Restriction fragment length polymorphism of the major histocompatibility complex of the dog

Assessment of the quality and quantity of genomic DNA recovered from canine blood samples by three different extraction methods

The ideal method for genomic DNA (gDNA) extraction should recover high quantities of pure, integral gDNA from the original sample source with minimal co-extraction of inhibitors of downstream processes. Canine ethylenediamine tetra-acetic acid (EDTA) treated and clotted blood samples were extracted by three different methods (a silica column method, a phenol-chloroform method and a modified salt precipitation method). Phenol-chloroform and modified salt precipitation based extractions demonstrated similar relative recovery of gDNA with EDTA preserved blood, but were less efficient at recovering gDNA from clotted blood. Spectrophotometer measurement of phenol-chloroform based extractions tended to overestimate the quantity of gDNA recovered from extractions, and was associated with the greater co-extraction of PCR inhibitors. The silica column method recovered gDNA with equal efficiency, purity and integrity irrespective of the sample type or method of quantification.

High-Resolution Characterization of the Canine DLA-DRB1 Locus Using Reference Strand-Mediated Conformational Analysis

Several methods exist for genotyping class II DLA gene polymorphisms in the dog. The most accurate method is sequence-based typing, which involves direct sequencing of polymerase chain reaction products. However, this method is expensive and unsuitable for large-scale studies. Recently, reference strand-mediated conformation analysis (RSCA) has been shown to be effective for characterizing major histocompatibility complex genes in humans, sheep, horse, and cats. RSCA is a cheap and rapid method, ideal for large epidemiological studies. We have developed RSCA for typing DLA-DRB1 in the dog. Control panels including dogs typed by sequence-based typing and cloned major histocompatibility complex class II alleles in plasmids were used to establish migration patterns for each allele using 20 different fluorescent labeled references, of which 5 were selected to allow for clear identification and discrimination of all known DLA-DRB1 alleles. We have compared 168 dogs typed by RSCA for DLA-DRB1 and characterized by sequence-based typing, with less than 1% discrepancy. These differences were due to missing alleles because of a weak polymerase chain reaction. To date, we have RSCA-typed 1,394 dogs. RSCA is likely to become the method of choice for characterizing DLA genes in the dog and will prove a useful tool for dissecting the immune response of dogs in clinical studies.

The HLA-DOB gene displays limited polymorphism with only one amino acid substitution

The HLA-DO molecule is a non-classical class II heterodimer composed of alpha and beta chains. We have previously recognized that all eight of the allelic variations of the HLA-DOA gene represent non-synonymous amino acid substitution. In the present study, to analyze genetic polymorphism and allelic variation of the HLA-DOB gene which may affect the efficiency of class II restricted antigen presentation thereby being involved in the susceptibility of HLA associated diseases, we conducted direct DNA sequencing of HLA-DOB in 36 HLA class II homozygous typing cells and identified six new allelic variations (DOB*0101101, *0101102, *01012, *01022, *0104101 and *0104102) including five single nucleotide polymorphisms with only one amino acid substitution. Furthermore, strong linkage disequilibrium was detected between DOB*01022 and DRB1*1502 only, with no linkage disequilibrium between the DOA and the DOB genes. The HLA-DOB gene has been identified in other mammals, and their nucleotide sequences are well conserved. These facts suggest that limited polymorphism in the DOB gene is profitable to execute their unique function as a co chaperone and so strong selective pressure is operating to prevent generic variation against the DOB molecule interacting with the DM molecule and thus maintaining the specified immunological function of regulating antigen presentation.

Analysis of cDNA coding MHC class II beta chain of the chimpanzee (Pan troglodytes)

The chimpanzee (Pan troglodytes, Patr) is the closest zoological living relative of humans and shares approximately 98.6% genetic homology to human beings. Although major histocompatibility complex (MHC) plays a critical role in T cell-mediated immune responses in vertebrates, the information on Patr MHC remains at a relatively poor level. Therefore, we attempted to isolate Patr MHC class II genes and determine their nucleotide sequences. The cDNAs encoding Patr MHC class II DP, DQ and DR beta chains were isolated from the cDNA library of a chimpanzee B lymphocyte cell line Bch261. As a result of screening, the clone 6-3-1 as a representative of Patr DP clone, clone 30-1 as a Patr DQ clone, and clones 4-7-1 and 55-1 having different sequences as Patr DR clones were detected. The clone 6-3-1 consisted of 1,062 nucleotides including an open reading frame (ORF) of 777 bp. In the same way, clone 30-1 consisted of 1,172 nucleotides including ORF of 786 bp, clones 4-7-1 and 55-1 consisted of 1,163 nucleotides including ORF of 801 bp. Except for five nucleotide changes, clones 4-7-1 and 55-1 were the same sequence. By comparison with the nucleotide sequences already reported on chimpanzee MHC class II beta 1 genes, clones 6-3-1, 30-1, 4-7-1 and 55-1 were classified as PatrDPB1*16, PatrDQB1*0302, PatrDRB1*0201 and PatrDRB1*0204, respectively. This is the first report to describe complete cDNA sequences of Patr DP and DQ molecules. The nucleotide sequence data of Patr MHC class II genes obtained in this study will be useful for the genotyping of Patr MHC class II genes in individual chimpanzees.

