1
|
Amaral MD. Using the genome to correct the ion transport defect in cystic fibrosis. J Physiol 2022; 601:1573-1582. [PMID: 36068724 DOI: 10.1113/jp282308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/31/2022] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Human genome information can help finding drugs for human diseases. 'Omics' allow unbiased identification of novel drug targets. High-throughput (HT) approaches provide a global view on disease mechanisms. As a monogenic disease CF has led the way in multiple 'Omic' studies. 'Multi-omics' integration will generate maximal biological significance. ABSTRACT Today Biomedicine faces one of its greatest challenges, i.e. treating diseases through their causative dysfunctional processes and not just their symptoms. However, we still miss a global view of mechanisms and pathways involved in pathophysiology of most diseases. In fact, disease mechanisms and pathways can be achieved by holistic studies provided by 'Omic' approaches. Cystic Fibrosis (CF), caused by mutations in the CF transmembrane conductance regulator (CFTR) gene which encodes an anion channel, is paradigmatic for monogenic disorders, namely channelopathies. A high number of 'omics studies' have focussed on CF, namely several cell-based high-throughput (HT) approaches were developed and applied towards a global mechanistic characterization of CF pathophysiology and the identification of novel and 'unbiased' drug targets. Notwithstanding, it is likely that, through the integration of all these 'layers' of large datasets into comprehensive disease maps that biological significance can be extracted so that the enormous potential of these approaches to identifying dysfunctional mechanisms and novel drugs may become a reality. Abstract figure legend Schematic overview of the 3 main approaches to discovery of new drugs/drug targets. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande-C8 bdg, Lisboa, 1749-016, Portugal
| |
Collapse
|
2
|
Valdivieso ÁG, Santa‐Coloma TA. The chloride anion as a signalling effector. Biol Rev Camb Philos Soc 2019; 94:1839-1856. [DOI: 10.1111/brv.12536] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/20/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Ángel G. Valdivieso
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical SciencesPontifical Catholic University of Argentina Buenos Aires 1107 Argentina
- The National Scientific and Technical Research Council of Argentina (CONICET) Buenos Aires 1107 Argentina
| | - Tomás A. Santa‐Coloma
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical SciencesPontifical Catholic University of Argentina Buenos Aires 1107 Argentina
- The National Scientific and Technical Research Council of Argentina (CONICET) Buenos Aires 1107 Argentina
| |
Collapse
|
3
|
Braccia C, Tomati V, Caci E, Pedemonte N, Armirotti A. SWATH label-free proteomics for cystic fibrosis research. J Cyst Fibros 2018; 18:501-506. [PMID: 30348611 DOI: 10.1016/j.jcf.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND Label-free proteomics is a powerful tool for biological investigation. The SWATH protocol, relying on the Pan Human ion library, currently represents the state-of-the-art methodology for this kind of analysis. We recently discovered that this tool is not perfectly suitable for proteomics research in the CF field, as it lacks assays for several proteins crucial for the CF biology, including CFTR. METHODS We extensively investigated the proteome of a very popular model for in vitro research on CF, CFBE41o-, and we used the corresponding data to improve the power of SWATH proteomics for CF investigation. We then used this improved tool to explore in depth the proteome of primary bronchial epithelial (BE) cells deriving from four CF individuals compared with that of four corresponding non-CF controls. By means of advanced bioinformatics tools, we outlined the presence of a number of protein networks being significantly altered by CF. RESULTS Our analysis on patients' BE cells identified 154 proteins dysregulated by the CF pathology (94 upregulated and 60 downregulated). Some known CFTR interactors are present among them, but our analysis also revealed the alteration of other proteins not previously known to be related with CF. CONCLUSIONS The present work outlines the power of SWATH label free proteomics applied to CF research.
