1
|
Bene Z, Fejes Z, Macek M, Amaral MD, Balogh I, Nagy B. Laboratory biomarkers for lung disease severity and progression in cystic fibrosis. Clin Chim Acta 2020; 508:277-286. [PMID: 32428503 DOI: 10.1016/j.cca.2020.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 04/20/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022]
Abstract
Although the clinical outcomes of cystic fibrosis (CF) have been markedly improved through the recent implementation of novel CF transmembrane conductance regulator (CFTR) modulator drugs, robust and reliable biomarkers are still demanded for the early detection of CF lung disease progression, monitoring treatment efficacy and predicting life-threatening clinical complications. Thus, there is an unmet need to identify and validate novel, ideally blood based biomarkers with strong correlations to the severity of CF lung disease, which represents a major contribution to overall CF morbidity and mortality. In this review, we aim to summarize the utility of thus far studied blood-, sputum- and bronchoalveolar lavage (BAL)-based biomarkers to evaluate inflammatory conditions in the lung and to follow treatment efficacy in CF. Measurements of sweat chloride concentrations and the spirometric parameter FEV1 are currently utilized to monitor CFTR function and the effect of various CF therapies. Nonetheless, both have inherent pitfalls and limitations, thus routinely analyzed biomarkers in blood, sputum or BAL samples are required as surrogates for lung disorders. Recent discovery of new protein (e.g. HE4) and RNA-based biomarkers, such as microRNAs may offer a higher efficacy, which in aggregate may be valuable to evaluate disease prognosis and to substantiate CF drug efficacy.
Collapse
Affiliation(s)
- Zsolt Bene
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Department of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Fejes
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Milan Macek
- Department of Biology and Medical Genetics, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - István Balogh
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Béla Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| |
Collapse
|
2
|
Ivády G, Madar L, Dzsudzsák E, Koczok K, Kappelmayer J, Krulisova V, Macek M, Horváth A, Balogh I. Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system. BMC Genomics 2018; 19:158. [PMID: 29466940 PMCID: PMC5822529 DOI: 10.1186/s12864-018-4544-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/13/2018] [Indexed: 01/14/2023] Open
Abstract
Background Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis. Results In the plasmid system average correct genotyping was 95.8% in 4-mers, 87.4% in 5-mers and 72.1% in 6-mers. Despite the experienced low genotyping accuracy in 5- and 6-mers, it was possible to generate amplicons with more than a 90% adequate detection rate in every homopolymer tract. When homopolymers in the CFTR gene were sequenced average accuracy was 89.3%, but varied in a wide range (52.2 – 99.1%). In all but one case, an optimal amplicon-sequencing primer combination could be identified. In that single case (7A tract in exon 14 (c.2046_2052)), none of the tested primer sets produced the required analytical performance. Conclusions Our results show that pyrosequencing is the most reliable in case of 4-mers and as homopolymer length gradually increases, accuracy deteriorates. With careful primer selection, the NGS system was able to correctly genotype all but one of the homopolymers in the CFTR gene. In conclusion, we configured a plasmid test system that can be used to assess genotyping accuracy of NGS devices and developed an accurate NGS assay for the molecular diagnosis of CF using self-designed primers for amplification and sequencing. Electronic supplementary material The online version of this article (10.1186/s12864-018-4544-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gergely Ivády
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - László Madar
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Erika Dzsudzsák
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Katalin Koczok
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.,Division of Clinical Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - János Kappelmayer
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Veronika Krulisova
- Department of Biology and Medical Genetics, Second Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Attila Horváth
- Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen, Hungary
| | - István Balogh
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary. .,Division of Clinical Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.
