A Novel Mutation in the Cystic Fibrosis Gene in Patients with Pulmonary Disease but Normal Sweat Chloride Concentrations
W. Edward Highsmith, Lauranell H. Burch, Zhaoqing Zhou, John C. Olsen, Thomas E. Boat, Alexander Spock, Jack D. Gorvoy, Lynne Quittell, Kenneth J. Friedman, Lawrence M. Silverman, Richard C. Boucher, and Michael R. Knowles
Background Many patients with chronic pulmonary disease similarto that seen in cystic fibrosis have normal (or nondiagnostic)sweat chloride values. It has been difficult to make the diagnosisof cystic fibrosis in these patients because no associated mutationin the cystic fibrosis transmembrane conductance regulator (CFTR)gene has been identified.
Methods We evaluated 23 patients with pulmonary disease characteristicof cystic fibrosis but with sweat chloride concentrations inthe normal range. Mutations in the CFTR gene were sought bydirect sequencing of polymerase chain reaction-amplified nasalepithelial messenger RNA and by testing the functioning of affectedepithelium.
Results A cytidine phosphate guanosine dinucleotide C-to-T pointmutation in intron 19 of the CFTR gene, termed 3849+10 kb Cto T, was identified in 13 patients from eight unrelated families.This mutation was found in patients from three different ethnicgroups with three different extended haplotypes. The mutationleads to the creation of a partially active splice site in intron19 and to the insertion into most CFTR transcripts of a new84-base-pair "exon," containing an in-frame stop codon, betweenexons 19 and 20. Normally spliced transcripts were also detectedat a level approximately 8 percent of that found in normal subjects.This mutation is associated with abnormal nasal epithelial andsweat acinar epithelial function.
Conclusions We have identified a point mutation in intron 19of CFTR and abnormal epithelial function in patients who havecystic fibrosis-like lung disease but normal sweat chloridevalues. The identification of this mutation indicates that thissyndrome is a form of cystic fibrosis. Screening for the mutationshould prove diagnostically useful in this population of patients.
Cystic fibrosis is an autosomal recessive genetic disorder thatreflects mutations in the cystic fibrosis transmembrane conductanceregulator (CFTR) gene,1,2,3 which codes for a cyclic AMP (cAMP)-regulatedchloride channel4,5. The disorder has a broad range of severitybut has traditionally been manifested by chronic pulmonary disease,pancreatic exocrine insufficiency, elevated concentrations ofchloride in sweat, and identified mutations, most commonly F5083,6.
There is a group of patients, however, who have chronic lungdisease similar to that seen in cystic fibrosis but who havenormal sweat chloride values6. These patients have no commonmutation in the CFTR gene detectable by conventional geneticanalysis of genomic DNA and thus present a diagnostic problem.To evaluate the diagnosis of cystic fibrosis in such patients,we characterized the physiologic functioning of epithelium inaffected organs and sought mutations in the CFTR gene by directsequencing of messenger RNA (mRNA) transcripts obtained fromnasal epithelium and amplified by the polymerase chain reaction(PCR).
Methods
Patients
We evaluated 23 patients in 13 families who had disease resemblingcystic fibrosis (obstructive airways disease and characteristicmicrobiologic contents of sputum, i.e., Staphylococcus aureus,Pseudomonas aeruginosa, or both) but who had sweat chloridevalues7 in the nondiagnostic or normal range8 (<60 mmol perliter in patients older than 15 years and <40 mmol per literin patients 15 years old or younger, calculated as the medianof at least three determinations). Pancreatic exocrine functionwas assessed by the measurement of stool fat during a 72-hourperiod (normal, <7 g per day per 100 g of fat ingested) orby clinical features and the measurement of serum vitamin E(normal, 5 to 20 mg per milliliter of solution), serum trypsinogen(normal, 10 to 57 ng per milliliter of solution), or both. Eachpatient was screened for 29 different mutations of CFTR9. Thestudy protocol was approved by the institutional review boardof the University of North Carolina, and informed consent wasobtained.
