Characterization of Renal Chloride Channel (CLCN5) Mutations in Dent's Disease
KATSUSUKE YAMAMOTO*,
JEREMY P. D. T. COX*,
THOMAS FRIEDRICH,
PAUL T. CHRISTIE*,,
MARTIN BALD,
PETER N. HOUTMAN§,
MARTA J. LAPSLEY||,
LUDWIG PATZER¶,
MICHEL TSIMARATOS#,
WILLIAM G VAN'T HOFF**,
KANJI YAMAOKA,
THOMAS J. JENTSCH and
RAJESH V. THAKKER*,
*MRC Molecular Endocrinology Group, Hammersmith Hospital, London, United
Kingdom ZMNH Centre for Molecular Neurobiology, University of Hamburg,
Germany Department of Paediatric Nephrology, University of Essen,
Germany §Department of Paediatrics, Leicester Royal Infirmary, United
Kingdom ||Department of Chemical Pathology and Metabolism, St Helier Hospital,
Surrey, United Kingdom ¶Children's Hospital "Jussuf Ibrahim," Friedrich-Schiller
University, Jena, Germany #Department of Paediatric Nephrology, Children's Hospital of the Timone,
Marseille, France **Department of Paediatric Nephrology, Great Ormond Street Hospital, London,
United Kingdom Department of Paediatrics, Osaka Prefectural Hospital, Osaka,
Japan Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United
Kingdom
Correspondence to Dr. Rajesh V. Thakker, Molecular Endocrinology Group,
Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford
OX3 9DU, United Kingdom. Phone: +44 1865 222043; Fax: +44 1865 222049; E-mail:
rajesh.thakker{at}ndm.ox.ac.uk
Abstract. Dent's disease is an X-linked renal tubular disorder
characterizedby low molecular weight proteinuria, hypercalciuria,
nephrocalcinosis,nephrolithiasis, and renal failure. The disease is caused by
mutationsin a renal chloride channel gene, CLCN5, which encodes a 746amino
acid protein (CLC-5), with 12 to 13 transmembrane domains.In this study, an
additional six unrelated patients with Dent'sdisease were identified and
investigated for CLCN5 mutationsby DNA sequence analysis of the 11 coding
exons of CLCN5. Thisrevealed six mutations: four frameshift deletions
involvingcodons 392, 394, 658, and 728, one nonsense mutation (Tyr617Stop),
andan A to T transversion at codon 601 that would result in
eithera missense mutation (Asp601Val) or creation of a novel donorsplice
site. These mutations were confirmed by restriction endonucleaseor
sequence-specific oligonucleotide hybridization analysisand were not common
polymorphisms. The frameshift deletionsand nonsense mutation predict
truncated and inactivated CLC-5.The effects of the putative missense
Asp601Val mutant CLC-5were assessed by heterologous expression in
Xenopus oocytes,and this revealed a chloride conductance that was
similar tothat observed for wild-type CLC-5. However, an analysis of the
mutantCLCN5 transcripts revealed utilization of the novel donor splicesite,
resulting in a truncated CLC-5. Thus, all of the six mutationsare likely to
result in truncated CLC-5 and a loss of function,and these findings expand
the spectrum of CLCN5 mutations associatedwith Dent's disease.
Dent's disease is a renal tubular disorder characterized bylow molecular
weight proteinuria, hypercalciuria, nephrocalcinosis,nephrolithiasis, and
progressive renal failure
(1,2).
The diseasealso may be associated with aminoaciduria, phosphaturia,
glycosuria,kaliuresis, uricosuria, and impaired urinary acidification,and is
complicated by rickets or osteomalacia in some patients.Thus, Dent's disease
may be considered a form of the renal Fanconisyndrome
(2,3).
The etiology of Dent's disease, and three otherphenotypically similar
disorders referred to as X-linked recessivenephrolithiasis
(4,5,6),
X-linked recessive hypophosphatemicrickets
(7), and the idiopathic low
molecular weight proteinuriaof Japanese children
(8,9,10,11,12),
has been established tobe due to inactivating mutations of a renal chloride
channelgene designated CLCN5
(11,
13,
14).
