an intronic mutation causes long qt syndrome · linkage analysis demonstrated a logarithm of odds...

9
An Intronic Mutation Causes Long QT Syndrome Li Zhang, MD,* G. Michael Vincent, MD, FACC,*† Marco Baralle, PHD,‡ Francisco E. Baralle, MD, PHD,‡ Blake D. Anson, PHD,§ D. Woodrow Benson, MD, PHD, Bryant Whiting, BA,* Katherine W. Timothy, BS,† John Carlquist, PHD,*† Craig T. January, MD, PHD, FACC,§ Mark T. Keating, MD,¶ Igor Splawski, PHSalt Lake City, Utah; Trieste, Italy; Madison, Wisconsin; Cincinnati, Ohio; and Boston, Massachusetts OBJECTIVES The purpose of this research was to determine whether an intronic variant (T19456C) in KCNH2 is a disease-causing mutation, and if expanded phenotyping criteria produce improved identification of long QT syndrome (LQTS) patients. BACKGROUND Long QT syndrome is usually caused by mutations in conserved coding regions or invariant splice sites, yet no mutation is found in 30% to 50% of families. In one such family, we identified an intronic variant in KCNH2. Long QT syndrome diagnosis is hindered by reduced penetrance, as the long QT phenotype is absent on baseline electrocardiogram (ECG) in about 30%. METHODS Fifty-two family members were phenotyped by baseline QTc, QTc maximum on serial ECGs (Ser QTc-max), and on exercise ECGs (Ex QTc-max) and by T-wave patterns. Linkage analysis tested association of the intronic change with phenotype. The consequences of T19456C on splicing was studied using a minigene system and on function by heterologous expression. RESULTS Expanded phenotype/pedigree criteria identified 23 affected and 29 unaffected. Affected versus unaffected had baseline QTc 484 48 ms versus 422 20 ms, Ser QTc-max 508 48 ms versus 448 10 ms, Ex QTc-max 513 54 ms versus 444 11 ms, and LQT2 T waves in 87% versus 0%. Linkage analysis demonstrated a logarithm of odds score of 10.22. Splicing assay showed T19456C caused downstream intron retention. Complementary deoxyribonucleic acid with retained intron 7 failed to produce functional channels. CONCLUSIONS T19456C is a disease-causing mutation. It alters KCNH2 splicing and cosegregates with the LQT2 phenotype. Expanded ECG criteria plus pedigree analysis provided accurate clinical diagnosis of all carriers including those with reduced penetrance. Intronic mutations may be responsible for LQTS in some families with otherwise negative mutation screening. (J Am Coll Cardiol 2004;44:1283–91) © 2004 by the American College of Cardiology Foundation Hereditary long QT syndrome (LQTS) is caused by over 250 mutations in five genes, four encoding potassium channel subunits KCNQ1 (KVLQT1, LQT1), KCNH2 (HERG, LQT2), KCNE1 (minK, LQT5), KCNE2 (MiRP1, LQT6), and the cardiac sodium channel gene SCN5A (LQT3) (1). Mutations of ANKB (2) and KCNJ2 (3) have been reported to cause LQT4 and LQT7, respec- tively. Our recent reports on the ANKB and KCJN2 disor- ders (4,5) have shown that the mean QTc is within the normal range, the majority of patients have normal to borderline QT intervals, and patients in each disorder have other clinical features that are distinctly different from LQT1 to 3. Thus, classification of ANKB and KCNJ2 mutations as LQTS disorders is uncertain and remains to be fully elucidated. Genetic screens for mutations in coding regions or flanking intronic sequences of the five LQTS genes have been performed frequently during the past decade. Currently, even after improvements in sequence detection technology, a mutation cannot be identified in about 30% of LQTS families. Many of these patients exhibit characteristic T-wave patterns of the known LQTS genotypes (6), prompting us to believe that mutations in noncoding regions of the known genes may be the cause of LQTS in some of these families. One such Caucasian family from the LDS Hospital LQTS program was the stimulus for this study. In 1994, the 27-year-old proband experienced a cardiac arrest triggered by activity and excitement, with subsequent documented torsade de pointes (Fig. 1). He had no prior symptoms, but siblings had experienced recurrent syn- cope. Electrocardiogram (ECG) screening of the nuclear family showed QTc prolongation and typical LQT2 T-wave patterns (Fig. 2)(6) in several members, sug- gesting a KCNH2 mutation. Mutation analysis was performed in one affected family member, but failed to find a sequence variation in the coding sequences of any of the five known LQTS genes. The only sequence variant identified was a single nucleotide substitution, T19456C, at the 5= splice (donor) site of intron 7 in KCNH2. This substitution was not found in 320 ethni- cally matched normal control subjects. From the *LDS Hospital, Salt Lake City, Utah; †University of Utah School of Medicine, Salt Lake City, Utah; ‡International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; §University of Wisconsin, Madison, Wisconsin; Cin- cinnati Children’s Hospital Medical Center, Cincinnati, Ohio; and ¶Children’s Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, Massachusetts. Sources of funding: LDS Hospital/Deseret Foundation grant DF400, Salt Lake City, Utah; Telethon Onlus Foundation grant E1038, Trieste, Italy; NHLBI grant R01 HL60723, Madison, Wisconsin; NIH grants R01 HL46401 and SCOR HL52338, Salt Lake City, Utah. Manuscript received April 12, 2004; revised manuscript received June 3, 2004, accepted June 7, 2004. Journal of the American College of Cardiology Vol. 44, No. 6, 2004 © 2004 by the American College of Cardiology Foundation ISSN 0735-1097/04/$30.00 Published by Elsevier Inc. doi:10.1016/j.jacc.2004.06.045