Identification and Characterization of the Mutation in Intron 19
Total RNA was prepared by the method of Chirgwin et al.10 orthe Ultraspect system (Biotecx, Houston) from nasal epithelialcells (5 x 105) obtained by scraping the inferior turbinateswith a Rhinoprobe11. For the sequence analysis, reverse transcriptionwas performed with CFTR-specific primers and avian moloney virusreverse transcriptase (Red Module, Invitrogen, San Diego, Calif.).The complementary DNA (cDNA) was amplified (for 35 cycles) toyield segments of cDNA of approximately 1 kilobase (kb). Eachfirst-round PCR product was reamplified (for 35 cycles) withnested primers, resulting in overlapping products of 400 to600 base pairs (bp). The second-round products were purifiedon low-melting-temperature agarose gels; single-stranded DNAwas prepared by asymmetric PCR12 and purified by two roundsof spin dialysis (Centricon 100, Amicon, Beverly, Mass.). Dideoxysequencing was done with Sequenase (United States Biochemical,Cleveland).
The region of CFTR cDNA spanning exon 18 to exon 20 was amplifiedwith a primer complementary to bases 3552 to 3596 (exon 18)and a primer complementary to the junction of exons 20 and 21(bases 3991 to 4009). After electrophoresis in composite gelsconsisting of 3 percent NuSieve agarose and 1 percent Seakemagarose (FMC Bioproducts, Rockland, Me.), the amplified fragmentwas detected by Southern hybridization with 32P-labeled oligonucleotidecomplementary to bases 3600 through 3619. EcoRI digests of phageclones (TE24II and TE28), which together span intron 19, wereanalyzed by the Southern blot assay with an insert-bearing PCRproduct (542 bp). The primers (forward primer, 5'TTGACTTGTCATCTTGATTTC3';reverse primer, 5'CATTTTAATACTGCAACAGAT3') derived from theinsert sequence (as described in the next section) were usedto amplify DNA from a plasmid subclone (pTE24II-6) to providesequences in regions flanking the 84-bp insert. In sequencingkey regions of intron 19, primers were used to amplify a 437-bpPCR product from genomic DNA (forward primer 4712, 5'AGGCTTCTCAGTGATCTGTTG3';reverse primer 4713, 5'GAATCATTCAGTGGGTATAAGCAG3').
Quantitation of CFTR mRNA
Total RNA was prepared from nasal epithelium with the Ultraspectsystem (Biotecx). Two microgs of total RNA was used to synthesizecDNA (in 20-microl reactions) with reverse transcriptase (SuperScript, Life Technologies, Gaithersburg, Md.). After 20-folddilution in water, 10-microl aliquots of cDNA were includedin the 50-microl PCR reactions. The normal CFTR sequence wasamplified with primer 051193-1 and a primer complementary tothe junction of exons 19 and 20 (bases 3843 to 3867). Amplificationof -actin sequences was performed in parallel with primers HAG3and HAG413. CFTR and -actin sequences were amplified by 25 cyclesof PCR (94 °C for 30 seconds, 65 °C for 30 seconds,and 72 °C for 1 minute) with the rapid-initiation technique(HotStart AmpliWax paraffin beads, Perkin-Elmer, Norwalk, Conn.).Plasmids carrying the CFTR sequence (pCFTR474) or the -actinsequence (pHF1)14 were amplified in parallel; the initial copynumber of each plasmid was increased serially (10-fold, from10 to 105). Amplification products were analyzed by Southernblot hybridization with 32P-labeled oligonucleotides complementaryto CFTR (bases 3600 to 3619) or -actin15 (bases 1072 to 1096).The DNA fragments were quantitated by phosphor-screen autoradiography(PhosphorImager, Molecular Dynamics, Sunnyvale, Calif.).
Haplotype Determination
Extended haplotypes were constructed from an analysis of PCR-amplifiedDNA for the diallelic markers XV.2c and KM-1916 and the markerloci J44, GATT, M470, and TUB1817.
Sweat-Gland and Nasal Epithelial Function
Sweat ductal function was assessed by measurement of sweat chloride7and by measurement of the potential difference (PD), or voltage,across the epithelium of the sweat duct18,19. Sweat acinar epithelialchloride secretion mediated by cAMP was assessed by measuringsweat formation after an intradermal injection of isoproterenol,aminophylline, and atropine20,21,22. We tested the nasal PDand the response to sequential superfusion with amiloride (10-4M), chloride-free amiloride (in which the chloride is replacedby gluconate), and a combination of isoproterenol (10-5 M) andchloride-free amiloride23,24,25. The chloride-diffusion PD (anindex of basal chloride permeability) indicates the change withchloride-free superfusion; values reported here are corrected(by adding -9 mV) for the change in voltage caused by the replacementof chloride by gluconate. The change in PD with isoproterenolcorrelates with the cAMP-activated permeability of chloride;a negative value indicates chloride secretion.