The human CLCN5 gene, which is located on chromosome Xp11.22,has a 2238-bp
coding sequence that consists of 11 exons thatspan 25 to 30 kb of genomic DNA
and encode a 746 amino acidprotein (Figure
1) (15,
16). CLCN5 belongs to the
family ofvoltage-gated chloride channel genes (CLCN1-CLCN7, and CLCKaand
CLCKb) that have approximately 12 transmembrane domains
(17,
18).These chloride channels
have an important role in the controlof membrane excitability,
transepithelial transport, and possiblycell volume
(17,
18). Heterologous expression
studies of wild-typeCLCN5 in Xenopus oocytes have revealed that the
channel, CLC-5,conducts chloride currents that are outwardly rectifying and
time-independent(19), and
similar expression of disease-associated CLC-5 mutantshas demonstrated
markedly reduced or absent currents
(9,
11,12,13,14).
Theexpression of CLC-5 in the human nephron has been shown to bein the
proximal tubule, the thick ascending limb, and the intercalatedcells of the
collecting duct (20).
Furthermore, CLC-5 has beenlocalized intracellularly to the subapical
endosomes and withthe vacuolar H(+)-ATPase, thereby suggesting that it may
havea role in the counterion transport mechanism that facilitates
acidificationwithin endosomes
(20,21).
These endosomes form part of the receptor-mediatedendocytic pathway that
transports proteins such as albumin
(20,21,22),
andthus CLC-5 dysfunction in this pathway may help provide an explanationfor
the observed low molecular weight proteinuria in Dent'sdisease
(20,21).
However, the mechanisms by which CLC-5 dysfunctionresults in hypercalciuria
and the other features of Dent's diseaseremain to be elucidated. The
identification of additional CLCN5mutations may help in these studies, and we
have pursued suchstudies in patients with Dent's disease.
Figure 1. Schematic representation of CLCN5 mutations within the framework of the
predicted topology of CLC-5, which consists of 746 amino acids
(13,
16). The correct topology of
the CLC-5 putative transmembrane domains (D1 to D13) is not established, and
this representation is based on a model reported previously (Inset)
(13). The consensus
phosphorylation and glycosylation sites are indicated by the asterisks and
branch sites, respectively. The locations of the six mutations detected by the
present study (Table 2) are
indicated by the filled arrowheads, and the mutations are illustrated in bold
and within boxes. These six mutations consist of four deletional frameshifts
(392delGT, 394delT, 658delC, and 728del23bp), one nonsense (Tyr617Stop), and
the loss of codons 601 to 645 (filled arrowheads, marked 601 and 645) due to
the novel donor splice-site mutation (gacagt to gtcagt). Of
the 52 CLCN5 mutations reported from previous studies
(6,
9,10,11,12,13,14,
26,
37,38,39),
31 are shown and eight of these have been observed to occur more than once; in
addition, two large deletions encompassing the entire CLCN5 gene
(10,
13), two small intragenic
deletions (12,
13), and four splice-site
mutations (two donor and two acceptor splice mutations)
(11,
13,
39), which are not shown, have
been reported. The two intragenic deletions would result in a loss of codons
132 to 241 (12,
13) and codons 132 to 449
(12). The two donor splice
sites would both result in a loss of codons 132 to 172
(13), and of the two acceptor
splice sites, one was shown to result in a loss of codons 173 to 241
(39) and the effects of the
other one were not characterized
(11).
Patients
Six probands who suffered from Dent's disease
(Table 1) wereinvestigated
after giving informed consent. All six of the probandshad low molecular
weight proteinuria, five had hypercalciuria,four had nephrocalcinosis and/or
nephrolithiasis, and threehad renal impairment. None of the probands suffered
from rickets.Five of the six probands were of Northern European origin and
oneproband (26/97, Table 1)
was of Japanese origin. A family historyof Dent's disease could be
established in four of the probands,while in the remaining two probands
family members were notavailable for study to establish an inherited basis
for thedisease. Venous blood samples were obtained from these six probands
andfrom three affected and six unaffected family members for mutational
analysisof the CLCN5 gene.