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Page 1: An intronic mutation causes long QT syndrome · Linkage analysis demonstrated a logarithm of odds score of 10.22. Splicing assay showed T19456C caused downstream intron retention

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Journal of the American College of Cardiology Vol. 44, No. 6, 2004© 2004 by the American College of Cardiology Foundation ISSN 0735-1097/04/$30.00Published by Elsevier Inc. doi:10.1016/j.jacc.2004.06.045

n Intronic Mutation Causes Long QT Syndromei Zhang, MD,* G. Michael Vincent, MD, FACC,*† Marco Baralle, PHD,‡rancisco E. Baralle, MD, PHD,‡ Blake D. Anson, PHD,§ D. Woodrow Benson, MD, PHD,�ryant Whiting, BA,* Katherine W. Timothy, BS,† John Carlquist, PHD,*†raig T. January, MD, PHD, FACC,§ Mark T. Keating, MD,¶ Igor Splawski, PHD¶

alt Lake City, Utah; Trieste, Italy; Madison, Wisconsin; Cincinnati, Ohio; and Boston, Massachusetts

OBJECTIVES The purpose of this research was to determine whether an intronic variant (T1945�6C) inKCNH2 is a disease-causing mutation, and if expanded phenotyping criteria produceimproved identification of long QT syndrome (LQTS) patients.

BACKGROUND Long QT syndrome is usually caused by mutations in conserved coding regions or invariantsplice sites, yet no mutation is found in 30% to 50% of families. In one such family, weidentified an intronic variant in KCNH2. Long QT syndrome diagnosis is hindered byreduced penetrance, as the long QT phenotype is absent on baseline electrocardiogram(ECG) in about 30%.

METHODS Fifty-two family members were phenotyped by baseline QTc, QTc maximum on serial ECGs(Ser QTc-max), and on exercise ECGs (Ex QTc-max) and by T-wave patterns. Linkageanalysis tested association of the intronic change with phenotype. The consequences ofT1945�6C on splicing was studied using a minigene system and on function by heterologousexpression.

RESULTS Expanded phenotype/pedigree criteria identified 23 affected and 29 unaffected. Affectedversus unaffected had baseline QTc 484 � 48 ms versus 422 � 20 ms, Ser QTc-max 508 �48 ms versus 448 � 10 ms, Ex QTc-max 513 � 54 ms versus 444 � 11 ms, and LQT2 Twaves in 87% versus 0%. Linkage analysis demonstrated a logarithm of odds score of 10.22.Splicing assay showed T1945�6C caused downstream intron retention. Complementarydeoxyribonucleic acid with retained intron 7 failed to produce functional channels.

