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* Department of Immunology, Hospital Clinico San Carlos, and
Immunology Unit, La Paz Hospital, Madrid, Spain
| Abstract |
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| Introduction |
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Within the MHC, primary association with both class II HLA genes (10, 18) and class III genes (8, 11, 12, 15) has been claimed. In recent years, despite the development of high-density genetic maps and large kindred studies, the point has not been completely settled; although the telomeric part of the MHC class III region is usually favored (13, 15), a report points to the telomeric part of the MHC class II region (19). Most studies published in recent years (13, 14, 19, 20) have focused on IgAD patients bearing the B8-DR3 haplotype, because this is the most common haplotype associated with IgAD in Caucasians. However, in Spanish white IgAD patients, HLA-DR1 and HLA-DR7 are even more frequent than HLA-DR3 (21), reflecting the distribution of HLA-DR alleles and extended haplotypes in southern Europe, where HLA-DRB1*0102 (carried on the B14-DR1 haplotype) and DR7 are more frequent than in northern Europe and the U.S. (22). Studies performed in Italy have also shown the DRB1*0102 allele and the B14-DR1 extended haplotype as the most frequently associated with IgAD patients in their population (7, 23).
Taking advantage of the high frequency of association of IgAD with
HLA-DR1 and DR7 in addition to DR3 in
the Spanish white population, this study aimed to map the predisposing
locus (or loci) of the IGAD1 candidate region within the MHC
by investigating the pattern of association of the disease with these
three HLA-DR alleles and other markers in this region. In
all, six microsatellites (9N2, D6S273,
BAT2, TNFa, TNFb, and MHC class
I chain-related gene A (MICA)), three single
nucleotide polymorphisms (TNF-376, -308, and
-238) on the TNF gene, and four polymorphic genes
(HLA-DRB1, -DQA1, -DQB1, and
HLA-B) were typed (Fig. 1
).
Therefore, when we refer to conserved extended haplotypes in the IgAD
families studied we refer to fragments extending from
HLA-DQB1 to HLA-B.
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| Materials and Methods |
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The study group consisted of 182 IgAD patients (as defined by the World Health Organization Group on Primary Immunodeficiencies (24), all ascertained at the Immunology Unit of La Paz Hospital (Madrid, Spain)) and 343 healthy controls. All patients and controls were unrelated Spanish Caucasians. Recurrent infections were present in 24 patients, allergy was present in 26 patients, autoimmune diseases were present in 27 patients, and celiac disease was present in 14 patients. Additionally, we investigated parents and siblings of 100 of these patients. Of the 100 families, 13 were found to have a second (or more) IgAD patient (nine siblings, four fathers, and eight mothers of the probands). In all, 412 family members were studied (to set haplotype phase and clarify ambiguities), but only data obtained from patients and their parents were used. All were white individuals of Spanish origin and all parental haplotypes were established in each family (n = 400).
Molecular biology methods
DNA was isolated by standard methods from peripheral blood leukocytes by a salting-out procedure with 6 M NaCl after overnight incubation with proteinase K (25). HLA-B was typed using the Low Resolution SSP Typing kit by Biosynthesis (Lewisville, TX). DRB1 typing (and subtyping) and DQA1 and DQB1 typing were conducted by PCR amplification and hybridization with allele-specific oligonucleotides; both primers and probes were used according to the Eleventh International Histocompatibility Workshop (26). Because we were interested in positive associations, only DR1 was subtyped. Positive associations were also observed (as previously published) with DR3 and DR7, but in our population only one subtype of DR3 and one subtype of DR7 are found; therefore, no subtyping was performed on them. TNFA alleles at positions -376, -308, and -238 were investigated by PCR and dot blot hybridization according to the method of Brinkman et al. (27). The TNFa and b microsatellite typing was performed as described by Nedospasov et al. (28). PCR amplification and sizing of DNA fragments containing TNFa and b microsatellites separately and of a larger fragment containing both microsatellites made TNFab haplotype assignment possible; the two longer fragment lengths were a combination of the sizes of the two individual microsatellites in each DNA molecule plus the intervening 22-bp sequence (28). MICA transmembrane exonic microsatellite was amplified using primers and conditions described by Ota et al. (29). The MICA R primer was labeled with FAM. D6S273 microsatellite was amplified using primers described by Martin et al. (30). The 142-3 primer were labeled with tetrachloro-6-carboxyfluorescein. BAT2 (821) and 9N2 microsatellites were amplified using primers described by Vorechovsky et al. (19). The 821-1 primer was labeled with tetrachloro-6-carboxyfluorescein and the 9N2-1 primer was labeled with FAM. The PCR fragments were subsequently run on an ABI Prism 310 automatic sequencer (PE Applied Biosystems, Foster City, CA). The microsatellite samples were analyzed using the Genescan software (PE Applied Biosystems) with the TAMRA 500-pb marker (added to each sample) and the local Southern size-calling method under denaturing conditions.