Table 1. Clinical and biochemical abnormalities in six male probands with Dent's
disease
DNA Sequence Analysis of the CLCN5 Gene
Leukocyte DNA was extracted and used with CLCN5-specific primers
(9)for PCR amplification,
using methods described previously
(9).The DNA sequence of PCR
products was determined by Taq polymerasecycle sequencing, using a
semiautomated detection system (ABI373XL sequencer; Applied Biosystems,
Foster City, CA) (23).DNA
sequence abnormalities were confirmed by either restrictionendonuclease
analysis or sequence-specific oligonucleotide (SSO)hybridization analysis of
the appropriate genomic PCR products
(23,24).
TheDNA sequence abnormalities were demonstrated to be absent ascommon
polymorphisms in the DNA obtained from 74 unrelated normalindividuals (34
males, 40 females), and to cosegregate withthe disorder in the available
members from three of the families.
CLCN5 mRNA Analysis
RNA was extracted from Epstein-Barr virus (EBV)-transformedlymphoblastoid
cell lines established from peripheral bloodcells of proband 15/97
(Table 1), and from three
unrelated normalindividuals. Reverse transcription (RT)-PCR was performed
usingpairs of nested CLCN5-specific primers (outer primers: forward
5'-CTTGGAGGAGTC-CAGAAGGCC-3',and reverse 5'-
GGTACCAGTTAATACAA-CATATCC-3'; inner primers:forward
5'-AGTCAGGGAGCTGATTG-CATCAC-3', and reverse
5'-CATATCCATGGTCTGTAATGTCC-3'),at an annealing temperature of
65°C for both the first andsecond rounds, which consisted of 20 and 30
cycles, respectively.The PCR products were gel-purified, and the DNA
sequences ofboth strands were determined as described
(23).
Functional Expression in Xenopus Oocytes
Wild-type and mutant CLC-5 were expressed in Xenopus oocytesas
described previously
(9,11,13,14).
A cDNA encoding the humanCLC-5 protein was inserted into the expression
vector PTLN (25).Mutations
were introduced by recombinant PCR. Capped cRNA wassynthesized using SP6-RNA
polymerase after linearization ofthe construct. About 10 ng of cRNA was
injected into manuallydefolliculated Xenopus oocytes and incubated
for 2 d at 17°C.Currents were measured by standard two-electrode
voltage-clamptechniques, using a Turbo TEC-05 amplifier (NPI, Tamm, Germany)
andpCLAMP software (Axon Instruments, Foster City, CA). Measurementswere
carried out in ND96 (96 mM NaCl, 2 mM KCl, 1.8 mM CaCl2,1 mM
MgCl2, and 5 mM Hepes, pH 7.4). The oocyte membrane washeld at the
resting potential and stepped for 500 ms to potentialsranging from -100 to
+80 mV in 20-mV steps. Currents were determinedat a membrane potential of +80
mV. Results were expressed asmean values ± SEM.
Determination of Protein Expression in Xenopus Oocytes
Oocytes were pooled after measurement and stored at -20°C.After
homogenization in 5 mM ethylenediaminetetra-acetic acid,10 mM Tris-HCl, and a
protease inhibitor mix (Complete; BoehringerMannheim, Mannheim, Germany) on
ice, the yolk platelets wereremoved by three low-speed centrifugations. From
the supernatant,the equivalent of two oocytes was dissolved in sodium dodecyl
sulfate(SDS)-Laemmli buffer and loaded onto a 6% SDS-polyacrylamidegel
electrophoresis. After separation, the proteins were blottedon polyvinylidene
difluoride membranes, and CLC-5 protein wasdetected using a rabbit polyclonal
antiserum raised againsta peptide encompassing the 13 carboxy-terminal amino
acid residuesof hCLC-5
(11,21).
Detection was carried out using a ProteinA-peroxidase-based kit (Renaissance;
DuPont, Boston, MA).
DNA sequence analysis of the entire 2238-bp coding region andexon-intron
boundaries of the CLCN5 gene from the six probands
(Table 1)with Dent's disease
revealed six novel mutations that consistedof four deletional frameshifts
(Figure 2), one nonsense
mutation,and an A to T transversion in the second base of
codon 601 (Figure 3,Table 2). The deletional
frameshifts occurred in exons 8,11, and 12, and the nonsense mutation
(Tyr617Stop) and A toT transversion both occurred in exon
10 (Table 2). Three ofthese
mutations (Tyr617Stop, 392delGT, and 728del23bp) resultedin an alteration of
a restriction enzyme site (Table
2) thatfacilitated their confirmation
(Figure 1). The other three
mutations(394delT, 658delC, and the A to T transversion in
codon 601)were not associated with altered restriction enzyme sites, andthe
method of SSO hybridization analysis
(Figure 3) was used
(Table 2).The absence of each
of these six DNA sequence abnormalitiesin 110 alleles from 74 unrelated
normal individuals establishedthat these abnormalities were not sequence
polymorphisms thatwould be expected to occur in >1% of the population.