CONCLUSIONS T1945�6C is a disease-causing mutation. It alters KCNH2 splicing and cosegregates withthe LQT2 phenotype. Expanded ECG criteria plus pedigree analysis provided accurateclinical diagnosis of all carriers including those with reduced penetrance. Intronic mutationsmay be responsible for LQTS in some families with otherwise negative mutationscreening. (J Am Coll Cardiol 2004;44:1283–91) © 2004 by the American College ofCardiology Foundation

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ereditary long QT syndrome (LQTS) is caused by over50 mutations in five genes, four encoding potassiumhannel subunits KCNQ1 (KVLQT1, LQT1), KCNH2HERG, LQT2), KCNE1 (minK, LQT5), KCNE2MiRP1, LQT6), and the cardiac sodium channel geneCN5A (LQT3) (1). Mutations of ANKB (2) and KCNJ23) have been reported to cause LQT4 and LQT7, respec-ively. Our recent reports on the ANKB and KCJN2 disor-ers (4,5) have shown that the mean QTc is within theormal range, the majority of patients have normal toorderline QT intervals, and patients in each disorder havether clinical features that are distinctly different fromQT1 to 3. Thus, classification of ANKB and KCNJ2utations as LQTS disorders is uncertain and remains to be

ully elucidated. Genetic screens for mutations in codingegions or flanking intronic sequences of the five LQTS

From the *LDS Hospital, Salt Lake City, Utah; †University of Utah School ofedicine, Salt Lake City, Utah; ‡International Centre for Genetic Engineering and

iotechnology, Trieste, Italy; §University of Wisconsin, Madison, Wisconsin; �Cin-innati Children’s Hospital Medical Center, Cincinnati, Ohio; and ¶Children’sospital, Harvard Medical School, Howard Hughes Medical Institute, Boston,assachusetts. Sources of funding: LDS Hospital/Deseret Foundation grant DF400,

alt Lake City, Utah; Telethon Onlus Foundation grant E1038, Trieste, Italy;HLBI grant R01 HL60723, Madison, Wisconsin; NIH grants R01 HL46401 andCOR HL52338, Salt Lake City, Utah.Manuscript received April 12, 2004; revised manuscript received June 3, 2004,

cccepted June 7, 2004.

enes have been performed frequently during the pastecade. Currently, even after improvements in sequenceetection technology, a mutation cannot be identified inbout 30% of LQTS families. Many of these patientsxhibit characteristic T-wave patterns of the known LQTSenotypes (6), prompting us to believe that mutations inoncoding regions of the known genes may be the cause ofQTS in some of these families.One such Caucasian family from the LDS Hospital

QTS program was the stimulus for this study. In 1994,he 27-year-old proband experienced a cardiac arrestriggered by activity and excitement, with subsequentocumented torsade de pointes (Fig. 1). He had no priorymptoms, but siblings had experienced recurrent syn-ope. Electrocardiogram (ECG) screening of the nuclearamily showed QTc prolongation and typical LQT2-wave patterns (Fig. 2) (6) in several members, sug-esting a KCNH2 mutation. Mutation analysis waserformed in one affected family member, but failed tond a sequence variation in the coding sequences of anyf the five known LQTS genes. The only sequenceariant identified was a single nucleotide substitution,1945�6C, at the 5= splice (donor) site of intron 7 inCNH2. This substitution was not found in 320 ethni-

ally matched normal control subjects.

Page 2: An intronic mutation causes long QT syndrome · Linkage analysis demonstrated a logarithm of odds score of 10.22. Splicing assay showed T19456C caused downstream intron retention

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An analysis of 400 vertebrate genes (7) has yieldedonsensus sequences near intron-exon boundaries that aressential for correct splicing. The 10 base pair (bp) (�4 to6) including the GT at the 5= start of the intron constitute

he 5= (donor) splice site. The G and T at positions �1 and2, respectively, are highly conserved (100%), and, conse-

uently, sequence alterations at these locations are readilyecognized as mutations. Several adjacent nucleotides at theplice donor site are less well-conserved, and the nucleotidet position �6 is a T in �50% of the introns.

Intronic KCNH2 mutations in LQTS have been infre-uently reported. For example, Splawski et al. (1) re-orted only three (�4%) such mutations in an analysis of2 KCNH2 mutations. These three mutations alteredbligatory (�100% conservation) nucleotides within do-or or acceptor splice sites and, in the absence ofunctional analysis, were assumed to alter transcriptplicing. By contrast, T1945�6C changes a less highlyonserved (�50%) intronic nucleotide of a donor spliceite and could not be assumed to alter transcript splicing.herefore, to determine whether this is a disease-causingutation or a simple polymorphism, we expanded the

edigree, used enhanced ECG and pedigree criteria forhenotyping, tested the association of genotype withhenotype using linkage analysis, and elucidated theplicing effect and molecular mechanism of the1945�6C through well-established cellular splicing

ssay and heterologous expression studies.