Statistical analysis
The joint segregation of DRB1, DQA1, DQB1, 9N2, D6S273, BAT2, TNF-376, -308, -238, TNFab, MICA, and HLA-B in the families led to the establishment of the haplotypes involved.
Allele or haplotype transmission from heterozygous parents to affected
offspring was studied using the transmission disequilibrium test. The
distributions of transmitted and nontransmitted alleles were compared
using a Monte Carlo computer simulation with 20,000 iterations under
the null hypothesis of a probability of transmission of 0.5. These were
confirmed with a
2 test (or Fishers exact
test) for each individual allele. When a difference between the two
methods was found we preferred the Monte Carlo simulation, although the
p values were slightly higher, because it is considered more
exact.
For stratified transmission test (when the null hypothesis of a
probability of transmission of 0.5 is no longer feasible) and for all
case control comparisons, a
2 test (or
Fishers exact test when an expected cell value was <5) was used.
Strength of associations was given as odds ratios (OR). A standard
statistical software package (EPI-INFO version 6.02; World Health
Organization, Geneva, Switzerland) was used.
Because IgAD was associated with more than one allele or haplotype in the MHC region, the relative predispositional effects (RPE) of some alleles or haplotypes could not be readily determined. A primary association could mask a second positive association because of the expected decreased frequency of the latter imposed by the former. Therefore, we used the RPE method (31) to identify several associations sequentially. Thus, the possibility that an association with an allele or haplotype could create misleading deviations in the frequencies of other alleles was eliminated.
| Results |
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Table I
shows the frequency of
HLA-DR alleles in IgAD patients and controls. All three
alleles (DR1, DR3, and DR7) previously
reported to be associated with IgAD were found to be increased in
frequency in patients. When HLA-DR1-positive patients were
subtyped (Table I
), a very strong association with DRB1*0102
was observed (OR = 6.35). DR3 and DR7 were
not subtyped, because only one subtype for each group is present in our
population (DRB1*0301 and DRB1*0701,
respectively).
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DR3-positive haplotypes
We analyzed the 400 haplotypes from the 100 IgAD patients families studied to identify the extended haplotypes and to look for transmission disequilibrium of the associated marker allele or haplotype from a heterozygous parent to an affected offspring. Sixty-eight haplotypes carried HLA-DR3. Of these DR3-positive haplotypes, we found 32 carrying haplospecific markers of the B8-DR3 haplotype (TNF-308A, TNFa2b3, and HLA-B8) in addition to DR3; therefore, they were considered to be B8-DR3 conserved haplotypes. Additionally, 12 were found carrying DR3, TNF-376A, TNFa1b5, and HLA-B18, all of them haplotypic markers of the B18-DR3 conserved haplotype. All other DR3-positive haplotypes present had multiple combinations of alleles at the tested loci not shared by more than four of them. The B8-DR3 haplotype was transmitted more frequently than not from heterozygous parents to IgAD patients (23 vs 7; p = 0.027), whereas no statistically significant difference was seen for the B18-DR3 haplotype or for all other DR3-positive haplotypes.
All DR3, TNF-308A, TNFa2b3, and
HLA-B8 haplotypes were carrying MICA allele
A5.1, except in one instance where allele A5 was
present. Concerning D6S273 and BAT2
microsatellites, two different patterns were present: allele
136 at D6S273, always coupled with allele
2 at BAT2, was found in eight instances, whereas
all other 24 haplotypes were carrying allele 140 at
D6S273 coupled with allele 1 at BAT2
in most instances (allele BAT2-2 was present on two
haplotypes and alleles 3 and 4 were present on
one each). Transmission from the 30 heterozygous parents was
significantly increased for both groups of DR3,
TNF-308A, TNFa2b3, and HLA-B8
haplotypes (Table II
).
