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*
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190;
American Red Cross, National Histocompatibility Laboratory, Baltimore, MD 21201; and
National Marrow Donor Program, Minneapolis, MN 55413
| Abstract |
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1 in 100 samples
typed. These new HLA-C alleles result from 29 nucleotide substitutions
of which 4 are silent, such that coding substitutions concentrated
about the Ag-binding groove predominate. Polymorphism at the HLA-C
locus therefore resembles that at the HLA-A and HLA-B loci more than
previously believed, indicating that antigenic stress is driving HLA-C
evolution. However, sequence conservation in the
-helix of the first
domain and a clustering of unique amino acids around the B pocket
indicate that HLA-C alleles respond to antigenic pressures differently
than HLA-A and HLA-B. Finally, because the samples characterized were
predominantly from Caucasians, we hypothesize that HLA-C polymorphism
will equal or exceed that of the HLA-A and -B loci as DNA
sequence-based typing is extended to include more non-Caucasian
individuals. | Introduction |
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The extent and characteristics of HLA-A and -B polymorphism support the
hypothesis that antigenic stress drives class I HLA diversification.
For example, comparative analysis of the
200 HLA-B alleles now
recognized demonstrates that nonsynonymous nucleotide substitutions
predominate in the evolution of HLA-B alleles, that HLA-B polymorphism
is focused about the Ag-binding groove, and that particular alleles
such as HLA-B*5301 are found at a high frequency in regions where these
alleles convey disease resistance (3, 8, 9). The HLA-C locus, on the
other hand, has remained more of an enigma largely because reagents
capable of distinguishing HLA-C molecules from one another and from
HLA-A and -B molecules are difficult to obtain (10, 11, 12, 13). Indeed, the
inability to accurately establish the HLA-C type of patients with
disease resistances, autoimmune disorders, or in need of a transplant
has resulted in the functional contribution of HLA-C molecules being
comparatively unexplored. Less cell surface expression of HLA-C
compared with HLA-A and -B has led to speculation that the HLA-C
molecules are deteriorating or lack function, while apparent
stimulation of allograft rejection and their recognition by NK cells
indicate that HLA-C molecules play an important role in stimulating
cellular immune responses (14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25). However, without the ability to
determine accurately the HLA-C type of a transplant donor/recipient
pair or of an individual in which cellular immune responses induce
disease susceptibility/resistance the enigma of HLA-C remains
unresolved.
Nucleotide sequencing represents an accurate means of determining an
individuals HLA-C type, and we have adapted DNA sequencing such that
it can be applied to HLA-C typing in a high throughput, robust, and
cost-efficient manner. By applying this class I HLA-C DNA
sequence-based typing (SBT)3
protocol to
2000 bone marrow donor/recipient pairs in the National
Marrow Donor Programs (NMDP) research repository, we accurately
establish parameters such as HLA-C homozygosity rates, HLA-C allele
frequencies, and the frequency of serologic blanks in the samples
typed. In terms of HLA-C polymorphism, positions both conserved and
polymorphic within the class I Ag-binding groove become apparent while
the pool of nucleotide sequence provided identifies synonymous and
nonsynonymous nucleotide substitution rates. The data interpretation
herein is significantly different from that of other studies due to the
large number of new HLA-C alleles we have contributed for comparative
analyses, and the HLA-C SBT data presented here provide a step forward
in unraveling the polymorphic nature of HLA-C molecules and how these
HLA-C polymorphisms might impact cellular immune responses.
| Materials and Methods |
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Genomic DNA from 1823 individuals were prepared from 200 µl of frozen whole blood (citrate/EDTA), PBLs, granulocytes, or EBV cell lines, provided by the NMDP repository in North America, using the commercially available Qiagen QIAamp (Qiagen, Valencia, CA) blood kit according to manufacturers protocol.