Collapse
Affiliation(s)
- Clarissa Braccia
- D3Pharmachemistry, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; Dipartimento di Chimica, Università degli Studi di Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Valeria Tomati
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Emanuela Caci
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry Lab, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
| |
Collapse
|
4
|
Massip-Copiz MM, Santa-Coloma TA. Extracellular pH and lung infections in cystic fibrosis. Eur J Cell Biol 2018; 97:402-410. [PMID: 29933921 DOI: 10.1016/j.ejcb.2018.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/01/2018] [Accepted: 06/12/2018] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by CFTR mutations. It is characterized by high NaCl concentration in sweat and the production of a thick and sticky mucus, occluding secretory ducts, intestine and airways, accompanied by chronic inflammation and infections of the lungs. This causes a progressive and lethal decline in lung function. Therefore, finding the mechanisms driving the high susceptibility to lung infections has been a key issue. For decades the prevalent hypothesis was that a reduced airway surface liquid (ASL) volume and composition, and the consequent increased mucus concentration (dehydration), create an environment favoring infections. However, a few years ago, in a pig model of CF, the Na+/K+ concentrations and the ASL volume were found intact. Immediately a different hypothesis arose, postulating a reduced ASL pH as the cause for the increased susceptibility to infections, due to a diminished bicarbonate secretion through CFTR. Noteworthy, a recent report found normal ASL pH values in CF children and in cultured primary airway cells, challenging the ASL pH hypothesis. On the other hand, recent evidences revitalized the hypothesis of a reduced ASL secretion. Thus, the role of the ASL pH in the CF is still a controversial matter. In this review we discuss the basis that sustain the role of CFTR in modulating the extracellular pH, and the recent results sustaining the different points of view. Finding the mechanisms of CFTR signaling that determine the susceptibility to infections is crucial to understand the pathophysiology of CF and related lung diseases.
Collapse
Affiliation(s)
- María Macarena Massip-Copiz
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED UCA-CONICET), The National Scientific and Technical Research Council (CONICET), and School of Medical Sciences, The Pontifical Catholic University of Argentina (UCA), Buenos Aires, Argentina
| | - Tomás Antonio Santa-Coloma
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED UCA-CONICET), The National Scientific and Technical Research Council (CONICET), and School of Medical Sciences, The Pontifical Catholic University of Argentina (UCA), Buenos Aires, Argentina.
| |
Collapse
|
5
|
Valdivieso ÁG, Mori C, Clauzure M, Massip-Copiz M, Santa-Coloma TA. CFTR modulates RPS27 gene expression using chloride anion as signaling effector. Arch Biochem Biophys 2017; 633:103-109. [DOI: 10.1016/j.abb.2017.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 09/13/2017] [Accepted: 09/20/2017] [Indexed: 12/13/2022]
|
6
|
c- Src and its role in cystic fibrosis. Eur J Cell Biol 2016; 95:401-413. [DOI: 10.1016/j.ejcb.2016.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/08/2016] [Accepted: 08/10/2016] [Indexed: 12/15/2022] Open
|
7
|
Meneghello A, Antognoli A, Sonato A, Zacco G, Ruffato G, Cretaio E, Romanato F. Label-free efficient and accurate detection of cystic fibrosis causing mutations using an azimuthally rotated GC-SPR platform. Anal Chem 2014; 86:11773-81. [PMID: 25359284 DOI: 10.1021/ac503272y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plasmonic nanosensors are candidates for the development of new sensors with low detection limits, high sensitivity, and specificity for target detection: these characteristics are of critical importance in the screening of mutations responsible for inherited diseases. In this work, we focused our study on the detection of some of the most frequent mutations responsible for cystic fibrosis (CF) among the Italian population. For the detection of the CF mutations we adopted a recently developed and highly sensitive Grating Coupled-Surface Plasmon Resonance (GC-SPR) enhanced spectroscopy method for label-free molecular identification exploiting a conical illumination configuration. Gold sinusoidal gratings functionalized with heterobifunctional PEG were used as sensing surfaces, and the specific biodetection was achieved through the coupling with DNA hairpin probes designed for single nucleotide discrimination. Such substrates were used to test unlabeled PCR amplified homozygous wild type (wt) and heterozygous samples, deriving from clinical samples, for the screened mutations. Hybridization conditions were optimized to obtain the maximum discrimination ratio (DR) between the homozygous wild type and the heterozygous samples. SPR signals obtained from hybridizing wild type and heterozygous samples show DRs able to identify univocally the correct genotypes, as confirmed by fluorescence microarray experiments run in parallel. Furthermore, SPR genotyping was not impaired in samples containing unrelated DNA, allowing the platform to be used for the concomitant discrimination of several alleles also scalable for a high throughput screening setting.
