(Hypertension. 1995;25:6-13.)
© 1995 American Heart Association, Inc.
Articles |
From INSERM U358, Hôpital St Louis (T.N., M.J., C.J., M.L.), and INSERM U36, College de France (T.N., A.B., X.J., P.C., F.S.), Paris, France.
Correspondence to Florent Soubrier, MD, PhD, INSERM U36, College de France, 3 rue d'Ulm, 75005, Paris, France.
| Abstract |
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Key Words: hypertension, essential genetics sibling relations rat, inbred SHR
| Introduction |
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Another approach to determine genetic loci that could be involved in hypertension consists of the isolation of new candidate genes that are differentially expressed in target tissues from hypertensive and normotensive rat strains. The example of the SA gene illustrates how the mapping of such candidate genes can be combined with genetic linkage studies of blood pressure to obtain new information on the loci potentially involved in the disease. SA is a gene of unknown function identified in screening for genes with increased expression in the kidney of the spontaneously hypertensive rat (SHR) compared with the kidney of the normotensive Wistar-Kyoto rat at the early hypertensive stage.10 The SA gene exhibits a 10-fold difference in expression in the target tissue from the two strains and is also expressed in the liver. The gene was mapped to rat chromosome 1,11 12 and SA or genetic markers of the same region were shown to be linked to blood pressure levels in a number of different crosses. These include crosses involving the SHR,13 14 15 the stroke-prone SHR,11 16 and the Dahl salt-sensitive hypertensive rat.17
These observations by independent groups suggest that SA is a likely candidate for a causative gene of hypertension in some models of hereditary hypertension in the rat. Since these hypertensive rat strains share many pathophysiological characteristics of the human disease,18 it is of interest to examine the possible relation of the SA gene to essential hypertension in humans. Alternatively, the SA gene in the rat may be linked to another locus involved in blood pressure regulation. Therefore, it is also of interest to test other markers that could be in the region of conserved synteny around the human SA gene.
To assess these points, we first isolated and sequenced a human SA cDNA that was cloned from a liver cDNA library. This was used to screen for a human yeast artificial chromosome (YAC) clone containing the SA gene. A highly polymorphic microsatellite marker was isolated from the YAC and mapped to human chromosome 16 by linkage. This marker and other microsatellites from the same region of chromosome 16 were examined for linkage to hypertension in affected sib pairs. A frequent polymorphism was detected by single-strand conformation polymorphism (SSCP) analysis in one of the introns of the SA gene, and this was examined for association with the disease by comparison of genotype and allele frequencies in hypertensive patients and normotensive control subjects. This study illustrates the methodology that can be applied to evaluate novel candidate loci in human hypertension after identification from studies of rat models.
| Methods |
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Polymerase Chain Reaction Amplification
We performed polymerase chain reaction (PCR) amplifications
using various primers under the following conditions: 2.5 ng/µL of
genomic DNA, 0.5 nmol/L of each primer, 1.5 mmol/L MgCl2,
0.02 U/mL of Taq polymerase (Boehringer-Mannheim), 1x
Taq polymerase buffer provided by the supplier, and 63
nmol/L of dNTPs in 10 or 20 µL of reaction mixture. PCR was started
with the initial denaturing step at 96°C for 4 minutes, followed by
35 cycles, each of which consisted of 1 minute at 94°C, 1 minute at
annealing temperatures depending on primers, and 10 seconds at 72°C.
Cloning of the Human SA cDNA
A human liver cDNA library constructed in
gt11 was screened
with a fragment of rat SA cDNA as a probe. This was made by reversed
transcription of total RNA extracted from the rat kidney. Primers
(5'-ATGGCAATGTTACTTCGTG-3', 5'-AGGATGTCTTTCTGGGTCA-3') were designed
based on the published sequence of rat SA cDNA to amplify a 460-bp DNA
fragment positioned between nucleotide 289 and 749.10
Reverse transcription was done for 60 minutes at 37°C in a reaction
mixture containing 3 µg of total RNA, 25 pmol of the designed
primers, 25 nmol dNTPs, and 200 U Moloney-murine leukemia virus reverse
transcriptase (Gibco BRL). PCR amplification was then performed on the
synthesized cDNA with the same primers. The amplified fragment was
purified on agarose gel and sequenced.