| |
Collapse
|
3
|
Soltysova A, Tothova Tarova E, Ficek A, Baldovic M, Polakova H, Kayserova H, Kadasi L. Comprehensive genetic study of cystic fibrosis in Slovak patients in 25 years of genetic diagnostics. CLINICAL RESPIRATORY JOURNAL 2017; 12:1197-1206. [PMID: 28544683 DOI: 10.1111/crj.12651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/25/2017] [Accepted: 05/02/2017] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Cystic fibrosis (CF) has one of the longest histories in hereditary disease molecular diagnostics. However, identification of causative mutations in the CFTR gene is complicated by over 2000 currently identified mutations; with more still being discovered. Knowledge of mutation spectrum may improve effective routine diagnostics and is obligatory in mutation-specific treatment. OBJECTIVES This study presents comprehensive mutation screening of the CFTR gene; with 275 unrelated, clinically confirmed and treated cystic fibrosis (CF) patients diagnosed in 25 years genetic testing in Slovakia. METHODS Detection of the most common CFTR mutations was performed by ELUCIGENE 29 and ELUCIGENE CF EU2 kits. HRM and dHPLC mutation screening methods with subsequent Sanger sequencing were applied for minor mutation screening, and MLPA analysis for deletion/duplication detection. RESULTS A total of 70 different mutations were identified, from which the most common mutation F508del accounted for 60.36% of all disease alleles and 8 mutations have currently been observed only in Slovak patients. Two large deletions identified on chromosomes 2 and 22 were further characterized to identify breakpoints. Based on mutation screening results and neonatal screening we estimated incidence in Slovakian newborns at approximately 1:6000-7000. CONCLUSION In our study, we identified mutations in 98.54% of all disease chromosomes, while 86.54% were identified using ELUCIGENE kits, 0.54% by MLPA analysis and 11.46% by sequencing analysis. Knowledge of the mutation spectrum in genetically diagnosed patients improves possibilities of genetic counseling and cascade screening in the affected families and Slovak population.
Collapse
Affiliation(s)
- Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia.,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia.,Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Eva Tothova Tarova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia
| | - Marian Baldovic
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia
| | - Helena Polakova
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Hana Kayserova
- Center for Cystic Fibrosis, Department of Pediatric Pneumology Slovak Medical University, Krajinska 91, Bratislava 825 56, Slovakia
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia.,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia.,Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| |
Collapse
|
4
|
Nagy B, Nagy B, Fila L, Clarke LA, Gönczy F, Bede O, Nagy D, Újhelyi R, Szabó Á, Anghelyi A, Major M, Bene Z, Fejes Z, Antal-Szalmás P, Bhattoa HP, Balla G, Kappelmayer J, Amaral MD, Macek M, Balogh I. Human Epididymis Protein 4: A Novel Serum Inflammatory Biomarker in Cystic Fibrosis. Chest 2016; 150:661-72. [PMID: 27105680 DOI: 10.1016/j.chest.2016.04.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Increased expression of the human epididymis protein 4 (HE4) was previously described in lung biopsy samples from patients with cystic fibrosis (CF). It remains unknown, however, whether serum HE4 concentrations are elevated in CF. METHODS Seventy-seven children with CF from six Hungarian CF centers and 57 adult patients with CF from a Czech center were enrolled. In addition, 94 individuals with non-CF lung diseases and 117 normal control subjects with no pulmonary disorders were analyzed. Serum HE4 levels were measured by using an immunoassay, and their expression was further investigated via the quantification of HE4 messenger RNA by using quantitative reverse transcription polymerase chain reaction in CF vs non-CF respiratory epithelium biopsy specimens. The expression of the potential regulator miR-140-5p was analyzed by using an UPL-based quantitative reverse transcription polymerase chain reaction assay. HE4 was measured in the supernatants from unpolarized and polarized cystic fibrosis bronchial epithelial cells expressing wild-type or F508del-CFTR. RESULTS Median serum HE4 levels were significantly elevated in children with CF (99.5 [73.1-128.9] pmol/L) compared with control subjects (36.3 [31.1-43.4] pmol/L; P < .0001). This observation was replicated in adults with CF (115.7 [77.8-148.7] pmol/L; P < .0001). In contrast, abnormal but lower HE4 concentrations were found in cases of severe bronchitis, asthma, pneumonia, and bronchiectasis. In patients with CF, the concentrations of HE4 were positively correlated with overall disease severity and C-reactive protein concentrations, whereas a significant inverse relationship was found between HE4 and the spirometric FEV1 value. Relative HE4 mRNA levels were significantly upregulated (P = .011) with a decreased miR-140-5p expression (P = .020) in the CF vs non-CF airway biopsy specimens. Twofold higher HE4 concentrations were recorded in the supernatant of polarized F508del-CF transmembrane conductance regulator/bronchial epithelial cells compared with wild-type cells. CONCLUSIONS HE4 serum levels positively correlate with the overall severity of CF and the degree of pulmonary dysfunction. HE4 may thus be used as a novel inflammatory biomarker and possibly also as a measure of treatment efficacy in CF lung disease.