Figure 2. Detection of mutation in exon 12 by restriction enzyme analysis. DNA
sequence analysis of the proband 26/97
(Table 1) revealed a 23-bp
deletion commencing at codon 728. This led to a frameshift that resulted in
five missense amino acids (Gly, Glu, Pro shown) followed by a termination
signal (Stop) at codon 733 (A). This deletion also resulted in the loss of an
MseI restriction enzyme site (T/TAAA). PCR amplification and
MseI digestion (B) would result in four fragments of 116, 82, 46 (not
shown), and 10 bp (not shown) from the normal sequence, but only three
products of 175, 46 (not shown), and 10 bp (not shown) from the mutant
sequence, as illustrated in the restriction map (C). This deletion was not
present in 74 normal individuals (N1 to N3 shown), indicating that it is not a
common DNA sequence polymorphism. The standard size marker (S in Panel B) in
the form of a 1-kb ladder is indicated. Similar restriction enzyme analysis
was used to confirm the 392delGT and Tyr617Stop mutations
(Table 2). The symbols denoting
the phenotype in the individual are as described in
Figure 3.
Figure 3. Detection of the mutation in exon 10 by sequence-specific oligonucleotide
(SSO) hybridization analysis. DNA sequence analysis of the affected proband
II.1 from family 15/97 (Table
1) revealed an A to T transversion in the second
base of codon 601 (A). This transversion would alter the wild-type sequence
GAC, which encodes an aspartic acid (Asp), to GTC, which
encodes a valine (Val), or to a novel donor splice site (gacagt to
gtcagt). This mutation, which did not result in an altered
restriction enzyme site, was confirmed and demonstrated to cosegregate with
Dent's disease in the family by the use of SSO hybridization analysis (B). The
affected male II.1 is hemizygous for the mutant allele, and the mother I.1 is
heterozygous for the mutant (m) and wild-type (WT) alleles. The absence of
this mutation in 74 unrelated normal individuals (N1 to N3 shown) indicated
that it was not a common DNA sequence polymorphism. Squares, male; circles,
female; open sections, unaffected; filled sections, affected.
The four deletional frameshift mutations and the nonsense mutationare
predicted to result in truncated CLC-5 that lack from 14to 346 amino acids
(Table 2). The functional
effect of suchtruncated CLC-5, which has been assessed previously
(9,
11,
13,
14),is likely to be a loss of
function, and this was confirmed bythe expression of the CLC-5 mutant due to
the 23-bp deletionalframeshift (Figure
2) at codon 728 (Figure
4). The effects ofthe A to T transversion in
codon 601 were more difficult topredict. This transversion may result in
either a missense mutation,Asp601Val, or a novel donor splice site. The
functional effectsof such missense mutations may be to abolish or markedly
reduceCLC-5 chloride conductance
(9,
11,12,13,14).
The heterologousexpression, in Xenopus oocytes, of the Asp601Val
CLC-5 mutantrevealed that Cl- conductance was unaffected and
remained similarto that of the wild-type CLC-5
(Figure 4); translation of both
thewild-type and mutant CLC-5 proteins was confirmed by Westernblot analysis
(data not shown) of the Xenopus oocyte membranes,using an antibody
directed against the carboxy terminus
(21).However, an analysis of
CLCN5 transcripts resulting from thisA to T transversion
revealed that the mutation was associatedwith a novel donor splice site
(Figure 5). This novel donor
splicesite led to skipping of the 3' portion of exon 10 that encoded
codons601 to 645. Thus, the mutant CLCN-5 transcript consisted ofthe
5' portion of exon 10 (encoding codons 512 to 600) splicedto exon 11.