DLA-DQB1 alleles and bone marrow transplantation experiments in narcoleptic dogs

Human narcolepsy is a neurological disorder known to be tightly associated with HLA-DQB1*0602. A clinically similar disorder has been described in various dog breeds. The canine form of the disease is inherited as an autosomal recessive disorder in Labrador retrievers and Doberman pinschers (canarc-1) but occurs sporadically in other breeds, most typically dachshunds and poodles. In this study, we have examined if there is a relationship between the development of narcolepsy and specific dog leukocyte antigen (DLA)-DQB1 alleles. Ninety-nine dogs were typed for DLA-DQB1-31 with narcolepsy and 68 control animals. Recent studies have linked the development of autosomal recessive canine narcolepsy to a disruption of the hypocretin receptor 2 (Hcrtr2) gene on the same chromosome as the canine MHC region (CFA12), but not close to the DLA. Four Hcrtr2-positive families (two Doberman pinscher families, one Labrador retriever family, one dachshund family) were analyzed at the DLA-DQ level. No relationship was found between narcolepsy and DLA in Hcrtr2-mediated narcolepsy but loose genetic linkage was observed (Zmax=2.3 at theta=25%, m= 40). Bone marrow transplantation between two DLA identical affected (Hcrtr2-/-) and unaffected (Hcrtr2+/-) siblings was also performed and found not to be successful neither in transmitting narcolepsy nor in relieving the symptoms in Doberman pinschers. DLA-DQB1 was next studied in 11 dogs with sporadic (non-familial) narcolepsy and in unrelated control animals of the same and different breeds. The allelic and carrier frequencies of various DLA-DQB1 alleles were analyzed. There was no strong positive or negative correlation between the development of narcolepsy and specific DLA-DQB1 alleles. These results do not support the involvement of DLA-DQ in canine narcolepsy, whether of sporadic or familial origin.

DLA-DQA1 polymorphisms in dogs defined by sequence-specific oligonucleotide probes (SSOP)

Several recent studies have identified DNA sequences for alleles of the DLA-DQA1 locus in the dog. To date, 10 DQA1 alleles have been reported. No data exists on the frequencies of these alleles within the general dog population, nor is there any indication of whether alleles are breed specific. We have addressed this issue by establishing a molecular-based sequence-specific oligonucleotide probing (SSOP) method to identify all published DQA1 alleles and have used these methods to type a large number of dogs. Oligonucleotide probes were designed to detect all the polymorphic sites in exon 2. This allowed assignment at the allele level. Three hundred and thirty dogs were typed for DQA1. All but two of the published DQA1 alleles were identified in these animals. One new allele was identified, and confirmed by DNA cloning and sequencing. This typing method provides a powerful tool for generating data that will be essential for studies investigating the genetic relationships between different breeds.

Interbreed variation of DLA-DRB1, DQA1 alleles and haplotypes in the dog

Although 36 DLA-DRB1 and 10 DLA-DQA1 allele sequences have been published to date, no data on individual allele frequencies exists, either for specific breeds or cross breeds, and the full extent of the polymorphism at each of these loci is still not known. We have used sequence-specific oligonucleotide probing (SSOP) to characterise a series of 367 dogs for their DRB1 and DQA1 alleles. These included individual animals from over 60 different breeds, with numbers per breed ranging from 1 to 39. DLA types were generated from 218 dogs for DRB1 and from 330 dogs for DQA1, while 181 dogs were characterised for both these loci. The frequency of individual DRB1 and DQA1 alleles showed considerable interbreed variation, e.g. 83% of West Highland White Terriers were DRB1*01 as opposed to 9% of Collies. No breed had >9 of the 22 DRB1 types defined in this study; several breeds had only two DRB1 types. DLA-DQA1 showed less variation in allele numbers per breed, but also showed considerable interbreed frequency variation. Haplotype analysis revealed over 44 different DRB1/DQA1 combinations. Of these, 25 were in a number of animals, and also in an animal that was homozygous for one or both of these loci. Some DRB1 alleles could be found in combination with several different DQA1 alleles, while others were only present in one haplotypic combination. DLA allele frequency data in normal dogs will be critical for disease association studies. It may also be possible to use haplotype data to establish the genetic relationships between different dog breeds.