Results
Clinical Phenotype of Patients
The patients referred for study had obstructive lung disease,chest radiographs consistent with cystic fibrosis, and characteristicmicrobiologic features of sputum -- that is, mucoid P. aeruginosa,S. aureus, or both. Thirteen patients from eight families (Table 1)had at least one copy of the mutation in intron 19, as describedbelow. Except for Patient 8A, these patients tended to havelung disease similar to or milder than that expected for theirage as compared with a large population of patients with cysticfibrosis who were homozygous for F50827. Six of these studypatients had never been hospitalized for their lung disease.Their sweat chloride values were nondiagnostic of cystic fibrosis,and the median value on multiple sweat tests was within thenormal range. Most of the patients (10 of 13) had preservationof pancreatic exocrine function. One adult man (Patient 6A)who underwent fertility testing had an undeveloped vas deferensand obstructive azoospermia.
Table 1. Clinical Features and Genotype of Patients with Pulmonary Disease and Normal Sweat Chloride Levels.
Sweat-Gland and Nasal Epithelial Function
Eight patients underwent physiologic assessment of epithelialfunction. Sweat ductal PD measurements for all eight were normal(Table 2), in a manner consistent with effective sweat chlorideabsorption and normal sweat chloride concentrations. In contrast,the assessment of sweat acinar epithelial chloride secretoryfunction revealed that none of these patients secreted chloridein response to the -agonist isoproterenol, a pattern typicalof classic cystic fibrosis. The patients' nasal bioelectricproperties were also abnormal, similar to those seen in patientshomozygous for F508 (Table 2): the base-line PD and amiloride-sensitivePD were greater than normal, and the chloride diffusion PD (anindex of chloride permeability) and the cAMP-mediated chloridesecretory response to isoproterenol were smaller than normal.
Table 2. Physiologic Studies of Sweat-Gland and Nasal Epithelial Function in Eight Patients with Pulmonary Disease and the Mutation in Intron 19 of CFTR.
Genetic Analysis of Patients
The initial studies were of a 20-year-old woman (Patient 1 inTable 1). She was homozygous for the B haplotype16 and was theproduct of consanguineous mating (her paternal grandparentswere first cousins, as were her parents). No mutation was identifiedwhen the coding region of her CFTR gene was sequenced. However,PCR amplification of cDNA spanning from exon 18 to exon 20 revealedtwo products that hybridized to an oligonucleotide complementaryto exon 19 (Figure 1A). The smaller product (474 bp), foundin both normal subjects and the sample from the homozygous patient,corresponded to the normal CFTR sequence. The larger species(558 bp), found only in the sample from the patient, containedan 84-bp insert between exons 19 and 20 that included an in-frameTAA stop codon (Figure 1B). Hybridization of the relevant PCRproduct to EcoRI digests of phage clones TE24II and TE28 revealed,in addition to the expected bands overlapping exons 19 and 20,a 6.0-kb fragment common to both clones (Figure 1C). This fragmentbegins approximately 10 kb downstream of exon 19. Sequence analysisof DNA flanking the 84-bp insert from the 6.0-kb fragment revealedcryptic splice lariat and acceptor sequences 5' to the insertand a consensus splice-donor site 3' to the insert, except forthe C residue at position 2 (Figure 1D).
Figure 1. Identification and Characterization of the Mutation in Intron 19.