The cDNA library was screened following a standard protocol.20 Hybridized replica filters were washed in 1x SSC/0.1% sodium dodecyl sulfate (SDS) at 55°C. One positive clone was identified, which was subcloned into pBluescript (Stratagene) and sequenced.
Detection of SSCP
Two introns were identified in the SA gene by PCR amplification
of human genomic DNA with primers obtained from the cDNA sequence
(introns a and b in Fig 1). Primers for the SSCP study were designed
based on sequences of the introns and of their flanking exons of the SA
gene to obtain overlapping fragments (Table 2). PCR
fragments were labeled either with 32Pend-labeled primers
or with
[32P]dCTP included in the reaction mixture.
Fragments that were greater than 300 bp in length were digested with
restriction enzymes listed in Table 2 to maximize the probability of
detecting SSCP.21 22 Samples were analyzed on
nondenaturing 6% polyacrylamide/methylene-bis-acrylamide (49:1) gel
with or without 5% glycerol as described previously.21
Forty-seven unrelated individuals were screened to search for SSCP.
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Isolation of a Microsatellite Marker at the SA Locus
The Centre d'Etude du Polymorphisme Humain (CEPH) (Paris,
France) YAC library23 (23 700 clones, 8 haploid genome
equivalent) was screened with primers used in the SSCP study. One
positive clone, 933F8 (insert size, 1.1 megabase [Mb]), was
identified, and DNA was extracted in agarose plugs. The YAC was
subcloned into cosmids by constructing a cosmid library in the triple
helix vector (Stratagene) using Sau3AI partially digested
clone DNA. The first screening of the library was done with
32P-labeled human genomic DNA. Positive colonies were
picked up and were secondarily screened with
32P-end-labeled oligomers (CA)15 and
(GA)15. Hybridization with the oligomers was performed in
6x SSC, 0.5% SDS, and 5x Denhardt's solution at 55°C, and filters
were washed in 0.1x SSC/0.1% SDS at 55°C or 60°C. Nine positive
clones were identified and were digested with a combination of
Alu I, Hae III, and Rsa I for plasmid
library construction. After screening of these libraries with
32P-labeled (CA)15 and (GA)15,
positive clones were picked up and sequenced.
Genotype Characterization
Primers and annealing temperatures for microsatellite markers
are listed in Table 3. PCR reactions were made with
32P-labeled primers, and the products were analyzed on
standard sequencing gels. SSCP analysis (as described above) or
allele-specific oligonucleotide hybridizations were performed for
characterization of a single-nucleotide substitution in the SA gene
(cytosine to thymidine substitution in intron b). Allele-specific
oligonucleotide hybridizations were done as follows. Based on the
sequence data of homozygotes of the two alleles, two oligomers,
5'-ATAATCATAAGGAGACTG-3' (reverse strand) and 5'-GTCTCCTCATGATTA-3',
were designed for alleles 1 and 2 (see Fig 3), respectively. PCR
products were denatured in 0.4N sodium hydroxide, and half of the
volume was separately spotted on two membranes. Membranes were then
neutralized in 2x SSC and cross-linked with UV light. Each membrane
was hybridized in 7% polyethylene glycol/10% SDS at 42°C for 3 to
12 hours, with one of the two oligomers end labeled with
[32P]ATP. At the end of hybridization, membranes were
rinsed in 1x SSC/0.1% SDS at room temperature and once for 10 minutes
either at 50°C for allele-1 or at 45°C for allele-2 oligomer. After
autoradiography, membranes were dehybridized in boiling water and
rehybridized with the other oligomer to avoid misreading of genotypes.
Genotypes obtained by SSCP and by allele-specific oligonucleotide
hybridization were in complete accordance in 48 individuals screened by
both methods.
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Statistical Analyses
We performed two-point and multipoint linkage analyses with
LINKAGE24 using the CEPH database version 6.
Linkages between hypertensive state and selected markers in sibships
were analyzed with the affected sib pair method described by Lange
using Hodge's weighting for different sibship sizes25 26
and by a method developed by C. Amos as implemented in the program
SIBPAL.27 The SIBPAL program
provides estimates of the identity-by-descent (IBD) probabilities for
affected sib pairs (ie, the probability that affected siblings receive
the same allele from either parent), taking into account all
information on the markers in each family, including information on
genotypes of parents and unaffected siblings when these are available.