PCR amplification
Exons 2 and 3 of HLA-C loci were amplified as previously
described by Cereb et al. (26) using primers 5'CI1 and 3'BCI3 (Table I
). This first round PCR, C1, was diluted
1:100 and used as template for nested PCR reactions that amplify exons
2 and 3 separately (Fig. 1
). The four
nested PCR reactions, two for each exon, include 10 pM concentrations
of each HLA class I generic primer mix (Table I
): C2 (biotin-5'I1E2C +
3'I2E2ABC-U); C3 (5'I1E2C-U + biotin-3'I2E2ABC); C4 (biotin-5'I2E3C +
3'BCI3-U); and C5 (5'I2E3C-U + biotin-3'BCI3); 1.5 mM
MgCl2; 50 mM KCl; 10 mM Tris-HCl (pH 8.3); 200 mM
concentrations each of dATP, dTTP, dGTP, and dCTP; and 0.5 U of
Taq polymerase in a final volume of 60 µl. Amplifications
were accomplished on an MJ Research Tetrad (MJ Research, Watertown,
MA), PTC-225 (heated bonnet) thermocycler using the following cycling
conditions: 30 cycles of 95°C for 1 min; 54°C for 1 min; and 72°C
for 1 min; and a final cycle of 72°C for 5 min.
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Bidirectional sequencing of each exon was performed. A Cy5 dye-labeled -21-mer M13 Universal primer and an AutoLoad Kit (Amersham Pharmacia Biotech, Piscataway, NJ) were used for the sequencing of each nested PCR product (45 µl). Sequencing reactions were then loaded onto a 6% Page Plus (Amresco, Solon, OH) gel and run on a Pharmacia ALFexpress automated DNA sequencer. Data were analyzed using the Pharmacia HLA SequiTyper software (version 2.0).
Cloning and sequencing
Putative new HLA-C alleles were reamplified from genomic DNA as
previously described using HLA class I locus-specific primers, C1 mix
(Table I
) and cloned into the blunt-end TA vector using the TA cloning
kit (Invitrogen, Carlsbad, CA) according to the manufacturers
instructions. Ten white colonies from each sample were picked and grown
overnight in 10 ml of Luria-Bertani medium containing 50 mg/ml
ampicillin. Plasmid DNA was isolated using the Promega Wizard kit
(Promega, Madison, WI) according to the manufacturers instructions.
Each clone underwent EcoRI digestion and was run on a 0.8%
agarose gel to screen for insert. Screen sequencing of clones
containing the insert was achieved with -21-mer M13 Universal primer
and a Thermosequenase cycle sequencing kit (Amersham Pharmacia
Biotech, Piscataway, NJ). Bidirectional sequencing of clones from
the desired populations was performed as before using M13 reverse
primer. Sequencing reactions were loaded onto a 5% Page Plus (Amresco,
Solon, OH) gel run on a Pharmacia ALFexpress automated DNA sequencer.
Sequence data were analyzed using the Wisconsin GCG (Genetics Computer
Group, Madison, WI) sequence analysis system on a Digital Equipment
Corporation VAX 6610.
Accession numbers and nomenclature
The new HLA-C alleles detected here have been submitted to
GenBank and assigned the accession numbers detailed in Table II
, which also contains the names
officially assigned by the World Health Organization (WHO) Nomenclature
Committee (27). This follows the agreed policy that, subject to the
conditions stated in the Nomenclature Report, names will be assigned to
new sequences as they are identified. Lists of such new names will be
published in the next WHO Nomenclature Report.
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| Results and Discussion |
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The most surprising aspect of this study was the number of new
alleles that were uncovered, in total 19, all of which were confirmed
by traditional cloning (31, 32). This number of new alleles gives a
rate of
1 new HLA-C allele in every 100 samples typed. Because HLA-C
has historically been characterized as less polymorphic than HLA-A and
-B (33), we analyzed the nature of these previously undetected HLA-C
polymorphisms to learn more about HLA-C diversification. A total of 29
nucleotide substitutions give rise to the 19 new alleles with only 4 of
the new alleles not resulting from a coding substitution; coding
substitutions predominate in HLA-C. Twelve of the new HLA-C alleles
differ from their closest HLA-C relative by 1 nucleotide while the
remaining 7 new alleles differ from their closest relative by
2
nucleotides (Table III
). On the surface,
these single nucleotide polymorphisms indicate that point mutations
predominate over recombinations in the generation of HLA-C
diversification. However, few (3 of 12) of the point mutations creating
new alleles are unique to a particular HLA-C allele such that most
point substitutions can be explained through gene conversion with DNA
sequences present in another HLA-C molecule. As with HLA-A and -B,
intralocus gene conversion in exons 2 and 3 therefore appears to be the
primary mechanism driving HLA-C diversification.