Panel A shows an autoradiograph of PCR products from the region spanning exon 18 to exon 20 of CFTR cDNA from a normal subject (lane 1) and a patient with cystic fibrosis who is homozygous for the mutation in intron 19 (lane 2). The 474-bp product is the normal CFTR sequence, and the 558-bp product contains the 84-bp insert from intron 19. Panel B shows the sequence of the 84-base insert; the in-frame stop codon TAA appears in capital letters. The diagram shows alternative splicing (above) and normal splicing (below); the hatched box represents the 84-bp insert, and the solid boxes represent exon 19 and exon 20. Panel C shows an EcoRI restriction map of CFTR intron 19 and a schematic drawing of Southern blot analysis of EcoRI-digested phage clones TE24II and TE28, with an insert-bearing PCR product used as the hybridization probe; the heavy lines indicate hybridization to the probe. R denotes EcoRI recognition site. Panel D shows sequences flanking the 84-bp insert in intron 19. The flanking regions demonstrate homology to splice lariat, acceptor, and donor sites; the bases matching the consensus sequence are capitalized. The index patient had a C-to-T mutation in the second base 3' of the insert sequence (arrow).
The sequence of genomic DNA (Figure 2) revealed that the inbredpatient had a T residue two bases downstream of the 84-bp insert,whereas a C residue was present in the normal subject. The fatherwas heterozygous for the C-to-T mutation at this position. Thissubstitution creates a sequence with strong homology to a splice-donorsite (Figure 1D).
Figure 2. Sequence of the PCR Product from Intron 19 in the Index Patient, Her Father, and a Normal Control.
The patient is homozygous for a G-to-A mutation (arrow) on the antisense strand. Her father is a heterozygous carrier.
The C-to-T mutation in intron 19 is termed a 3849+10 kb C-to-Tmutation (3849 is the number of the last base in exon 19, and10 kb indicates that the mutation is approximately 10 kb downstreamfrom 3849). The mutation creates a new HphI restriction site,and we used HphI restriction digestion to screen the other patientswith cystic fibrosis who had normal sweat chloride values. Thirteenpatients had at least one copy of the mutation in intron 19(Table 1): two were homozygous for the mutation, nine were compoundheterozygotes with F508, and two siblings were compound heterozygoteswith W1282X. The mutation in intron 19 was associated with threedifferent ethnic origins (Pakistani, Ashkenazi Jewish, and northernEuropean white) and at least three different extended haplotypes(data not shown).
Correlation of Mutation with Disease
One patient who was homozygous for the mutation in intron 19(Patient 2 in Table 1) was homozygous for the C haplotype; althoughconsanguinity could not be documented, both parents traced theirancestry to the same Jewish community in Eastern Europe. Thepedigree of this patient's family shows the correlation of thedisease with the mutation in intron 19 (Figure 3); neither oftwo clinically unaffected sisters was homozygous for the mutation.Sixteen siblings or parents of affected persons were genotyped,and the mutation in intron 19 was associated with known cysticfibrosis mutations only in persons who had clinical diseasecompatible with cystic fibrosis. We screened 137 cystic fibrosischromosomes with unidentified mutations from patients with cysticfibrosis who had clearly elevated sweat chloride values and60 non-cystic fibrosis chromosomes derived from obligate carriers.No mutations in intron 19 were found.
Figure 3. Detection of the 3849+10 kb C-to-T Mutation by PCR and HphI Digestion.
The figure shows the pedigree of a patient (Patient 2 in Table 1) who is homozygous for the 3849+10 kb C-to-T mutation. The square denotes a male family member, circles female family members, the solid symbol a homozygous family member, the open symbol a normal family member, and half-solid symbols heterozygous family members. DNA from each family member was amplified with primers 4712 and 4713 and digested with HphI. The normal allele has one HphI site, yielding bands of 349 and 88 bp (the noncarrier sister, lane 6). The C-to-T mutation creates a new HphI restriction site, and the mutant allele shows bands of 222, 127, and 88 bp (lane 4). Plus and minus signs indicate whether samples were treated with HphI. Lane 1 shows a sample of undigested DNA from the patient.
Expression of Normally Spliced CFTR mRNA
Normally spliced CFTR mRNA was detected in the nasal epithelialsample from one patient homozygous for the mutation in intron19 (Figure 4A, lanes 1 through 5) relative to the normal sample(Figure 4A, lanes 6 through 10). The amount of normal CFTR mRNAin the sample from the patient was only 8 percent of that inthe normal sample (Figure 4B). Similar results were obtainedby an alternative method using quantitative competitive PCRwith other samples from this patient. The amount of normal CFTRmRNA was only 5 to 10 percent of that in nasal epithelial samplesfrom three normal subjects.