Abbreviations and AcronymsEx QTc-max � maximum QTc value during the

exercise test, either exercise or recoveryLQTS � long QT syndromeLQT2 � second described variant of LQTS, due

to mutations of the KCNH2 (HERG)gene

RT-PCR � reverse transcription-polymerase chainreaction

Ser QTc-max � maximum QTc value among serialelectrocardiograms during follow-up

igure 1. Electrocardiogram monitor strip showing torsade de pointes re

ears.

ETHODS

henotyping. A five-generation pedigree was constructed,nd 52 blood-related family members were evaluated byistory and ECG (Fig. 3). History evaluation includedQTS-related syncope, cardiac arrest, and sudden death.lectrocardiogram analysis was from supine, resting ECGs,

nd included baseline QTc interval (Bazett’s formula) and-wave pattern (6) on all subjects. During follow-up, webtained ECGs at yearly clinic visits and at other times asndicated by clinical needs. Twenty-two members receiveddditional ECG evaluation, either bicycle exercise testing (n

18) and/or serial ECGs (n � 19) (�2 ECGs/person).rom these, the maximum QTc during exercise or recovery

Ex QTc-max) and on serial ECGs (Ser QTc-max) wasvaluated. None of the patients was on beta-blockers at timef initial ECG data acquisition, and the phenotyping waserformed without knowledge of genotype.Family members were determined to be phenotypically

ffected if they met one of the following criteria: 1) aiagnostic QTc interval (�470 ms in males or �480 ms inemales) (8) with or without the presence of an LQT2-wave pattern, on baseline, Ex QTc-max, or Ser QTc-maxCGs; 2) a QTc of 460 ms with an LQT2 T-wave pattern

f other family member(s) met the diagnostic criterion 1;nd 3) identification as an obligate gene carrier on familyedigree; members could be classified as an obligate genearrier if offspring plus other blood relative(s) showed aefinite LQT2 phenotype (Fig. 3).enotyping. Informed consent (approved by and in accor-

ance with the guidelines of the Institutional Review Boardt LDS Hospital of Intermountain Health Care, Inc.) wasbtained from all participants before genetic testing.DNA was collected from buccal swabs and extracted

sing the QIAamp DNA Mini Kit (Qiagen, Valencia,alifornia). The region containing the T1945�6C intronic

ariant was amplified at LDS Hospital using previouslyublished oligonucleotides (9). Samples were sequenced byRUP Laboratories (Associated Regional University Pa-

hologists, Salt Lake City, Utah) using the Applied Biosys-ems 377 (Foster City, California) deoxyribonucleic acid

d from the proband during resuscitation from cardiac arrest at age of 27

corde
Page 3: An intronic mutation causes long QT syndrome · Linkage analysis demonstrated a logarithm of odds score of 10.22. Splicing assay showed T19456C caused downstream intron retention

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1285JACC Vol. 44, No. 6, 2004 Zhang et al.September 15, 2004:1283–91 Intronic Mutation Causes LQTS

igure 2. Examples of typical LQT2 T-wave patterns in the affected family members. (a) Low bifid T waves in the proband, QTc 500 ms. (b and c) Subtleifid T waves in two other affected members, QTc of 500 ms and 480 ms, respectively. Overall, 87% of T1945�6C mutation carriers presented typical

QT2 T-wave patterns on baseline electrocardiogram.
Page 4: An intronic mutation causes long QT syndrome · Linkage analysis demonstrated a logarithm of odds score of 10.22. Splicing assay showed T19456C caused downstream intron retention