Collapse
Affiliation(s)
- Anna Meneghello
- Veneto Nanotech S.C.p.A. , Via S. Crispino 106, Padova, Italy , c/o Nanofab, Via delle Industrie 5, 30175 Marghera (VE), Italy
| | | | | | | | | | | | | |
Collapse
|
8
|
Disruption of interleukin-1β autocrine signaling rescues complex I activity and improves ROS levels in immortalized epithelial cells with impaired cystic fibrosis transmembrane conductance regulator (CFTR) function. PLoS One 2014; 9:e99257. [PMID: 24901709 PMCID: PMC4047112 DOI: 10.1371/journal.pone.0099257] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 05/13/2014] [Indexed: 12/22/2022] Open
Abstract
Patients with cystic fibrosis (CF) have elevated concentration of cytokines in sputum and a general inflammatory condition. In addition, CF cells in culture produce diverse cytokines in excess, including IL-1β. We have previously shown that IL-1β, at low doses (∼30 pM), can stimulate the expression of CFTR in T84 colon carcinoma cells, through NF-κB signaling. However, at higher doses (>2.5 ng/ml, ∼150 pM), IL-1β inhibit CFTR mRNA expression. On the other hand, by using differential display, we found two genes with reduced expression in CF cells, corresponding to the mitochondrial proteins CISD1 and MTND4. The last is a key subunit for the activity of mitochondrial Complex I (mCx-I); accordingly, we later found a reduced mCx-I activity in CF cells. Here we found that IB3-1 cells (CF cells), cultured in serum-free media, secrete 323±5 pg/ml of IL-1β in 24 h vs 127±3 pg/ml for S9 cells (CFTR-corrected IB3-1 cells). Externally added IL-1β (5 ng/ml) reduces the mCx-I activity and increases the mitochondrial (MitoSOX probe) and cellular (DCFH-DA probe) ROS levels of S9 (CFTR-corrected IB3-1 CF cells) or Caco-2/pRSctrl cells (shRNA control cells) to values comparable to those of IB3-1 or Caco-2/pRS26 cells (shRNA specific for CFTR). Treatments of IB3-1 or Caco-2/pRS26 cells with either IL-1β blocking antibody, IL-1 receptor antagonist, IKK inhibitor III (NF-κB pathway) or SB203580 (p38 MAPK pathway), restored the mCx-I activity. In addition, in IB3-1 or Caco-2/pRS26 cells, IL-1β blocking antibody, IKK inhibitor III or SB203580 reduced the mitochondrial ROS levels by ∼50% and the cellular ROS levels near to basal values. The AP-1 inhibitors U0126 (MEK1/2) or SP600125 (JNK1/2/3 inhibitor) had no effects. The results suggest that in these cells IL-1β, through an autocrine effect, acts as a bridge connecting the CFTR with the mCx-I activity and the ROS levels.
Collapse
|
9
|
Schuierer MM, Langmann T. Molecular diagnosis of ATP-binding cassette transporter-related diseases. Expert Rev Mol Diagn 2014; 5:755-67. [PMID: 16149878 DOI: 10.1586/14737159.5.5.755] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
ATP-binding cassette (ABC) transporters are involved in a variety of physiologic processes such as xenobiotic defense, lipid metabolism, ion homeostasis and immune functions. A large number of ABC proteins have been causatively linked to rare and common human genetic diseases including familial high-density lipoprotein deficiency, retinopathies, cystic fibrosis, diabetes and cardiomyopathies. Furthermore, genetic variations in ABC transporter genes and dysregulated expression patterns of these molecules significantly contribute to drug resistance in human cancer cells and alter the pharmacokinetic properties of a variety of drugs. In order to analyze DNA sequence alterations or define disease-associated mRNA expression patterns of the complete ABC transporter superfamily, novel high-throughput molecular methods such as quantitative real-time PCR and DNA microarray analysis are emerging. The aim of this review is to provide an overview and to present some examples of human ABC transporters involved in monogenic diseases, cancer and pharmacogenetics. Methodologic aspects of molecular diagnostics applied to analyze genetic variations, mRNA and protein expression levels and functional characteristics of ABC transporters are discussed.
Collapse
Affiliation(s)
- Marion M Schuierer
- University of Regensburg, Institute of Pathology, Franz-Josef-Strauss Allee 11, D-93053, Germany.
| | | |
Collapse
|
10
|
Valdivieso AG, Santa-Coloma TA. CFTR activity and mitochondrial function. Redox Biol 2013; 1:190-202. [PMID: 24024153 PMCID: PMC3757715 DOI: 10.1016/j.redox.2012.11.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 11/12/2012] [Indexed: 12/21/2022] Open
Abstract
Cystic Fibrosis (CF) is a frequent and lethal autosomal recessive disease, caused by mutations in the gene encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). Before the discovery of the CFTR gene, several hypotheses attempted to explain the etiology of this disease, including the possible role of a chloride channel, diverse alterations in mitochondrial functions, the overexpression of the lysosomal enzyme α-glucosidase and a deficiency in the cytosolic enzyme glucose 6-phosphate dehydrogenase. Because of the diverse mitochondrial changes found, some authors proposed that the affected gene should codify for a mitochondrial protein. Later, the CFTR cloning and the demonstration of its chloride channel activity turned the mitochondrial, lysosomal and cytosolic hypotheses obsolete. However, in recent years, using new approaches, several investigators reported similar or new alterations of mitochondrial functions in Cystic Fibrosis, thus rediscovering a possible role of mitochondria in this disease. Here, we review these CFTR-driven mitochondrial defects, including differential gene expression, alterations in oxidative phosphorylation, calcium homeostasis, oxidative stress, apoptosis and innate immune response, which might explain some characteristics of the complex CF phenotype and reveals potential new targets for therapy.