Collapse
Affiliation(s)
- Béla Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Béla Nagy
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Libor Fila
- Department of Pulmonology, Charles University, 2nd Faculty of Medicine, Motol University Hospital, Prague, Czech Republic
| | - Luka A Clarke
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | | | - Olga Bede
- Department of Pediatrics, Szent-Györgyi Albert Medical University, Szeged, Hungary
| | - Dóra Nagy
- Department of Pediatrics, Szent-Györgyi Albert Medical University, Szeged, Hungary
| | | | - Ágnes Szabó
- Department of Pediatrics, Szent-Györgyi Albert Medical University, Szeged, Hungary
| | | | - Miklós Major
- Markusovszky Lajos County Hospital, Szombathely, Hungary
| | - Zsolt Bene
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Fejes
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Antal-Szalmás
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Harjit Pal Bhattoa
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - György Balla
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Kappelmayer
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Milan Macek
- Department of Biology and Medical Genetics, Motol University Hospital, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - István Balogh
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Division of Clinical Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| |
Collapse
|
5
|
Molecular Analysis of Cystic Fibrosis Patients in Hungary - An Update to the Mutational Spectrum. J Med Biochem 2014; 34:46-51. [PMID: 28356823 PMCID: PMC4922332 DOI: 10.2478/jomb-2014-0055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/25/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND In this study the authors present an update to the CFTR mutation profile in Hungary, utilizing data from a selected cohort of 45 cystic fibrosis (CF) patients from different regions of the country. METHODS Depending on the preceding analysis, four different mutation detection methods were used. A commercial assay targeting the most common CF-causing mutations was performed as the first test followed by an allele specific PCR for CFTRdele2,3(21kb), Sanger sequencing and MLPA analysis of the coding region of the CFTR gene. RESULTS In our recent study 27 different mutations were detected, including 2 novel ones (c.1037_1038insA and c.1394C>T). Besides F508del (c.1521_1523delCTT), the following mutations were found at a frequency of ≥ 4.0%: W1282X (c.3846G>A), N1303K (c.3909C>G), CFTRdele2,3(21kb) (c.54-5940_273+10250del21kb) and 2184insA (c.2052_2053insA). In addition, four mutations (G542X, Y1092X, 621+1G>T, and 2143delT) were found in more than one allele. CONCLUSIONS The updated database of Hungarian mutations not only enables to increase the efficiency of the existing diagnostic approach, but also provides a further refined basis for the introduction of the molecular newborn screening (NBS) program in Hungary.
Collapse
|
6
|
CFTR mutations spectrum and the efficiency of molecular diagnostics in Polish cystic fibrosis patients. PLoS One 2014; 9:e89094. [PMID: 24586523 PMCID: PMC3935850 DOI: 10.1371/journal.pone.0089094] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/15/2014] [Indexed: 01/20/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane regulator gene (CFTR). In light of the strong allelic heterogeneity and regional specificity of the mutation spectrum, the strategy of molecular diagnostics and counseling in CF requires genetic tests to reflect the frequency profile characteristic for a given population. The goal of the study was to provide an updated comprehensive estimation of the distribution of CFTR mutations in Polish CF patients and to assess the effectiveness of INNOLiPA_CFTR tests in Polish population. The analyzed cohort consisted of 738 patients with the clinically confirmed CF diagnosis, prescreened for molecular defects using INNOLiPA_CFTR panels from Innogenetics. A combined efficiency of INNOLiPA CFTR_19 and CFTR_17_TnUpdate tests was 75.5%; both mutations were detected in 68.2%, and one mutation in 14.8% of the affected individuals. The group composed of all the patients with only one or with no mutation detected (109 and 126 individuals, respectively) was analyzed further using a mutation screening approach, i.e. SSCP/HD (single strand conformational polymorphism/heteroduplex) analysis of PCR products followed by sequencing of the coding sequence. As a result, 53 more mutations were found in 97 patients. The overall efficiency of the CF allele detection was 82.5% (7.0% increase compared to INNOLiPA tests alone). The distribution of the most frequent mutations in Poland was assessed. Most of the mutations repetitively found in Polish patients had been previously described in other European populations. The most frequent mutated allele, F508del, represented 54.5% of Polish CF chromosomes. Another eight mutations had frequencies over 1%, 24 had frequencies between 1 and 0.1%; c.2052-2053insA and c.3468+2_3468+3insT were the most frequent non-INNOLiPA mutations. Mutation distribution described herein is also relevant to the Polish diaspora. Our study also demonstrates that the reported efficiency of mutation detection strongly depends on the diagnostic experience of referring health centers.