In the presence of linkage, we expect that the IBD probability will be
greater than 0.5; otherwise it should be equal to 0.5. Estimates and
SEMs of the IBD probabilities were obtained with the SIBPAL
program. For a biallelic marker, comparisons of genotype distributions
and of allelic frequencies were assessed by the
2 test
with 2 and 1 df, respectively. Deviation from Hardy-Weinberg
equilibrium was tested by the
2 test with 1
df.
| Results |
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Localization of the SA Gene and Identification of Flanking
Microsatellite Markers
Microsatellite markers were obtained from YAC clone 933F8
containing the SA gene as described above. Four distinct dinucleotide
repeats [3 (CA)n and 1 (GA)n] were
identified, and one of these (p4546) was further characterized. Primers
for genotyping p4546 were designed to amplify a 108-bp fragment
constituting the repeat (Table 3). Members of 12 families from the CEPH
panel were characterized for this marker, and lod scores were
calculated for markers in the CEPH database. Several markers in the
region of chromosome 16p13.11-12.3 showed highly significant evidence
of linkage with p4546. The localization of the 933F8 YAC clone to
chromosome 16p was confirmed by fluorescent in situ hybridization (data
not shown). The placement of p4546 was estimated with respect to
chromosome 16 markers in the recent Généthon map by
multilocus linkage analysis.29 These results showed
that the SA gene lies in the interval spanned by markers AFM165yb6
(D16S410) and AFM191wb10 (D16S412) with odds greater than 1000:1 (Fig 2).
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SSCP Polymorphism of the SA Gene
Two introns were identified by PCR amplification of human genomic
DNA with primers selected from the sequence of the human SA cDNA (see
Fig 1). The introns were located at residues 406 and 1119 of the cDNA
sequence (at points a and b in Fig 1) and were 1323 bp and 969 bp in
length, respectively. Primers for the SSCP study were designed based on
sequences of the introns and the flanking exons (Table 2). Among 11
fragments studied, one from intron b exhibited a frequent polymorphism
(Fig 3A). Direct sequencing of homozygotes for the two
alleles indicated that residue 79 of intron b was thymidine in allele 1
(the upper band on SSCP gel) instead of cytosine in allele 2 (the lower
on SSCP gel) (Fig 3). The allele frequencies of this polymorphism
(designated CT79) in 292 normotensive whites of French origin were 0.45
and 0.55 for alleles 1 and 2, respectively. Although we found four
other variants in the two introns, these were not analyzed further
because in each case the frequency of one of the two alleles was less
than 5%.
Eighty parents of CEPH reference families were genotyped for the CT79 polymorphism using SSCP gels. Members of 17 informative families were characterized for CT79, and no recombination events were observed with p4546, which confirms that the two markers detect the same locus.
Linkage and Association Studies
Genotypes in the hypertensive sibships were characterized for the
SA microsatellite p4546 and for three other Généthon
microsatellite markers (AFM113xa9, AFM165yb6, and AFM191wb10) from the
region that spans the segment of chromosome 16 containing the gene (Fig 2).29 As shown in Table 4, no significant
excess of the identity-by-state statistics were observed for the four
microsatellites. An association study was also performed by comparing
genotype and allele frequencies for polymorphism CT79 in hypertensive
patients and normotensive control subjects; no significant differences
were observed between the two populations (Table 5). The
results were not changed when comparisons were made between control
subjects and subgroups of hypertensive subjects stratified by one of
the following criteria: SBP greater than 170 mm Hg and DBP greater
than 100 mm Hg, age of onset of hypertension younger than 35 years, or
body mass index less than 25.0 kg/m2 (results not shown).
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The genotype frequencies in the normotensive control population were
found to deviate significantly from Hardy-Weinberg expectations
(
2=9.77, P<.002). Since the
normotensive control subjects were selected from two different regions
of France, we further subdivided this population according to the city
of origin (Table 5). The genotype frequencies were similar in the two
groups, and both exhibited a deficit in heterozygotes compared with
that expected under Hardy-Weinberg equilibrium (Paris:
2=5.61 [P<.02]; Nancy:
2=4.72 [P<.05]). Although
the reasons for this deviation remain unclear, genotype and allelic
frequencies were not significantly different from the hypertensive
sample for either control group. The hypertensive population showed no
deviation from Hardy-Weinberg expectations.