DLA-DRB1 polymorphisms in dogs defined by sequence-specific oligonucleotide probes (SSOP)

To date, DNA sequences for 29 dog DLA-DRB1 alleles have been reported. However, no data exists on the frequencies of these alleles within the general dog population, nor is there any indication of whether there is interbreed variation of allele distribution. We have addressed this by establishing a molecular based sequence-specific oligonucleotide probing (SSOP) method to identify all of the known broad DRB1 types and we have used this to type a random panel of dogs. A series of oligonucleotide probes were designed to detect known polymorphisms in the three DRB1 hypervariable regions, together with two distinctive motifs in other regions of exon 2. This set of probes enabled us to assign broad DRB1 types. Two hundred and eighteen dogs were SSOP typed for DRB1. All but 4 of the published DLA-DRB1 alleles were identified in these animals. Interbreed variation in both allele distributions and allele frequencies were observed, which may be useful in the study of genetic variation between breeds. This variation also has implications for the selection of control groups for studies aimed at identifying MHC associations with disease susceptibility in the dog.

Canine major histocompatibility complex genes DQA and DQB in Irish setter dogs

Information about genetic variation within the canine major histocompatibility complex (MHC) class II genes is limited. In common with most other vertebrate species the canine MHC, or DLA, includes genes which are homologous to human DR, DQ, and DP. Recently, at least one functional DLA DQ gene-pair has been characterized, but so far systematic screening efforts have been lacking. In the present study, we sequenced both cDNA and genomic clones derived from DLA DQ genes of Irish setter dogs. This breed was of interest, since it shows a high prevalence of gluten sensitive enteropathy (GSE), which may be a useful animal model for celiac disease (CD) of man. Interestingly, few of the alleles found in Irish setters were identical to those previously detected in other breeds. Three novel DLA DQA and four novel DLA DQB alleles were discovered in 19 unrelated dogs. Strong association between certain HLA DQ alleles and CD of man prompted us to screen the DQ alleles of members of a family of gluten-sensitive Irish setter dogs. No haplotypes or alleles were shared by all affected dogs, but one frequent haplotype in this family was also detected in an unrelated gluten-sensitive Irish setter; this haplotype was absent in the healthy dogs. This observation warrants further investigation by screening the DQ alleles of a large population of unrelated gluten-sensitive Irish setters.

Molecular analysis of the DLA DR region

The dog is an important model for studying organ transplantation. In order to develop a DNA-based typing system, a genomic analysis of the canine DR region of the MHC was undertaken. Southern analysis suggests the presence of two DRB genes in most dogs and all have one DRA gene. One dog out of 200 examined contains only one DRB gene. The DRA gene was mapped in one lambda phage clone. One DRB gene (DRBB1) was localized to two overlapping phage clones. Another DRB gene (DRBB2) was localized to two overlapping phage clones. Sequence analysis of the two DRB genes suggests that one gene is intact (DRBB1) and one gene is a pseudogene (DRBB2) because it lacks a splice acceptor signal for exon 3 and lacks exons 2 and exon 4. Intron 1 and 2 sequence data from DRBB1 allow amplification of the polymorphic exon 2 which, in turn, can serve as a basis for developing a typing system for DRB.

A research on DLA-DRB1 genotyping by PCR-RFLP. I. To select a appropriate oligonucleotide primer pair

In order to study the DLA (Dog Leucocyte Antigen) class II region we utilized the polymerase chain reaction based restriction fragment length polymorphism (PCR-RFLP) method, which has been reported previously as an efficient and simple technique for accurate definition of the HLA class II alleles. To search for a appropriate primer pair a series of amplifications with 4 different primer pairs DLA-DR-SP/Stop, DLA-DR-SP/P3, HLA-DRB-GH46/50 and HLA-DRB-AMP-A/B were provided. Only one satisfactory amplification was obtained with the primer pair HLA-DRB-AMP-A/B. The analogous sequences of the primer pair are found in the sequence of HLA-DRB-cDNA. The amplification region of the primer pair includes also the three hypervariable regions (HVR) in the sequence of DLA-DRB cDNA. Southern blot hybridization analysis confirmed the specificity of the primer pair HLA-DRB-AMP-A/B. The results of Hae III and Hinfl digestion show high polymorphism in DLA-D region and allele specific polymorphic patterns. Therefore, it is suggested that the primer pair HLA-DRB-AMP-A/B is at present the only available and usefull primer pair in PCR-RFLP study of DLA-DRB1 gene.