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1286 Zhang et al. JACC Vol. 44, No. 6, 2004Intronic Mutation Causes LQTS September 15, 2004:1283–91

equencer with Big Dye Terminator chemistry. The resultsere read by a single investigator blinded to the phenotypeata.tatistical and linkage analyses. The QTc on baselineCG, the Ser QTc-max, and the Ex QTc-max were

ompared between affected and unaffected members usinghe Mann-Whitney test. The phenotype-genotype agree-ent was measured as a Kappa statistic. The statistical

nalyses were performed using SPSS 10.1 for WindowsSPSS Inc., Chicago, Illinois). Using KCNH2-T1945�6Cs an allele, we performed linkage analysis. A two-pointogarithm of odds (LOD) score was calculated usingIPED software (Rockefeller University, New York, Nework) (10), assuming an allele frequency of 0.1% and diseaseenetrance of 95%.unctional splicing assays. Normal and mutated (T1945�C change) sequences of the KCNH2 gene were amplifiedrom genomic deoxyribonucleic acid of an individual het-rozygous for the mutation using forward primer 5=-gaattccatatggaatcactgcacctgtcagtgc-3= and reverse primer=-ggaattccatatggaattgtacatctgcgctccagc-3=. The amplifica-ion generated a fragment that contained exon 7 with 248p of 5= and 202 bp of 3= intronic flanking sequences. Bothligonucleotides carry an Nde1 restriction enzyme site inheir 5= ends that was used to clone the product into aodified version of the alpha-globin-fibronectin EDBinigene (11). The splicing assay was performed by trans-

ecting 0.5 �g of each minigene plasmid into 3 � 105 He Laells with Qiagen Effectene transfection reagents. Ribonu-leic acid extraction and reverse transcription-polymerasehain reaction (RT-PCR) analysis were performed as pre-iously described (11). All of the fragments shown in Figure

(panel B) were cloned and sequenced to confirm theirdentity and exclude polymerase errors.

The parental U1 snRNA was pG3U1 (WT-U1), aerivative of PHU1 (12). The variant A�G U1 snRNA,

igure 3. Pedigree structure of the multigenerational family demonstrates thedigree was modified to protect patient and family privacy.

omplementary to the nucleotide change observed in the E

atient, was created by replacing the U1 snRNA 5= se-uence between the sites Bcl1 and BglII in the pG3U1lasmid with the mutant oligonucleotides. The effect of1945�6C mutation on ribonucleic acid processing was

tudied using a well-documented hybrid minigene system11,13,14).unctional expression assays. To study the effects of1945�6C, human embryonic kidney (HEK-293) cellsere transiently transfected with either KCNH2-WT

DNA or KCNH2 complementary deoxyribonucleic acidontaining T1945�6C and intron 7 (KCNH2-T�C).reen fluorescent protein (GFP) was cotransfected with

ach complementary deoxyribonucleic acid as a marker foruccessful transfection. The KCNH2-WT cDNA expres-ion vector has been described previously (15), and GFP wasxpressed with the mammalian expression vector pRK-5Clonetech, Mansfield, United Kingdom). The KCNH2-�C expression vector was generated by amplifying1945�6C genomic deoxyribonucleic acid, restricting atnique Bgl II and Xho I restriction sites in exons 7 and 8,nd subsequently ligating into the WT expression vector.ll amplified sequences were confirmed to be error-free

hrough Big Dye sequencing. Current levels were measuredrom GFP-expressing cells 24 to 48 h after transfectionsing tight-seal whole-cell voltage clamp recording tech-iques. Peak currents were assessed as peak tail current (Itail)Fig. 5, arrows) evoked by depolarizing cells from a holdingotential of �80 mV to 20 mV for 5 s followed byepolarization to �50 mV for 2.85 s. Details for both theransfection and recording techniques have been describedn detail previously (16).

ESULTS

henotyping. Phenotype was characterized in the 52lood-related family members based on medical history,

ociation between the T1945�6C mutation and the LQT2 phenotype. The

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CG assessment, and pedigree analysis. Twenty-three in-

Page 5: An intronic mutation causes long QT syndrome · Linkage analysis demonstrated a logarithm of odds score of 10.22. Splicing assay showed T19456C caused downstream intron retention

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1287JACC Vol. 44, No. 6, 2004 Zhang et al.September 15, 2004:1283–91 Intronic Mutation Causes LQTS

ividuals were considered affected and 29 unaffected (Fig.). The QTc on baseline ECG, Ex QTc-max, and the SerTc-max were all significantly longer in affected versus

onaffected members (Table 1). A total of 87% of affectedembers presented typical LQT2 patterns in baseline ECG

Table 1, Fig. 2). No significant gender differences wereound in the QTc interval and the T-wave patterns amongffected members.