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Location and nature of new HLA-C polymorphisms
A predominance of coding substitutions indicates that HLA-C genes
are under selective pressure, and the fact that a majority of
polymorphisms that result in new HLA-C alleles are focused in the
peptide-binding groove further substantiates the functional
significance of HLA-C. Twelve of the 19 new HLA-C alleles shown in
Table III
are polymorphic at amino acids with side chains positioned to
influence peptide presentation (36, 37, 38). Polymorphisms at residues 9
and 66 in the B specificity pocket distinguish the two new alleles
Cw*0308 and Cw*0603, and because positions 9 and 66 lie in the B
specificity pocket with the HLA-C unique glycine-45, it is likely that
peptides bound by Cw*0308 and Cw*0603 are unique at their N termini
(36, 39). In a similar fashion, 9 of the new HLA-C alleles listed in
Table III
are polymorphic in the E specificity pocket while 6 new
alleles have modified F specificity pockets (36, 39). Thus, a majority
of the new HLA-C polymorphisms reported here are positioned to
preferentially alter the anchoring of peptides near their N and C
termini.
While a majority (10 of 14) of the HLA-C amino acid polymorphisms
leading to new alleles represent polymorphisms also seen in HLA-A and
-B alleles, it is noteworthy that 4 of the new polymorphisms detected
in this study are unique to the HLA-C locus (Table III
; Fig. 3
). For example, while positions 80 and
114 are polymorphic across all three HLA class I loci, three of the new
HLA-C alleles (Cw*0306, Cw*0709, and Cw*12042) detected here have amino
acids previously unseen at one of these two positions. Furthermore, the
new alleles Cw*1206 and Cw*0405 have the unique amino acids
Val120 and Leu28, respectively; these positions
are conserved across all other HLA class I alleles (Table III
).
Polymorphisms unique to the HLA-C locus therefore continue to be
propagated both inside (positions 80 and 114) and outside (positions 28
and 120) of the Ag-binding groove.
|
The detection of 19 new alleles demonstrates that class I DNA SBT
is capable of unveiling characteristics of HLA-C not appreciated with
lower resolution typing methods. Indeed, SBT provides more precise data
concerning the distribution of existing HLA-C subtypes. For example,
from the SBT typing data, it was found that Cw*0701 was the most common
allele with an overall frequency of 15.66%, and the most prevalent
genotype was Cw*0701, Cw*0702. Contrasting the high incidence of
Cw*0701 was the less frequent Cw*0704 at a frequency of 1.73% and the
complete absence of Cw*0703 and Cw*0705 in this sample set. Perhaps one
of the most interesting findings was that 28% of the samples contained
"serologic blanks," Cw12-18, which would be undefined by serology
due to a lack of suitable reagents. That 28% of the samples typed here
contained at least one serologic Cw12-18 blank suggests many previously
typed homozygous samples may well be heterozygotes. Indeed, previous
studies have shown 18% homozygosity by PCR sequence-specific primers
and up to 50% homozygosity by serology (40, 41). In comparison, we
found the rate of HLA-C homozygosity to be 9.8% in the NMDP research
repository samples, suggesting that like the HLA-A and -B loci, a
heterozygous state of
90% is favored at the HLA-C locus.
The NMDP research pool contains ethnically diverse samples of which the
vast majority are Caucasian at an overall frequency of 66.85%. Of the
61 HLA-C sequences now in the database, our SBT detected 48 in the NMDP
research repository samples. The 12 HLA-C alleles not detected here
were primarily of restricted ethnic origin (Table IV
). Construction of an evolutionary tree
shows that alleles not detected in this study, as well as new alleles
detected here, were dispersed among all of the HLA-C families such that
no apparent SBT bias exists in the detection of HLA-C alleles (Fig. 4
). The Figure 4
dendrogram illustrates
that new alleles were detected in the Cw2, Cw3, Cw4, Cw7, Cw8, and
Cw12, 14, 15, 16 families, while the alleles not detected were
dispersed in a similar fashion. Thus, the SBT approach applied herein
did not favor the detection of alleles in any particular HLA-C family,
nor do alleles in any given HLA-C family represent SBT "blanks."