Collapse
Affiliation(s)
- Angel Gabriel Valdivieso
- Institute for Biomedical Research (BIOMED CONICET-UCA), Laboratory of Cellular and Molecular Biology, School of Medical Sciences, Pontifical Catholic University of Argentina (UCA), Buenos Aires, Argentina
| | | |
Collapse
|
11
|
Differential global gene expression in cystic fibrosis nasal and bronchial epithelium. Genomics 2011; 98:327-36. [DOI: 10.1016/j.ygeno.2011.06.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 06/23/2011] [Accepted: 06/24/2011] [Indexed: 01/08/2023]
|
12
|
|
13
|
Arranz JA, Riudor E, Marco-Marín C, Rubio V. Estimation of the total number of disease-causing mutations in ornithine transcarbamylase (OTC) deficiency. Value of the OTC structure in predicting a mutation pathogenic potential. J Inherit Metab Dis 2007; 30:217-26. [PMID: 17334707 DOI: 10.1007/s10545-007-0429-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 01/04/2007] [Accepted: 01/29/2007] [Indexed: 10/23/2022]
Abstract
Ornithine transcarbamylase deficiency (OTCD), the X-linked, most frequent urea cycle error, results from mutations in the OTC gene, encoding a 354-residue polypeptide. To date 341 OTCD clinical mutations, including 222 missense single nucleotide changes (mSNCs), have been compiled (Hum Mutat 2006;27:626). OTCD mutation detection might be simplified if the entire repertoire of OTCD-causing mutations were known. We estimate the size of this repertoire from 23 new OTCD patients exhibiting 22 different mutations, of which 9, including 4 mSNCs, are novel. The complete repertoire of OTCD-causing mutations is estimated as 560 mutations (95% confidence interval, 422-833 mutations), including 290 mSNCs (95% confidence interval, 230-394 mSNCs). Thus, OTCD diagnosis based on the screening for known mutations might attain 90% sensitivity in <5 years. Since disease-causing mSNCs represent <20% of the 2064 possible OTC mSNCs, simple approaches are essential for discrimination between causative and trivial mSNCs. Observation of the OTC structure appears a simple approach for such discrimination, comparing favourably in our sample with three formalized structure-based and/or sequence-based in silico assessment methods, and supporting the causation of complete deficiency by the mutations p.Pro305Arg and p.Ser96Phe, and of partial deficiency by p.Asp41Gly, p.Glu122Gly, p.Leu179Phe, p.Pro220Thr and p.Glu273del. Five non-mSNC novel mutations (p.Gly71X, a 7-nucleotide and a 10-nucleotide duplication and deletion in exon 5, G>A transitions at bases +1 and +5 of introns 4 and 9, respectively) are obviously pathogenic. The previously reported mSNCs p.Arg26Gln, p.Arg40His, p.Glu52Lys, pLys88Asn, p.Arg129His, p.Asn161Ser, p.Thr178Met, p.His202Tyr, p.Ala208Thr and p.His302Arg, found in our cohort, are also discussed.
Collapse
Affiliation(s)
- J A Arranz
- Unitat de Metabolopaties, Hospital Materno-Infantil Vall d'Hebron, Barcelona, Spain
| | | | | | | |
Collapse
|
14
|
Ollero M, Brouillard F, Edelman A. Cystic fibrosis enters the proteomics scene: New answers to old questions. Proteomics 2006; 6:4084-99. [PMID: 16791827 DOI: 10.1002/pmic.200600028] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery in 1989 of the gene encoding for the cystic fibrosis transmembrane conductance regulator (CFTR) and its mutation as the primary cause of cystic fibrosis (CF), generated an optimistic reaction with respect to the development of potential therapies. This extraordinary milestone, however, represented only the initial key step in a long path. Many of the mechanisms that govern the pathogenesis of CF, the most commonly inherited lethal pulmonary disorder in Caucasians, remain even today unknown. As a continuation to genomic research, proteomics now offers the unique advantage to examine global alterations in the protein expression patterns of CF cells and tissues. The systematic use of this approach will probably provide new insights into the cellular mechanisms involved in CF dysfunctions, and should ultimately result in the finding of new prognostic markers, and in the generation of new therapies. In this article we review the current status of proteomic research applied to the study of CF, including CFTR-related interactomics, and evaluate the potential of these technologies for future investigations.