A total of 65% (15 of 23) of affected members wereorrectly diagnosed by baseline QTc (503 � 46 ms, range60 to 610 ms) and the presence of typical LQT2 T-waveatterns in 15 of 15. The other 35% (8 of 23) had a QTc of49 � 16 ms (420 to 460 ms) and were classified asuncertain,” as these values overlap with those of normals.he LQTS diagnosis was confirmed in six of the eight by

ollow-up assessment: Ser QTc-max (3 � 1 ECGs/personver 1.3 � 1.9 years of 467 � 10, range 460 to 480 ms), andx QTc-max (482 � 11 ms, range 470 to 490 ms) (Fig. 4).ll six met diagnostic criterion #2, typical T-wave pattern

oupled with a QTc of 460 ms or greater, and most metriterion #1. The remaining two members (II-9 and III-21)Fig. 3), an 86-year-old female and her daughter, both with

igure 4. Diagnostic value of Ex QTc-max in patients with a borderline bbaseline QTc of 440 ms during sinus bradycardia. An Ex QTc-max of 4

esting revealed he was a T1945�6C mutation carrier.

Tc of 460 ms and absence of an LQT2 T-wave pattern,

ere identified as obligate mutation carriers by pedigreenalysis. Altogether, therefore, 23 affected members weredentified, 21 by the expanded ECG phenotype criteria and

as obligate carriers by pedigree analysis.Sudden death of uncertain cause had occurred in 8.7% (2

f 23) before the LQTS diagnosis in the family, an8-year-old male (II-3) (Fig. 3) and a 59-year-old femaleIII-16) (Fig. 3). Four (17%) affected members had syncope,nd one had resuscitated cardiac arrest (IV-20) (Fig. 1),efore treatment with beta-blockers.enotyping. Sequence analyses revealed 22 T1945�6C

arriers and 29 noncarriers. An obligate carrier (II-1) (Fig.) was phenotyped as affected by baseline ECG (QTc 490s with an LQT2 T-wave pattern), but he died at age 85

efore genetic testing was available.enotype-phenotype correlation: advantage of the ex-

anded QTc criteria and pedigree analysis. The1945�6C variant cosegregated with affected status. Link-

ge analysis yielded a maximum two-point LOD score of0.22 at recombination fraction � � 0.0, indicating odds of1010 that the T1945�6C is linked to the disease

henotype.

e QTc interval. A 23-year-old male asymptomatic family member showsat 9 min of the bicycle exercise test identifies his affected status. Genetic

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Phenotype-genotype correlation showed concordance in

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1288 Zhang et al. JACC Vol. 44, No. 6, 2004Intronic Mutation Causes LQTS September 15, 2004:1283–91

igure 5. (A) Schematic representation of the KCNH2 exon 7 minigene construct. The human KCNH2 exon 7 was cloned into the Nde I site of the-globin fibronectin EDB minigene (black shaded and white boxes, respectively, with intervening sequences [IVS] shown as thin lines). The intronicutation T1945�6C is shown with exonic sequence in upper case and intronic sequence in lower case. The superimposed arrows indicate the primers

sed in the reverse transcription-polymerase chain reaction (RT-PCR) assay. (B) Agarose gel electrophoresis of the RT-PCR products generated from theplicing assay: T1945�6 (WT) generates a single band of approximately 637 base pairs (bp) (lane 2) while T1945�6C generates three different sized bandslane 3), whose specific identity was established by cloning and sequencing. On the right of the gel, there is a graphic representation illustrating the DNAontent of each band. The 239 bp band contains the fibronectin exons, the 637 bp band contains the fibronectin exons with exon 7 inserted between them,nd the 1,302 bp band contains the fibronectin exons, exon 7, as well as the intron 3= to this exon. Note that the mutation causes intron retention and somexon skipping. The modified snRNA (A�G-U1) rescues this splicing defect (lane 4). (C) Upper panel: Base pairing between U1 snRNA (WT-U1) andhe 3= end of KCNH2 exon 7. The nucleotide change T1945�6C reduces the base pairing between the RNA and the WT-U1 snRNA. Lower panel: Theariant snRNA (A�G-U1) modified to complement the nucleotide change seen in the patient’s pre-mRNA, and restored the appropriate base pairing.