| Discussion |
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To investigate the involvement of the gene in human hypertension, we looked for polymorphic nucleotide sequences by the SSCP method in a group of selected hypertensive subjects. Although we did not identify all of the introns in the gene, we found several polymorphisms in the two introns that we studied, and the most informative was used for a cross-sectional study based on a large series of hypertensive patients and normotensive control subjects. The most striking difference between the hypertensive and normotensive populations was the finding of significant deviations from Hardy-Weinberg equilibrium at the CT79 polymorphism, located in intron b, in the normotensive group. As shown in Table 5, this is due to a deficiency of heterozygotes in normotensive subjects compared with the number expected under Hardy-Weinberg equilibrium. Interestingly, this was observed in normotensive populations from both Paris and Nancy. Because a deficiency of heterozygotes is a known consequence of population admixture, our observation could be due to a previously undetected source of heterogeneity in these samples. However, this has not been observed with many markers previously characterized in the same control samples,19 30 31 and we cannot exclude the possibility that the SA locus has an effect on blood pressure that leads to a decrease in heterozygote frequency in the normotensive samples. If this effect exists, it is not strong enough to produce a significant difference in genotype distributions observed in the hypertensive and normotensive samples that we have studied.
To perform a linkage study with hypertensive families, we isolated a YAC clone containing the SA gene and subcloned it into cosmids to identify highly informative multiallelic markers. One CA repeat was further characterized and was found to be highly informative (83% heterozygosity). In the CEPH families, no recombination was found between the CT79 polymorphism and this microsatellite, confirming the localization of the CA repeat in immediate proximity to the SA coding region. The absence of chimerism in this YAC clone was verified by fluorescent in situ hybridization (results not shown). The search for linkage in the hypertensive families was performed by means of two different affected sib pair methods, and no significant evidence of linkage was found. Since the 95% confidence interval gave an upper boundary of 0.54 on IBD probability at the SA microsatellite, the results suggest that this locus is not a major determinant of increased familial risk of hypertension.
There are two possible explanations for the differences between the observed genetic effects of the SA locus in rat and human hypertension. The first is that genetic variation at the SA locus plays a role in blood pressure regulation in the rat but not in human hypertension. This hypothesis implies that, in rats, (1) the gene is important for blood pressure regulation by a mechanism that is as yet unknown and (2) the polymorphism of the gene existed in outbred rat populations from which hypertensive and control strains were constructed. One of these two conditions may not be fulfilled in humans. The gene might not be important for human blood pressure control in contrast to the rat, but this discrepancy is quite unlikely. Another possibility is that the SA gene is not involved in blood pressure variance because there is no functional polymorphism altering the regulatory or the coding part of the gene in humans. In contrast to this hypothesis, a recent case-control study performed in Japan provided evidence for an association between a restriction fragment length polymorphism (RFLP) of the human SA gene and hypertension.28 Our preliminary results indicate that this RFLP is also observed in whites, while allele frequencies are not significantly different between hypertensive and normotensive subjects (the frequencies of minor allele were 0.15 and 0.14 for 13 hypertensive and 18 normotensive subjects, respectively). If these results can be confirmed, they would suggest that the association of this RFLP with hypertension is only observed in some ethnic groups or might be also observed in some particular subgroups of hypertensive subjects.
Another possible explanation is that the SA gene is not itself implicated but is linked to another gene at which variation affects blood pressure regulation in the rat. Indeed, the differential screening strategy leads to the identification of genes for which a polymorphism of expression exists between the two strains of rats. The SA gene expression polymorphism might be therefore only a neutral marker, without any relation to blood pressure physiology. With regard to the low number of genes analyzed in the initial study (a total of three),10 the chances of finding a gene cosegregating with blood pressure is probably low. However, the possibility of identifying cosegregation at these loci still exists for two reasons. The first is that the number of loci that have a linkage with blood pressure could be higher than initially expected. More than eight blood pressure loci have been already identified to date, and the list keeps elongating rapidly.32 33 34 Second, the confidence interval for the localization of any quantitative trait locus identified through linkage in experimental crosses is extremely wide and will contain multiple candidate genes.