Researches on DLA-DRB1 genotyping by PCR-RFLP. II. A study of serology and cellularly defined DLA haplotypes and their segregation

The polymerase chain reaction based restriction fragment length polymorphism (PCR-RFLP) method was used to study DLA class II gene in dogs. Genomic DNA from 11 DLA homozygous reference dogs representing 8 different haplotypes and 2 families with a total of 16 animals were amplified by the oligonucleotide primer pair (HLA-DRB-AMP-A/B) cross-hybridizing HLA-DRB specific and fit for the amplification of DLA-DRB1 gene. The corresponding amplified DNA products were 235 base pairs. Amplified DNA was digested by 32 different restriction endonucleases, which could recognize allelic variations within DLA-DRB. After digesting only with Hae III, Hha I, Hinf I, Rsa I and Sau96 I high polymorphism was revealed respectively and 9 distinct RFLP pattern were shown, which could be correlate to the DLA haplotypes studied. The 8 cellular established DLA-D specificities present in the reference panel were defined unequivocally by PCR-RFLP and correlated with DLA-Dw5 and Dw6 two subtypes. The segregation pattern of four different DLA-DRB types could be demonstrated in two families. Based on these data we conclude that PCR-RFLP typing utilizing the above mentioned primer pair and endonucleases is a valuable tool to define DLA class II types in the dog.

Cloning of a polymorphic canine genetic marker which maps to human chromosome 9

We describe the cloning of a novel canine polymorphic genetic marker which maps to human chromosome 9. The sequence is 2092 bp, 59% GC rich, and contains three GC boxes. Chemiluminescent probing of zooblots showed evolutionary conservation. Dogs have three BamHI alleles: 2.3 kb, 2.1 kb and 1.7 kb. Allele frequencies in 17 unrelated dogs representing 13 breeds are presented. Polymorphism for the 1.7-kb allele in beagles is common. The 2.1-kb allele is probably the ancestral allele since it is the most common and is also noted in the Cape hunting dog. Interestingly, in more than 50 dogs tested to date, the 2.3-kb allele has been found only in miniature and giant schnauzers. This points to a common origin for these two breeds.

Towards covering immunological genes with highly informative markers: a trans-species approach

To establish a highly informative screening system for immunologically relevant genes ("immunoprinting") we co-amplified via polymerase chain reaction (PCR) polymorphic exons plus adjacent intronic simple repetitive dinucleotide stretches in the T-cell receptor (Tcr) Vb6 and Major Histocompatibility Complex (MHC)-DRB loci in man and several ungulate species. In both gene families the basic structure of the simple repeat was found to be preserved for more than 70 x 10(6) years in all investigated species. The simple repeats exhibit extensive length variability. Distinct exon sequences are correlated with a defined repeat length and substructure. In addition, PCR and the oligonucleotides for typing were applicable to a broad range of species from different mammalian orders. Multiplex PCR of different members of the Tcr Vb6 family and MHC-DRB resulted in a complex pattern similar to an oligolocus fingerprint. Hence immunoprinting can be employed for searching for associations of immunologically relevant genes with diseases even across species barriers.

Immunological characterization of canine hematopoietic progenitor cells

Canine hematopoietic progenitor cells were characterized by separation with monoclonal antibodies. Depleted and enriched fractions were studied for growth of CFU-GM in semisolid agar and for repopulating capacity of lethally irradiated dogs. CFU growth was not reduced by depletion of marrow using monoclonal antibodies F 3-20-7 (anti-dog Thy-1), MT606 (anti-human CD 6), and IOT2a (anti-human DR). CFU growth was variable following treatment with the anti-canine T-cell antibody MdT-P 1 and immunomagnetic bead separation. It was regularly enriched when MdT-P 1 treatment was followed by immunorosetting with staphylococcal protein A-loaded sheep red blood cells and density gradient separation. Lethally irradiated dogs were reconstituted by autologous marrow depleted of MdT-P 1-positive cells using immunorosetting and density gradient centrifugation, whereas immunomagnetic bead-depleted marrow was ineffective. Fluorescence-activated cell sorting showed enrichment of hematopoietic progenitor cells in the weakly MdT-P 1-positive fraction.