Page 7: An intronic mutation causes long QT syndrome · Linkage analysis demonstrated a logarithm of odds score of 10.22. Splicing assay showed T19456C caused downstream intron retention

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1289JACC Vol. 44, No. 6, 2004 Zhang et al.September 15, 2004:1283–91 Intronic Mutation Causes LQTS

1 of 23 carriers and 29 of 29 noncarriers (Kappa � 0.96).wo obligate carriers were identified by pedigree analysis so

hat the combination of expanded ECG phenotyping cri-eria plus identification of obligate carriers revealed all 23utation carriers (Fig. 3).unctional effect of the intron 7 mutation. The effect of1945�6C on RNA processing was studied using aell-tested and documented hybrid minigene system

11,13,14) (Fig. 5, panel A). After transfection andxpression of the construct in He La cells, the mRNAerived from the minigene was analyzed for the KCNH2xon 7 splicing pattern by RT-PCR. As shown in Figure

(panel B, lanes exon 7 WT and exon 7 T�C), the1945�6C dramatically affected pre-mRNA processing.

n contrast with wild-type, T1945�6C processing re-ulted in three species of RNA that were unambiguouslydentified by cloning and complete sequencing. The

ajor band (1,302 bp) shows retention of the intronicequences downstream of the KCNH2 exon 7 in theature messenger ribonucleic acid. A lower level of

ormally spliced mRNA (637 bp) is also present as wells an additional faint band (239 bp) that results from thekipping of the exon.

Previous studies on a similar mutation in the NF-1 gene14) showed simple exon skipping but not intron retention.

owever, our hypothesis was that the same basic molecularechanism was involved, that is, the lack of recognition of

he 5= splice site in the mutant gene due to an imperfect baseairing with the U1 snRNP that is required for normalntron-exon splicing. Figure 4, panel C, is a schematicllustrating the decrease in complementarity between the

utant and U1 snRNA when compared with wild-typeequence. To functionally test this hypothesis, we simulta-eously introduced into the cells the T1945�6C minigeneith a variant U1 snRNA complementary to the mutation

Fig. 5, panel C). This resulted in the almost completeescue of the correct splicing pattern (Fig. 5, panel B, lanexon 7 T�C � U1 A�G).

The effect of intron retention on KCNH2 current wasxamined through heterologous expression of KCNH2-WTnd KCNH2-T�C cDNA in HEK-293 cells. Representa-ive current tracings from KCNH2-WT or KCNH2-T�Cransfected cells are shown in Figure 6 (upper and lowerracings, respectively). All recordings from cells transfectedith KCNH2-WT cDNA produced normal KCNH2 cur-

ents with a mean peak Itail of 938.3 � 157.6 pA (n � 15)hile none of the cells transfected with KCNH2-T�C

omplementary deoxyribonucleic acid produced currents

able 1. Electrocardiographic Findings in Phenotypically Affected

No.Age(yrs)

Gender(F/M)

QB

ffected 23 34 � 26 12/11 48naffected 29 35 � 22 14/15 42

Tc in ms. *p � 0.01 affected versus unaffected individuals using Mann-Whitney t

bove the basal noise level (7.9 � 2.6 pA; n � 20). Thus, T

omplementary deoxyribonucleic acid with a retained intronfailed to produce functional channels.

ISCUSSION

hese findings demonstrate that the T1945�6C sequencehange in intron 7 of KCNH2 is a mutation that causesQTS with a typical LQT2 phenotype. The functionalellular splicing assay demonstrated that T1945�6C pro-uces a major transcript that retains intron 7. Two minorranscripts include a WT transcript and a transcript result-ng from skipping of exon 7. Protein synthesized from theranscript containing intron 7 would be expected to undergo

translational frame-shift at amino acid residue 649 andrematurely truncate 21 amino acid residues further down-tream. This would drastically alter the protein’s 6th trans-embrane domain, completely delete the C-terminus, andost likely render the protein nonfunctional. Whole cell

ecordings from HEK-293 cells transfected with KCNH2T or T�C complementary deoxyribonucleic acid support

his conclusion. Although speculative, coassembly of mutantnd WT subunits could further inhibit the activity of theesidual correctly spliced protein as well as protein synthe-ized from the other allele. Our results also demonstratedhat the impaired splicing of T1945�6C was, at least inart, due to imperfect U1 snRNP recognition of the mutant