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Of the 44 DRB1*0102-positive haplotypes, 26
B14-DRB1*0102 conserved extended haplotypes (i.e., carrying
DRB1*0102, TNF-308G, TNFa2b1,
HLA-B14) were identified (Table IV
). All were D6S273-132, and
most were BAT2-3 positive (all but four) and
MICA-A6 positive (except two, carrying
MICA-A5.1). Two more haplotypes carried TNF-308G,
DRB1*0102, and TNFa2b1 but not HLA-B14
or the other tested markers present on the B14-DRB1*0102
extended haplotype. The other 16 DRB1*0102-positive
haplotypes present lacked TNFa2b1 and HLA-B14 and
had multiple combinations of alleles at the tested loci not
corresponding to any known conserved haplotype. As seen in Table IV
,
B14-DRB1*0102 conserved extended haplotype was transmitted
more frequently to IgAD offspring. Moreover,
DRB1*0102-positive haplotypes not carrying
B14-DRB1*0102 haplotypic TNF or HLA-B
alleles were also transmitted with increased frequency to IgAD patients
(11 transmitted vs 5 nontransmitted) (Table IV
).
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Because D6S273, BAT2, TNFab, and
MICA microsatellite alleles present on the
B14-DRB1*0102 haplotype were among the most common alleles
present in our population (and therefore were not very informative), we
looked for another microsatellite that could be considered as a more
specific marker of the B14-DRB1*0102 haplotype. We found
that allele 5 of the 9N2 microsatellite, located
25 kb centromeric to D6S273 (G7 region), was
present on 24 of 26 B14-DRB1*0102 haplotype as compared with
one of the 18 DRB1*0102-positive, B14-negative
haplotypes and could therefore be considered as a haplospecific marker
of the B14-DRB1*0102 haplotype. Six haplotypes
9N2-5, B14 positive and DRB1*0102
negative, were present. All six carried the alleles
D6S273-132, BAT2-3, TNF-308G,
TNFa2b1, and MICA-A6, haplotypic of the
B14-DRB1*0102 extended haplotype. As observed previously for
all DRB1*0102-negative haplotypes, no transmission
disequilibrium was seen (three transmitted vs three nontransmitted).
DR7-positive haplotypes
DR7-positive haplotypes were increased in frequency in
transmitted haplotypes (62 transmitted vs 19 nontransmitted;
p < 10-5). Because
HLA-DR7 is present on two DR-DQ haplotypes, both
were analyzed separately and a similar transmission disequilibrium was
observed (DR7, DQA1*0201, DQB1*0202:
53 transmitted vs 18 nontransmitted; p <
10-5; DR7, DQA1*0201,
DQB1*0303: 9 transmitted vs 1 nontransmitted;
p = 0.01). HLA-B and microsatellite typing
showed combinations of alleles corresponding to five different
DR7-positive conserved extended haplotypes (Table V
). In all instances, transmission of
these haplotypes to IgAD offspring was increased (Table V
) and no
statistical differences were found between them.
HLA-DR7-positive haplotypes not belonging to any known
conserved extended haplotype were also found more frequently in
transmitted haplotypes (14 transmitted vs 6 nontransmitted;
p = 0.056).
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Relative predispositional effects
Results presented above showed that the B8-DR3 and
B14-DRB1*0102 extended haplotypes, as well as all haplotypes
carrying HLA-DR7, were preferentially transmitted to the
IgAD patients. These primary associations could mask other positive
associations because of the expected decreased frequency of the latter
imposed by the former. Therefore, we used the RPE sequential study
(31) to identify several associations sequentially.
Excluding all B8-DR3, B14-DRB1*0102, and
DR7-carrying haplotypes, the centromeric fragment of the
B14-DRB1*0102 extended haplotype (the
DRB1*0102-carrying fragment) was preferentially transmitted
(Table IV
) and with this sequential study the difference between
transmitted and nontransmitted fragments appeared statistically
significant (11 of 99 transmitted vs 5 of 160 nontransmitted;
p = 0.009; OR = 3.88) (Table IV
). Conversely, no
preferential transmission of the telomeric fragment was observed. For
the B8-DR3 fragments, those carrying the telomeric
haplospecific markers (TNF-308A, TNFa2b3) were
preferentially transmitted (Table II
) and, in the RPE sequential study,
the OR, reflecting the strength of the association, was high; the
difference between transmitted and nontransmitted telomeric fragments
approached, but did not reach, statistical significance (5 of 99
transmitted vs 2 of 160 nontransmitted; p = 0.08;
OR = 4.20).
| Discussion |
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70% of the human haplotypes
are conserved, extended haplotypes or recombinants of no more than two
of them (17, 32, 33). It is generally accepted that a small number of these MHC conserved haplotypes are found in the majority of IgAD patients (5, 7, 8, 10, 11, 13, 19) and that these haplotypes share a susceptibility locus designated IGAD1. To track down this MHC susceptibility locus, most studies have either focused on the B8-DR3 haplotype (13, 14) or looked for a shared feature between different haplotypes associated with the disease (8, 10, 11, 12, 15, 18, 19). Conclusions from different groups map the susceptibility locus either to the telomeric class III region (8, 11, 12, 13, 15) or to the telomeric class II region (10, 18, 19).