If translated, this abnormal CLCN5 transcript wouldresult in 32 missense
amino acids from codons 601 to 632, followedby a termination signal (Stop)
(Figure 5,
Table 2). Such a truncated
CLC-5is likely to result in a loss of function that is similar tothose
observed by heterologous expression of the 23-bp deletioncommencing at codon
728 (Figure 4). Thus, all of
the six mutationsdetected in this study of patients with Dent's disease are
likelyto be associated with a loss of CLC-5 function.
Figure 4. Electrophysiologic analysis of Xenopus oocytes expressing human
wild-type (WT) CLC-5, the putative mutant Asp601Val
(Figure 3), and 728del23bp
(Figure 2) channels. The
Cl- currents were measured as described previously
(11,
13), and the averaged (mean
± SEM) whole cell currents measured at +80 mV in the Xenopus
oocytes injected with water control (0.34 ± 0.067), WT CLC-5 (2.54
± 0.45), the putative Asp601Val mutant (2.61 ± 0.44), and the
728del23bp mutant (0.33 ± 0.09) are shown. The Asp601Val mutant channel
had currents that were similar to that of the WT channel, whereas the
deletional mutant resulted in abolished Cl- currents. Western blot
analysis of the Xenopus oocyte membranes using an antibody directed
against a carboxy-terminal fragment
(21) identified translated
CLC-5 proteins (data not shown).
Figure 5. Novel donor splice site resulting from mutation in codon 601. The effects
of the A to T transversion at codon 601
(Figure 3) in exon 10 on CLCN5
transcripts was assessed by the detection of the illegitimate transcription
(13,
31) of exons 10 and 11, using
reverse transcription-PCR on RNA obtained from Epstein-Barr virus-transformed
lymphoblastoids of the proband from family 15/97 with Dent's disease and an
unrelated healthy (N1) individual. In the healthy individual, correctly
spliced CLCN5 cDNA was observed (A) at the expected size of 824 bp. However,
in the affected proband (15/97), an abnormally shortened CLCN5 cDNA of 691 bp
was detected. This mutant cDNA differed from the wild-type cDNA by 133 bp,
which corresponded to the size of the 3' portion of exon 10 that encodes
codons 601 to 645. DNA sequence analysis of the mutant cDNA showed that codon
600 within exon 10 had been spliced to exon 11 (B). Thus, the A to
T transversion had generated a novel donor splice site
(gacagt gtcagt), which resulted in a skipping of the
133 bp of exon 10. This is predicted to result in a frameshift with 32
missense amino acids followed by a termination signal (Stop). S, 1-kb size
marker; G, control genomic sample; Bl, blank water control.
Our results, which have identified six novel CLCN5 mutations
(Table 2),expand the spectrum
of mutations that are associated withDent's disease. All of the six CLCN5
mutations predict structuralalterations of CLC-5 that are likely to result in
a loss offunction. The total number of CLCN5 mutations now reported,
includingthe results of our present study, is 58, and these are scattered
throughoutthe channel (Figure
1) with no evidence for mutational hot spots.Furthermore, there
appears to be no correlation between themutations and phenotypes
(13,26).
Of the total 58 CLCN5 mutations,approximately 32% are nonsense mutations, 22%
are frameshiftdeletions or insertions, 2% are in-frame insertions, 4% are
donorsplice-site mutations, 3% are acceptor splice-site mutations,27% are
missense mutations, 8% are intragenic deletions, and2% are complete deletions
of the gene. The majority (>70%)are predicted to result in truncated or
absent CLC-5, whichwould lead to a complete loss of channel function. Only
fourof the mutations (30:His insertion, Gly57Val, Leu278Phe, andArg280Pro),
which are predicted not to result in truncated CLC-5and which are all located
outside the predicted trans-membranedomains, have been reported to be
associated with reduced, butnot abolished, Cl- currents
(Figure 1). Indeed, the
clusteringof such missense mutations (Leu278Phe, Arg280Pro), which are
associatedwith residual channel activity
(9,
11) in the putative loop
betweenD5 and D6 (Figure 1),
is of interest and suggests that thisloop may have a regulatory role in CLC-5
function (11). In relationto
this, our finding of the A to T transversion in codon 601,
whichpredicted a possible missense mutation Asp601Val, was intriguing.The
Asp601 is evolutionarily conserved in mouse
(27), rat
(19),and Xenopus
(28) and in other CLC members,
e.g., CLC-3 and CLC-4
(29,30).