Unaffected Family Members

atne Ser QTc-max Ex QTc-max

Typical LQT2T Waves

48* 508 � 48* 513 � 54* 87%*20 444 � 11 448 � 10 0

igure 6. Representative tight-seal whole-cell voltage clamp recordingsrom HEK-293 cells transfected with either KCNH2 or KCNH2 T�CDNA. The upper trace illustrates the voltage clamp protocol while the

iddle and lower tracings show WT and T�C currents, respectively. Tailurrents are denoted by the arrows. Note the complete absence of KCNH2ail current in the KCNH2-T�C tracing. The inset shows a series ofepolarizations from �70 to 40 mV for a cell expressing WT channels.

and

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he scale bar applies to the single traces and is 200 pA by 500 ms.

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1290 Zhang et al. JACC Vol. 44, No. 6, 2004Intronic Mutation Causes LQTS September 15, 2004:1283–91

= splice site. This conclusion is supported by the fact thatn artificial variant of the U1 snRNA, complementary to theutant sequence, was able to rescue the correct pre-essenger ribonucleic acid processing.Mutations in the GT splice donor and AG splice accep-

or sites in LQTS genes have been infrequently reported1,17–20). Because of the high conservation of these con-ensus sequences, such mutations have been assumed tolter splicing, but, until now, this hypothesis has remainedntested. By expanding the genotypic and phenotypic anal-ses performed in the proband to include a large kindred of2 individuals, we show that T1945�6C cosegregrates withhe LQT2 phenotype. Absence of this nucleotide substitu-ion in 320 ethnically matched control individuals furtheruggests that it is disease-causing. We have also clearlyefined the defective splicing pattern of T1945�6C androvided a mechanism for the molecular dysfunction, mak-ng this study the first demonstration that incorrect intron-xon splicing of pre-messenger ribonucleic acid transcriptsay result in LQT2. Furthermore, as T1945�6C is a less

ighly conserved (�50%) nucleotide position than eitherhe obligatory GT or AG of the donor and acceptor spliceites, this study clearly indicates that mutations of intronicucleotides other than invariant splice donor and acceptorites can cause LQTS. Of the 30% of LQTS families inhich no mutation has been found with exon screening, theajority have characteristic T-wave patterns of the known

enotypes (6). Consequently, in light of our results, it iseasonable to suggest that some of these families may haventronic mutations in the known LQTS genes rather thanefects in unidentified genes.At present, the function of introns is less well-understood

han that of exons. Introns are, on average, much larger thanxons and constitute about 25% of the human genome (21).hey may harbor promoters or other regulatory modules

hat modify gene expression and might influence penetrancend expressivity of phenotypes (13,22–28). Thus, it may behat, in some cases, intron variations contribute to thehenotypic heterogeneity of LQTS (8,29,30).The other important finding of this study is the high

ccuracy of diagnosis of affected family members using thenhanced QTc and T-wave morphology ECG criteria plusedigree analysis. The phenotypic heterogeneity and re-uced penetrance of the QT phenotype in LQTS (8,29,30)an impede accurate clinical diagnosis, leading to a missediagnosis in about 30% of LQTS patients by baseline ECG.he enhanced ECG criteria and pedigree analyses used in

his study correctly identified all the T1945�6C carriers,ncluding those who had baseline normal-to-borderline

Tc intervals of 400 to 460 ms, values that overlap those oformals. Large scale studies regarding the diagnostic valuef these enhanced criteria in LQTS patients with nondiag-ostic QTc intervals are currently underway. In addition tohe usefulness of typical LQT2 T-wave patterns for in-reased diagnostic accuracy, these patterns are also very

ccurate for genotype prediction (6). The high accuracy

rovides a strategy for deoxyribonucleic acid screening byndicating which gene to first examine, thus reducing

onetary and time costs.

cknowledgmentshe authors are grateful to Jay W. Mason, MD, and Robert. Lux, PhD, for their support in genotyping some familyembers.

eprint requests and correspondence: Dr. G. Michael Vincent,epartment of Medicine, LDS Hospital, 324 10th Avenue, Suite

30, Salt Lake City, Utah 84103. E-mail: [email protected].

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