Our patients showed, in agreement with previous reports, IgAD association with MHC haplotypes carrying HLA-DRB1*0102, DRB1*03, or DRB1*07. Therefore, we studied all three haplotypes groups to map the IGAD1 locus region in patients MHC haplotypes positive for any of these HLA-DR alleles. We typed polymorphic genes (HLA-DR, -DQA1, -DQB1, and -B), some single nucleotide polymorphisms (TNF-238, -308 and -376), and several microsatellites. These, in many instances, can be considered as markers of conserved haplotypes, because only one allele for each microsatellite is observed in most instances on these conserved extended haplotypes (34).
Moreover, HLA-DR2, DR5, and DR8 showed a negative association with the disease. HLA-DR2, the most significant negative association, has already been reported (10). The other two were seen to be secondary to the decreased frequency imposed by the well-known positive associations with HLA-DRB1*0102, DR3, and DR7 (data not shown).
Surprisingly, our results did not support the hypothesis of a unique susceptibility gene being shared by all the MHC susceptibility haplotypes. All HLA-DRB1*0102- and DR7-carrying haplotypes appeared to be preferably transmitted to IgAD offspring, independently of the markers present on the class III region, whereas for HLA-DR3-positive haplotypes transmission distortion was present only when the haplotype contained the alleles TNF-308A, TNFa2, and TNFb3. These three alleles at the TNF region are haplospecific markers of the B8-DR3 haplotype; therefore, our results indicated that a susceptibility allele was present in the B8-DR3 haplotype but not in other DR3-positive haplotypes. Although this ruled out as susceptibility alleles the HLA class II alleles present on all DR3-positive haplotypes (HLA-DR3, DQA1*0501, and DQB1*0201), it did not give any more clues on where the susceptibility locus was located.
Allele 140 of the D6S273 microsatellite
(D6S273-140) has been considered as a haplospecific marker
of the B8-DR3 haplotype (34, 35). We found it
in 75% of the B8-DR3 haplotypes (coupled with
BAT2-1), but in eight instances allele D6S273-136
(always coupled with BAT2-2) was present. This suggested the
presence of a double recombination at this level. Because in both
instances a statistically significant transmission disequilibrium was
observed, these two polymorphisms did not appear to play any role in
susceptibility to IgAD. Moreover, all genes lying between them, and
indeed all genes present in the whole fragment that had been
recombined, should also be excluded as the predisposing locus. Still,
the susceptibility gene on the B8-DR3 haplotype could be
either centromeric or telomeric to that fragment. However, in seven
families we have seen incomplete copies, or fragments, of the
B8-DR3 haplotype, positive for TNF-308A and
TNFa2b3 but not for DR3. In most instances (71%)
these haplotypes were transmitted to the IgAD offspring, suggesting
that the susceptibility locus was in linkage disequilibrium with these
markers and not with HLA-DR3, DQA1*0501, and
DQB1*0201. Still, the DR3-negative haplotypes
could have a class II gene that is involved in the deficiency. Because
this gene should be in linkage disequilibrium with the telomeric class
III markers of the B8-DR3 haplotype, but not with
DR3, recombination in these DR3-negative
B8-DR3 haplotype should have taken place in the class II
region. This was unlikely, because between HLA-DR and
HLA-B the preferential recombination site has been located
between D6S273 and TNF (36).
Moreover, of the seven haplotypes, only three carried D6S273
and BAT2 alleles present on the B8-DR3 haplotype
(two carried D6S273-140 and BAT2-1 and the third
one carried D6S273-140 and BAT2-3). Therefore, in
four recombinant haplotypes (three transmitted and one nontransmitted)
recombination appears to have taken place between D6S273 and
TNF (Table III
) and the susceptibility locus appears to be
telomeric to D6S273. This was in agreement with results from
most reports (8, 11, 12, 13, 15), notably from Schroeder et
al. (13), which in a large family study concluded that the
susceptibility locus was located between the class III markers
D821/D823 and HLA-B8.