In the latter case, a homologous gene responsible for high blood pressure could exist in humans, but at a distance from the SA locus. For this reason we have also performed linkage studies with microsatellite markers flanking the SA gene. Using two markers spanning an interval of approximately 5 cM on each side of the SA gene, we have not been able to detect any linkage with hypertension. We may thus be able to eliminate linkage within a 10-cM interval around the SA gene. However, it is likely that this interval includes genes that reside near the SA gene in rats but are on chromosome 11p in humans.35 Thus, a homologous locus in the human could be localized to regions other than chromosome 16p. Further studies will be needed to determine with precision the limits of the conserved synteny groups in humans that correspond to this region of rat chromosome 1 and to assess their relations to human hypertension.
As for every negative study, it is important to discuss the limitations of our study. We used several highly informative markers and large populations to obtain maximal power with the current approaches. However, we still could miss the effects of the SA locus on blood pressure as a quantitative trait because we studied blood pressure as a dichotomous trait (ie, hypertensive versus normotensive subjects). In addition, our study does not include any intermediate phenotypes related to the SA gene product, as it is not yet characterized. Using intermediate phenotypes may reinforce or add new information to such genetic studies, as was the case for angiotensinogen and angiotensin-converting enzyme genes.30 36 However, using the same study design, we successfully detected statistically significant linkage and/or association with hypertension on the angiotensinogen and angiotensin II receptor type I loci.19 30 Hence, the SA locus has only a minor effect, if it has any, on hypertension in the studied population.
In conclusion, our study of the SA gene illustrates a general approach that can be applied to evaluate candidate genes in humans. This requires cloning of the human equivalent of the gene, identification of YAC or other clones corresponding to the gene, development and mapping of microsatellite markers, and detection of polymorphisms within the gene by SSCP or by other techniques. In our case, the results coming from this strategy do not plead for the hypothesis that the SA gene itself plays a detectable role in hypertension among whites. More genetic studies in the rat will be required to further define the origin of the linkage of the SA locus, ie, the SA gene or a gene located at proximity of the SA gene, with blood pressure and to identify the physiological mechanism involved. The results of these investigations could lead to complementary investigations in humans.
Note added in proof. The insulin growth facter 2 (IGF2) locus was also tested since this gene is close to the SA gene in the rat genome, but located in 11p15.5 in humans. Using a tetranucleotide microsatellite marker located in the first intron of the tyrosine hydroxylase gene, close to the IGF2 gene, no linkage was observed in hypertensive families.
| Acknowledgments |
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Received May 9, 1994; first decision June 7, 1994; accepted October 3, 1994.
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N. Hubner, Y.-A. Lee, K. Lindpaintner, D. Ganten, and R. Kreutz Congenic Substitution Mapping Excludes Sa as a Candidate Gene Locus for a Blood Pressure Quantitative Trait Locus on Rat Chromosome 1 Hypertension, October 1, 1999; 34(4): 643 - 648. [Abstract] [Full Text] [PDF] |
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S. A. Frantz, M. Kaiser, S. M. Gardiner, D. Gauguier, M. Vincent, J. R. Thompson, T. Bennett, and N. J. Samani Successful Isolation of a Rat Chromosome 1 Blood Pressure Quantitative Trait Locus in Reciprocal Congenic Strains Hypertension, October 1, 1998; 32(4): 639 - 646. [Abstract] [Full Text] [PDF] |
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J. Rapp Editorial Commentary: The Sa Gene : What Does It Mean? Hypertension, October 1, 1998; 32(4): 647 - 648. [Full Text] [PDF] |
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P. Corvol and X. Jeunemaitre Molecular Genetics of Human Hypertension: Role of Angiotensinogen Endocr. Rev., October 1, 1997; 18(5): 662 - 677. [Abstract] [Full Text] |
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R. Kreutz, B. Struk, S. Rubattu, N. Hubner, J. Szpirer, C. Szpirer, D. Ganten, and K. Lindpaintner Role of the {alpha}-, {beta}-, and {gamma}-Subunits of Epithelial Sodium Channel in a Model of Polygenic Hypertension Hypertension, January 1, 1997; 29(1): 131 - 136. [Abstract] [Full Text] |
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T. Yang, S. A. Hassan, I. Singh, A. Smart, F. C. Brosius, L. B. Holzman, J. B. Schnermann, and J. P. Briggs SA Gene Expression in the Proximal Tubule of Normotensive and Hypertensive Rats Hypertension, March 1, 1996; 27(3): 541 - 545. [Abstract] [Full Text] |
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