Figure 4. Quantitation of Normally Spliced CFTR mRNA Expressed in Nasal Epithelial Cells from a Patient with the Intron 19 Mutation.
Panel A shows an autoradiograph of a Southern blot assay of PCR products from parallel reactions of CFTR cDNA and -actin cDNA from a patient with cystic fibrosis who was homozygous for the point mutation in intron 19 (lanes 1 through 5), a normal subject (lanes 6 through 10), and plasmid standards with sequential 10-fold increases (from 10 to 105) in the initial target copy numbers (lanes 11 through 15). Panel B shows the relative expression of normal CFTR mRNA in the sample from the patient who was homozygous for the mutation in intron 19, as compared with the sample from the normal subject. The level of expression was determined by a quantitative analysis of the hybridization in Panel A using phosphor-screen autoradiography. CFTR expression was standardized to -actin expression.
Discussion
Patients with clinical disease compatible with cystic fibrosiswho do not have diagnostic sweat chloride values are commonlyevaluated at cystic fibrosis centers6,26,28,29. It has beendifficult to establish firmly the diagnosis of cystic fibrosisin these patients, because testing for specific biologic markersfor cystic fibrosis18,23,24 is not widely available and onlyone mutation in CFTR (G551S), found infrequently in such patients,has been associated with this syndrome22.
We identified a change in a single base pair in intron 19, termeda 3849+10 kb C-to-T mutation, in 13 patients who had this syndromeof cystic fibrosis-like lung disease and normal sweat chloridevalues. The C-to-T mutation in intron 19 leads to novel alternativesplicing through the partial activation of a cryptic splicesite and the insertion into most CFTR transcripts of a new 84-bp"exon," complete with an in-frame stop codon between exons 19and 20 (Figure 1B). The C residue at position 2 of the cryptic(nonfunctional) splice-donor site in normal genomic DNA (Figure 1D)is part of a cytidine phosphate guanosine dinucleotide,which is the site of frequent point mutations30. No other sequencevariant was found in the coding region of a patient who washomozygous for the mutation in intron 19. This mutation wasnot found in 60 normal chromosomes or in 137 cystic fibrosischromosomes associated with elevated sweat chloride values.These findings, along with the correlation of this change ofa base pair with the disease, demonstrates that these 13 patientshave a form of cystic fibrosis.
The molecular nature of the mutation in intron 19 is compatiblewith the exon-shuffling theory,31 which proposes that pointmutations that create or destroy splice sites can cause theinsertion or deletion of clusters of amino acids ("exons"),thereby increasing the rate at which proteins can evolve. Asimilar intronic mutation has been described in the small secondintervening sequence of the beta-globin gene32. Such splicemutations are not easily detected with genomic DNA, and an approachusing mRNA offers a better opportunity to identify them. Oncethey are identified, the presence of new unique restrictionsites permits rapid diagnosis based on DNA analysis.
The 3849+10 kb C-to-T mutation is found in patients with sufficientsweat-duct epithelial chloride absorption to produce normalsweat. Patients with the mutation in intron 19 also appear tohave milder pulmonary disease than do patients homozygous forF508, although the varying severity of pulmonary disease amongpatients with the same genotype27 precludes a definitive analysisin our small and prospectively selected population. In thissmall group there was no obvious difference in clinical phenotypebetween patients homozygous for the mutation in intron 19 andthose heterozygous for the mutation.
A clue to the molecular basis of the variant phenotype was providedby the analysis of mRNA transcripts expressed in these patients.No full-length CFTR protein is expected to be translated fromthe mRNA containing the 84-bp insert with the in-frame stopcodon, but mRNA without the insert (occurring at approximately8 percent of the normal level in respiratory epithelium) wouldbe associated with the synthesis of normal CFTR protein. Whereasthese patients have lung disease, Chu et al. have reported thatsome people with in-frame splice skipping of exon 9 have nolung disease and only 8 to 12 percent of normal CFTR transcripts(i.e., those containing exon 9) in bronchial epithelium33. Theapparent difference between these two studies is probably dueto technical and molecular considerations.