Collapse
|
7
|
Distribution of CFTR mutations in the Czech population: Positive impact of integrated clinical and laboratory expertise, detection of novel/de novo alleles and relevance for related/derived populations. J Cyst Fibros 2013; 12:532-7. [DOI: 10.1016/j.jcf.2012.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/30/2012] [Accepted: 12/02/2012] [Indexed: 11/21/2022]
|
8
|
Balogh I, Koczok K, Szabó GP, Török O, Hadzsiev K, Csábi G, Balogh L, Dzsudzsák E, Ajzner E, Szabó L, Csákváry V, Oláh AV. Mutational spectrum of smith-lemli-opitz syndrome patients in hungary. Mol Syndromol 2012; 3:215-22. [PMID: 23293579 DOI: 10.1159/000343923] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Smith-Lemli-Opitz (SLO) syndrome is an autosomal recessive disorder characterized by multiple congenital abnormalities and mental retardation. The condition is caused by the deficiency of 7-dehydrocholesterol reductase (DHCR7) which catalyzes the final step in cholesterol biosynthesis. Biochemical diagnosis is based on increased concentration of 7-dehydrocholesterol (7-DHC) in the patient serum. Both life expectancy and quality of life are severely affected by the disease. The estimated prevalence of SLO syndrome ranges between 1:20,000 and 1:40,000 among Caucasians. Although the mutational spectrum of the disease is wide, approximately 10 mutations are responsible for more than 80% of the cases. These mutations show a large interethnic variability. There are no mutation distribution data from Hungary to date. Thirteen patients were diagnosed with SLO syndrome in our laboratory. As first-line tests, serum 7-DHC and total cholesterol were measured and, in positive cases, molecular genetic analysis of the DHCR7 gene was performed. Complete genetic background of the disease could be identified in 12 cases. In 1 case only 1 mutation was detected in a heterozygote form. One patient was homozygous for the common splice site mutation c.964-1G>C, while all other patients were compound heterozygotes. One novel missense mutation, c.374A>G (p.Tyr125Cys) was identified.
Collapse
Affiliation(s)
- I Balogh
- Department of Laboratory Medicine, University of Debrecen, Debrecen, Hungary
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
PURPOSE OF REVIEW Newborn screening for cystic fibrosis (CF) is now universal in the US and many other countries. The rapid expansion of screening has resulted in numerous publications identifying new challenges for healthcare providers. This review provides an overview of these publications and includes ideas on managing these challenges. RECENT FINDINGS Most CF newborn screening algorithms involve DNA mutation analysis. As screening has expanded, new challenges have been identified related to carrier detection and inconclusive diagnoses. Early descriptions of infants with CF-related metabolic syndrome (CRMS) indicate that the natural history of this condition cannot be predicted. Early identification has also provided an opportunity to better understand the pathophysiology of CF. However, few studies have been conducted in infants with CF to determine optimal therapy and recommendations are largely anecdotal. SUMMARY Newborn screening provides an opportunity to identify and begin treatment early in individuals with CF. Whereas a single, optimal approach to screening does not exist, all programs can benefit from new findings regarding sweat testing, carrier detection, early pathophysiology, and clinical outcomes.
Collapse
|