collaborating with the data collection.

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The authors contributed equally to this study.

Copyright © 2021. Sociedade Portuguesa de Pneumologia
Pulmonology

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