Modulation of the clinical phenotype associated with the reducedproduction of a normal protein has been reported. Mutationsin the regulatory elements of the beta-globin gene leading toreduced amounts of normal beta chain (i.e., beta-thalassemia)are associated with milder disease than are mutations leadingto nonfunctional or absent beta chains34. With respect to thesepatients with cystic fibrosis-like lung disease and normal sweatchloride values, the differences in disease expression at theorgan level, such as abnormal airway epithelial function ascompared with normal sweat ductal function, may reflect quantitativedifferences in the requirement for functional CFTR protein,differences in tissue-specific RNA splicing, or both.
The identification of a mutation in the CFTR gene in patientswith normal sweat chloride concentrations has several implicationsfor diagnosis and treatment. First, consideration of the diagnosisof cystic fibrosis must extend to patients with suppurativepulmonary disease and normal sweat chloride values. The mutationin intron 19 may be relatively common, because it was seen inthree ethnic groups and on three different extended haplotypes.Furthermore, this mutation has been noted on 104 chromosomesreported to the Cystic Fibrosis Gene Analysis Consortium sinceour initial report,35 and it accounts for about 4 percent ofthe mutations in Ashkenazi patients with cystic fibrosis inIsrael36. Whereas this mutation is common in patients with cysticfibrosis and normal sweat chloride values, it has also beenreported in patients with borderline or raised sweat chlorideconcentrations37,38.
Second, patients with the mutation in intron 19 have low levelsof normal CFTR mRNA. Future ability to quantitate the expressionof CFTR protein in patients with cystic fibrosis and this mutationwill provide information about the levels of CFTR expressionneeded to achieve a normal phenotype in a variety of affectedepithelial sites. This information may provide a better understandingof CFTR function and serve as a guide for protein or gene therapy.
Finally, increased understanding of CFTR gene regulation, mRNAsplicing, and protein expression may give patients with themutation in intron 19 therapeutic alternatives: the up-regulationof CFTR gene expression, the inhibition of alternative splicing,and the stabilization of CFTR protein would presumably all improvethe defense mechanisms of the lung.
Note added in proof: Since submitting this manuscript, we haveidentified 6 of approximately 45 men known to have this mutationwho do not have obstructive azoospermia according to semen analysisor who have fathered children, or both, including one of ourpatients (Patient 7A in Table 1)37 (and Bowman M, Cutting G,Dreyfus D, McCoy K, Gelfand E, Bethel R: personal communication).This is higher than the expected prevalence of fertility (<1percent) in men with other mutations in CFTR.
Supported by grants (HL34322 and RR000046) from the NationalInstitutes of Health, grants (R06 and Z440) from the CysticFibrosis Foundation, and a grant (R6041L) from the AmericanLung Association of North Carolina
We are indebted to Drs. John Bloom, Rebecca Buckley, GeraldFernald, Frank Kellogg, Peter Manos, Nathan Seriss, and GeraldStrope for providing information about patients; to Lynn Bonitz,R.N., B.S., for assistance in acquiring blood samples from patients;to Dr. Lloyd Edwards for statistical advice; to Drs. MichaelSwift and William Marzluff for thoughtful discussions; to Drs.Lap-Chee Tsui and Joanna Rommens for providing phage clonesTE28 and TE24II and plasmid pTE24II6, and for valuable discussions;to Nancy Callanan, M.S., for assistance in developing the familypedigrees; to Nina Church, M.Sc., Joe Robinson, M.Sc., and BeverlyM. Wood, M.T. (A.S.C.P.), for technical assistance; and to LisaBrown for editorial assistance.
Source Information
From the Applied Technology Genetics Corp., Malvern, Pa. (W.E.H.); the Department of Medicine (L.H.B., Z.Z., J.C.O., R.C.B., M.R.K.) and the Division of Molecular Pathology (Z.Z., K.J.F., L.M.S.), University of North Carolina, Chapel Hill; Children's Hospital Medical Center, Cincinnati (T.E.B.); the Department of Pediatrics, Duke University, Durham, N.C. (A.S.); Schneider Children's Hospital-Long Island Jewish Medical Center, New Hyde Park, N.Y. (J.D.G.); and the Pediatric Pulmonary Division, Columbia-Presbyterian Medical Center, New York (L.Q.).
Address reprint requests to Dr. Knowles at the Division of Pulmonary Diseases, 724 Burnett-Womack Bldg., CB 7020, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7020.
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