Correlation of RFLP typing and MLC reactivity in dogs

The human recombinant HLA-DRB1 gene probe was used for histocompatibility typing of two families of beagles for the DLA-D equivalent by using restriction fragment length polymorphisms (RFLP). This method was able to determine the segregation of these genes from the parental animals to the individual F1 offspring. Mixed lymphocyte culture (MLC) reactivity as well as serological typing for class I histocompatibility antigens were also performed for comparison. It was found that there was a high correlation between these three methods. We therefore conclude that RFLP typing is an effective procedure for predicting MLC reactivity in dogs and propose that it is a suitable genotyping method for assignment of class II antigen compatibility for donor-recipient pairs in conjunction with organ transplant studies.

Allelic variation in the DR subregion of the canine major histocompatibility complex

Allelic variation in the DR subregion of the canine major histocompatibility complex (DLA) has been analyzed by nucleic acid sequencing of cDNA clones of DRB genes amplified in vitro by the reverse transcriptase-polymerase chain reaction (RT-PCR). Sequence analysis of a panel of 19 homozygous typing cell dogs representing 12 different DLA-D types (defined by mixed leucocyte reaction) demonstrated the presence of one expressed DRB locus with at least nine distinct alleles in the dog. Unique DLA-DRB alleles were found in the DLA-D types Dw1, Dw3, Dw4, Dw8 (workshop assignments) and D4, D6, D7, D8, and D9 (Seattle assignments). In contrast, the DRB genes of the remaining three DLA-D types (D1, D10, and D16) were identical to those of Dw3/Dw4 (for D1), Dw8 (for D10), and D6 (for D16). The nucleotide sequences of all nine DLA-DRB alleles were typical of functional major histocompatibility complex (MHC) class II beta chains and contained three allelic hypervariable regions (HVRs) in the beta 1 domain at positions 8-16, 26-39, and 57-74. At each variable residue, two to five amino acid substitutions were found. The most polymorphic residues were located at positions 37 (with five amino acid substitutions), 11, 13, 28, and 71 (each with four substitutions). The DLA-DRB alleles had 96%-99% overall nucleotide sequence similarity and 93%-99% amino acid sequence similarity with each other. Cluster analysis of the nucleotide and predicted amino acid sequences subdivided the DLA-DRB alleles into three major allelic groups which may represent the canine counterparts of the supertypic groups described in man.

RFLP analysis of DLA class I genes in the dog

Human major histocompatibility complex (HLA) cDNA probes for class I genes HLA-A,B and HLA-E were used to analyze the Restriction Fragment Length Polymorphism (RFLP) of the class I region of the canine major histocompatibility complex (DLA) in 40 dogs. The Southern blot analysis demonstrated that the dog genome contains at least eight class I genes, including the canine homologues of HLA-A,B and HLA-E genes. The DNA polymorphism detected by the HLA-B7 probe corresponded to the serologically defined DLA-A allelic series. Restriction fragments that correlated with the DLA-A2, -A7 and -A9 antigenic specificities were identified in PstI digests of genomic DNA. The RFLP analysis was particularly useful in genotyping dogs which were not clearly DLA-A typable by serology. This technique can be used as a supplement to serotyping and as a genotyping tool for DLA antigenic specificities for which specific antisera are not available.

Characterization of class II alpha genes and DLA-D region allelic associations in the dog

Human major histocompatibility complex (HLA) cDNA probes were used to analyze the restriction fragment length polymorphism (RFLP) of the alpha genes of the DLA-D region in dogs. Genomic DNA from peripheral blood leucocytes of 23 unrelated DLA-D homozygous dogs representing nine DLA-D types (defined by mixed leucocyte reaction) was digested with restriction enzymes (BamHI, EcoRI, Hind III, Pvu II, Taq I, Rsa I, Msp I, Pst I and Bgl II), separated by agarose gel electrophoresis and transferred onto Biotrace membrane. The Southern blots were successively hybridized with radiolabelled HLA cDNA probes corresponding to DQ, DP, DZ and DR alpha genes. Clear evidence was obtained for the canine homologues of DQ and DR alpha genes with simple bi- or tri-allelic polymorphism respectively. Evidence for a single, nonpolymorphic DP alpha gene was also obtained. However, the presence of a DZ alpha gene could not be clearly demonstrated in canine genomic DNA. This report extends our previous RFLP analysis documenting polymorphism of DLA class II beta genes in the same panel of homozygous typing cell dogs, and provides the basis for DLA-D genotyping at a population level. This study also characterizes the RFLP-defined preferential allelic associations across the DLA-D region in nine different homozygous typing cell specificities.