Collapse
|
15
|
Ragoussis J, Elvidge G. Affymetrix GeneChip system: moving from research to the clinic. Expert Rev Mol Diagn 2006; 6:145-52. [PMID: 16512775 DOI: 10.1586/14737159.6.2.145] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Affymetrix Inc.'s GeneChip technology has become the industry standard in microarray-based research. Due to the high density of content per array that can be achieved today (an industry leading 6.5 million features) the GeneChips can be used for high-throughput mutation detection, single nucleotide polymorphism genotyping, expression profiling and detection of chromosomal aberrations. This in turn opens the way for clinical applications in genetics, cytogenetics, pharmacogenetics, oncology and pathogen recognition. Establishing standards is a central issue in improving data quality and, in combination with automatic, easy-to-interpret reports, will form the basis of the clinical applicability. Future pricing policies and the resolving of ethical considerations will also dictate the technology's full translation from research into clinical laboratories.
Collapse
Affiliation(s)
- Jiannis Ragoussis
- Genomics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK.
| | | |
Collapse
|
16
|
Eshaque B, Dixon B. Technology platforms for molecular diagnosis of cystic fibrosis. Biotechnol Adv 2006; 24:86-93. [PMID: 16171966 DOI: 10.1016/j.biotechadv.2005.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 08/01/2005] [Accepted: 08/01/2005] [Indexed: 11/19/2022]
Abstract
Cystic fibrosis (CF) is one of the most common recessive genetic diseases in North America. So far, 1200 mutations causing CF have been identified. Several techniques such as allele specific oligonucleotide (ASO) dot-blot, reverse dot-blot, amplification refractory mutation (ARMS), and an oligo-ligation assay, are available to detect the most common mutations. However, detecting compound heterozygotes between DeltaF508, the most common disease causing mutation, and other mutations which are rare is difficult as some mutations are common only to particular ethnic groups. Therefore, new diagnostic tests such as restriction enzyme assays and single stranded conformational polymorphism (SSCP) have been designed to recognize rare and population-specific mutations. This review will describe the most commonly used CF mutation detecting diagnostic techniques, as well as novel assays and techniques currently in development that might be employed in future.
Collapse
Affiliation(s)
- Bithi Eshaque
- Department of Biology, University of Waterloo, Ontario, Canada
| | | |
Collapse
|
17
|
Abstract
PURPOSE OF REVIEW To review the latest developments in screening and diagnosis of non-chromosomal genetic diseases. RECENT FINDINGS Major recent advances include the completion of the Human Genome Project, the use of microarray and related technologies for mass screening and diagnosis of thousands of genetic abnormalities, and non-invasive prenatal diagnosis using fetal DNA in maternal plasma. SUMMARY The rapid development in molecular biological technologies makes it possible to screen and to diagnosis thousands of genetic conditions, mutations and also predispositions to chronic diseases or traits, either prenatally or after birth. Clinical application of non-invasive prenatal diagnosis using fetal DNA in maternal plasma has become a reality. The arrival of the molecular genetic era also leads to many new ethical, social and medico-legal problems and dilemmas that obstetricians will have to face in the near future. There is an urgent need for the development of a new model for provision of genetic screening and diagnosis.
Collapse
Affiliation(s)
- Tze Kin Lau
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong.
| | | |
Collapse
|
18
|
Harris A. Nucleic acids analysis. J Cyst Fibros 2004. [DOI: 10.1016/j.jcf.2004.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
19
|
Amaral MD, Clarke LA, Ramalho AS, Beck S, Broackes-Carter F, Rowntree R, Mouchel N, Williams SH, Harris A, Tzetis M, Steiner B, Sanz J, Gallati S, Nissim-Rafinifa M, Kerem B, Hefferon T, Cutting GR, Goina E, Pagani F. Quantitative methods for the analysis of CFTR transcripts/splicing variants. J Cyst Fibros 2004; 3 Suppl 2:17-23. [PMID: 15463919 DOI: 10.1016/j.jcf.2004.05.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In cystic fibrosis (CF), transcript analysis and quantification are important for diagnosis, prognosis and also as surrogate markers for some therapies including gene therapy. Classical RNA-based methods require significant expression levels in target samples for appropriate analysis, thus PCR-based methods are evolving towards reliable quantification. Various protocols for the quantitative analysis of CFTR transcripts (including those resulting from splicing variants) are described and discussed here.
Collapse
Affiliation(s)
- Margarida D Amaral
- Department of Chemistry and Biochemistry, University of Lisboa, Lisboa, Portugal.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|