Thus,the replacement of this negatively charged conserved Asp residuewith
the nonpolar uncharged Val residue would be expected toabolish or reduce
Cl- currents, and yet our results revealedno alteration in
Cl- conductance (Figure
4). This suggestedthat the A to T transversion
was likely to be altering CLC-5structure and function by a mechanism other
than that of a missensemutation. An examination of the DNA sequence of codons
600,601, and 602 (Figure 3)
indicated that the A to T transversionmay have resulted in
a novel donor splice site (gacagt to gtcagt)in exon 10. The
first two bases (gt) of donor splice sites areinvariant
(31), and the effects of this
mutation leading toa putative novel donor splice site were demonstrated by an
analysisof RNA obtained from the patient's EBV-transformed lymphoblastoids
(Figure 5).This novel donor
splice site, which has not been previouslyreported in Dent's disease, led to
skipping of the 3' portionof exon 10 and a truncated, and likely
inactivated, CLC-5 (Table 2).The utilization of such novel donor splice sites, whichmay be used
preferentially to the wild-type, has been previouslyobserved to occur in
association with the Laron and Lesch-Nyhansyndromes
(32,33).
The mechanisms by which a functional loss of this renal chloridechannel
(CLC-5) leads to a generalized proximal renal tubulardefect with low
molecular weight proteinuria and hypercalciuriaremain to be elucidated.
Studies of CLC-5 expression in thehuman nephron have suggested some
possibilities, as CLC-5 isexpressed at multiple sites, including the proximal
tubule,thick ascending limb of Henle, and intercalated cells of the
collectingduct (20). CLC-5 is
located intracellularly and in the earlyendosomes, which contain the vacuolar
H(+)-ATPase and whichform part of the receptor-mediated endocytic pathway
(20). Thissuggests a role for
CLC-5 as a counterion transport mechanismallowing the action of the
electrogenic H(+)-ATPase in the acidificationof the endosomes
(20,21).
Indeed, CLC-5 has been shown to havea suitable pH dependence for its activity
(34), and endosomal
acidificationis inhibited by nonspecific chloride channel blockers. A
possibleexplanation for the proximal tubular reabsorptive defects seenin
Dent's disease may be as follows: Low molecular weight proteinuriamay be due
to defective endocytosis of these proteins, whichare known to be absorbed
through the receptor-mediated endocyticpathway, and the other features
(e.g., glycosuria and aminoaciduria)may be due to defective
endosomal recycling of plasma membranetransporters responsible for the
sodium-coupled reabsorptionof these solutes
(20,21,35).
The hypercalciuria, which is nota typical feature of proximal tubular
disorders, may partlybe of the absorptive type and may be due to the
associated highnormal to elevated serum concentrations of
1,25-dihydroxyvitaminD3 that are observed in patients with Dent's
disease (36). However,the
localization of CLC-5 to the thick ascending limb of Henle,where 60% of
calcium reabsorption occurs, suggests another interestingmechanism: The
possible changes in endosomal recycling stemmingfrom CLC-5 dysfunction in
this segment may lead to altered recyclingand activities of the surface
transporters (18),
e.g., the sodium-potassium-chloridecotransporter (NKCCT), the
chloride channel (CLC-Kb), and therenal outer medullary potassium channel
(ROMK), which are involvedin generating the transepithelial potential
difference thatis necessary for paracellular calcium uptake. The role of the
Dent'sdisease-associated CLC-5 mutants
(Figure 1) in these physiologic
mechanismsof calcium homeostasis still remains to be elucidated.
Acknowledgments
We are grateful to the Medical Research Council (MRC) (UnitedKingdom) (K.
Yamamoto, J. P. D. T. Cox, P. T. Christie, andR. V. Thakker) and the Deutsche
Forschungsgemeinschaft (T. Friedrichand T. J. Jentsch) for support. J. P. D.
T. Cox is an MRC TrainingFellow.
Footnotes
Dr. Katsusuke Yamamoto and Dr. Jeremy P. D. T. Cox contributedequally to
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Received for publication September 24, 1999.
Accepted for publication January 12, 2000.
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