The B14-DRB1*0102 haplotype was also observed to be
preferably transmitted to IgAD offspring. Both "complete" copies of
the B14-DRB1*0102 haplotype and fragments, recombinant
B14-DRB1*0102 haplotypes, carrying DRB1*0102,
showed transmission disequilibrium, whereas this was not so for the
telomeric end of the B14-DRB1*0102 haplotype, encompassing
from 9N2 and D6S273 microsatellites to
HLA-B but lacking DRB1*0102. Although this does
not necessarily mean that DRB1*0102 is the susceptibility
allele, it does establish that the predisposing locus on this haplotype
is in strong linkage disequilibrium with DRB1 and not
located in the telomeric class III region. Therefore, the
susceptibility locus to IgAD on the B14-DRB1*0102 haplotype
appears located centromeric to the predisposing region mapped on the
B8-DR3 haplotype (Fig. 1
).
The HLA-DRB1*07 allele was also seen preferably transmitted
to IgAD offspring. It is carried by the Spanish white population on
several conserved extended haplotypes (B13-DR7,
B44-DR7, B50-DR7, B57-DR7,
B64-DR7), all carrying different complotypes (17, 34, 37) and different alleles at the microsatellites typed in this
and previous studies (34, 37). Complete copies (from
HLA-DR to HLA-B) of all these haplotypes were
found in our IgAD families and all of them were preferentially
transmitted, irrespective of any other marker. We do not know whether
all of these haplotypes have any locus in common outside
HLA-DRB1. On the centromeric end this is very unlikely,
because transmission of two different DR-DQ haplotypes
(DR7-DQA1*0201-DQB1*0202 and
DR7-DQA1*0201-DQB1*0303) was significantly increased.
Therefore, the susceptibility locus must be either
HLA-DRB1*07 or any other in strong linkage with it and
present in most DR7-positive conserved extended haplotypes,
and definitely not in the telomeric end of the class III region
(Fig. 1
).
Our data point to the predisposing locus on the DRB1*0102-
and DR7-positive haplotypes located on the telomeric end of
the class II MHC region. This was advocated by Olerup and colleagues
(10, 18) more than 10 years ago. They found positive
associations of IgAD with DR1-DQ5, DR7-DQ2, and
DR3-DQ2 haplotypes and suggested that susceptibility and
resistance to IgAD was associated with different amino acids at
position 57 of the HLA-DQ
chain. However, our results do not point
to the DQB1 gene, even for DR7- and
DR1-positive haplotypes, because we have observed that both
DR7-DQA1*0201-DQB1*0202 and
DR7-DQA1*0201-DQB1*0303 haplotypes, differing at the
DQB1 gene, share susceptibility to IgAD, whereas only
DRB1*0102-positive haplotypes, of all associated with
DQA1*0101, DQB1*0501 in white populations (all
DR1- and DR10-positive haplotypes), confer
susceptibility to the disease.
IgAD is a complex disease that does not exhibit a simple mode of inheritance. As in any polygenic disease, no single gene is sufficient or, in general, necessary to cause the disease; therefore, although linkage with the HLA region has been detected in most IgAD patients and in all instances the risk attributable to this region is roughly equal, this does not indicate that just one MHC gene is conferring susceptibility to all of them. Functionally related genes are frequently linked to each other (38) and a single linkage signal to a region of a chromosome may actually be the result of disease-predisposing alleles in different linked genes in different pedigrees, as is the case for X-linked retinitis pigmentosa, where the existence of several genetic defects in the same chromosomal region has been proven (39). The MHC (HLA region in humans) is an extended cluster of genes that are remarkable for the number and importance of the immunological functions they encode (40, 41), and already, in some other immune-mediated diseases, more than one MHC gene has been primarily involved (42, 43, 44, 45).
IgAD appears as a good example of how, in complex diseases, individuals may be affected for different genetic reasons (38). More investigations are needed to pinpoint the predisposing genes in the different IgAD susceptibility-associated haplotypes, but our results clearly suggest the existence of more than one genetic defect in the same chromosomal region. This genetic complexity may be even greater within the HLA region and for diseases in which negative selection is not acting on phenotypes that do not strongly endanger reproduction. But we stress that genetics of complex diseases must always be investigated under the assumption that, at any linked locus, more than one predisposing gene and/or allele may be present.
| Acknowledgments |
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| Footnotes |
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2 Address correspondence and reprint requests to Dr. Emilio G. De la Concha, Department of Immunology, Hospital Universitario San Carlos, 28040 Madrid, Spain. E-mail address: egomezdela{at}hcsc.insalud.es ![]()
3 Abbreviations used in this paper: IgAD, IgA deficiency; OR, odds ratio; RPE, relative predispositional effect; MICA, MHC class I chain-related gene A. ![]()
Received for publication April 2, 2002. Accepted for publication August 8, 2002.
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