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Given a Caucasian ethnic disposition and a precise means of typing, it was anticipated that a majority of the samples exhibiting new alleles would stem from the Caucasian population. This is indeed the case as 13 of 19 new alleles were found in Caucasian individuals. A most interesting observation, however, was that new alleles found in non-Caucasians were often observed in multiple samples, whereas new alleles detected in samples of Caucasian origin were generally observed in single samples. For example, in Caucasians a new allele was seen in no more than 3 samples (Cw*02024 and Cw*16041), while Cw*03042 was detected in 6 African American samples and 1 Asian Pacific Islander and Cw*02024 was detected in 10 African Americans and 2 Hispanics. This suggests that new alleles are "hidden" in the Caucasian population although common in ethnic minorities. On the basis of this observation, we hypothesize that the SBT of non-Caucasian populations will reveal many more new alleles, ultimately demonstrating that HLA-C polymorphism is equivalent to that of the HLA-A and HLA-B loci.
HLA class I comparative analysis
The ribbon diagram of Figure 3
illustrates that four of the new
HLA-C alleles detected here result from unique polymorphisms (i.e.,
either location or amino acid residue) as compared with HLA-A and -B
molecules. A more encompassing comparison of all HLA-C amino acid
sequences demonstrates that this locus is distinguished by several
unique characteristics (Fig. 5
). In
building the HLA-C database to 61 alleles, we were able to revisit an
earlier observation that the
1
helix of the HLA-C
molecules is relatively conserved as is the glycine residue at amino
acid 45 (33). Indeed, the distribution of polymorphic residues around
the HLA-C peptide-binding groove is not uniform in that the
1
helix remains highly conserved in comparison with
other regions of the molecule: within the
1 and
2
helices, 16 polymorphisms were noted with 5 of
these located on the
1
helix (Table V
; Fig. 5
). Conservation of the
1
helix is positioned to affect Ag presentation and
receptor engagement. For example, conservation of the
1
helix might allow NK receptors specific for HLA-C to position
themselves on the conserved portion of the
1
helix
for examination of the polymorphic HLA-C NK epitope at amino
acids 77 and 80 (44). Alternatively, it has been proposed
that polymorphisms in the
1
helix induce major
changes in the peptides bound by class I HLA-B molecules, and a
conserved
1
helix might therefore conserve a
particular HLA-C peptide presentation property (45).
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2
helix from HLA-A and -B loci. The functional implication of these
HLA-C-specific characteristics is difficult to decipher because
comparatively little is known pertaining to the presentation of
peptides and the receptor ligands that recognize HLA-C molecules and
their peptide cargo (46, 47, 48, 49). For example, it is unclear how the unique
cluster of amino acids on the floor of the groove near the 45 pocket
relates to the observation that many HLA-C ligands do not have a
dominant P2 anchor, and it is also unclear how the HLA-C-unique
residues near the end of the
2
helix affect the
positioning of peptides in the 45 pocket. However, the observation that
dominant and strong anchors are more prevalent in the middle (P4P6)
of HLA-C ligands than for HLA-A and HLA-B suggests that these
HLA-C-unique residues impact how the N termini of peptide ligands lie
in the groove (44).
In summary, application of HLA-C DNA SBT provides structural, and
therefore functional, insights into HLA-C that were previously
unrealized. The 19-allele increase in HLA-C diversity reported here
demonstrates that the polymorphic nature of the HLA-C locus has been
underestimated and that greater HLA-C diversity will become apparent as
ethnic minorities are typed via DNA sequencing. That HLA-C
polymorphism, the generation of this polymorphism, and the frequency of
heterozygotes resemble the HLA-A and HLA-B loci more than previously
realized suggests that the pressures driving HLA-A and HLA-B evolution
also act on HLA-C. However, specific characteristics such as a
conserved
1
helix, a conserved Gly45,
and clustering of unique polymorphisms around the 45 pocket demonstrate
that some pressures faced by HLA-C molecules are unique to that locus.
Although the precise role that HLA-C plays in the adaptive immune
response, transplant compatibility, and autoimmunity is unclear, the
results presented here illustrate that understanding the function of
particular HLA-C alleles will first require a means to distinguish
among varied HLA-C subtypes.
| Acknowledgments |
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| Footnotes |
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2 Address correspondence and reprint requests to Dr. William Hildebrand, Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, P.O. Box 26901, Oklahoma City, OK 73190. ![]()
3 Abbreviations used in this paper: SBT, sequence-based typing; NMDP, National Marrow Donor Program. ![]()
Received for publication December 22, 1997. Accepted for publication April 6, 1998.
| References |
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1 helix of the HLA-B heavy chain can have an overriding influence on peptide-binding specificity. J. Immunol. 158:1660.[Abstract]
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