HLA class I and II typing using cells positively selected from blood by immunomagnetic isolation - a fast and reliable technique

This paper describes a new cell isolation and HLA typing technique, which permits cell separation and HLA class I or class II typing to be performed in 70 min. Magnetic monodisperse microspheres (Dynabeads TM) were coated with monoclonal antibodies (MAbs) specific for the CD8 T cell antigen or for HLA class II monomorphic epitopes. They could then be used to obtain HLA class I or class II positive cells directly from ACD blood in approximately 15 min by the use of magnetic separation. The cells (attached to the microspheres) were subsequently used in microcytotoxic HLA typing (total incubation time of 55 min) using acridin orange/ethidiumbromide to stain viable (yellow) and dead (red) cells. It was found that this immunomagnetic (IM) HLA typing technique was specific, has a sensitivity superior to that observed for conventional microcytotoxicity assays and gave low background staining. IM HLA-ABC typing of 50 healthy donors and 10 patients and IM HLA-DR typing of 25 healthy donors and 30 patients gave results corresponding well with that obtained independently by conventional HLA typing (concordancy rates 92-100%). Furthermore, the IM HLA typing technique permitted reliable HLA class II typing of blood cells from six patients where conventional HLA class II typing was impossible. The IM HLA typing technique also enables HLA class I and II typing to be quickly and reliably performed on cells from ACD blood of cadaveric donors.     

Techniques used to define human MHC antigens: serology

The classical, routine test employed for definition of HLA antigens expressed in humans (tissue typing) is the complement-mediated cytotoxicity assay developed by Terasaki and McClelland in the early 1960s. In both healthy persons and patients, the assay target cells are usually lymphocytes obtained from peripheral blood, but when typing cadaver donors, splenic or lymph node lymphocytes can be used. HLA-A, B, Cw (class I) antigens are expressed on all nucleated cells while HLA-DR, DQ (class II) are restricted to B lymphocytes and immune activated cells. Tissue typing has been achieved using culture cells from amniocentesis and typing of cell lines is possible with small modifications to the standardised cytotoxicity assay. Usually, target cells are incubated under oil with typing antisera at 22 degrees C in a 60- or 72-well Terasaki tray. After 30 min rabbit serum is added as a source of complement. After a further 60 min incubation the test is stained. A positive reaction results in target cell death. There are local variations to this test. Automation of the assay is now commonplace, from reagent dispensing to automated reading of finished assay. The use of antibody-coated magnetisable microspheres has enabled separation of pure B lymphocyte samples for class II typing and has reduced incubation times through antigen modulation. It is possible to define antibodies to HLA antigens in the same assay using target cells with known HLA phenotypes.     

DNA amplification for DQ typing as an adjunct to serological prenatal HLA typing for the identification of potential donors for umbilical cord blood transplantation.

It has recently been demonstrated that umbilical cord blood from genotypically human leukocyte antigen (HLA)-matched donors can provide sufficient numbers of progenitor cells for hematopoietic reconstitution. This technique has been successfully applied in the treatment of two children affected with Fanconi anemia (FA). Fetal cells from the potential sibling donors were first tested to determine that the fetus was not affected with FA. Unaffected fetal cells were then tested for HLA type. Cord blood from compatible donors can be harvested at birth and used immediately or frozen for subsequent use in hematopoietic reconstitution. We now show that fetal cell DNA amplification and hybridization for DQ typing can be an important adjunct procedure to verify serologically determined HLA class II types and/or to establish class II haplotype identity with the affected sibling.     

Recovery of lymphocytes from clotted blood for HLA typing

A method to recover lymphoid cells from clotted blood for the microcytotoxicity test used in HLA typing is described. The procedure consists of disruption of the clotted blood followed by Ficoll-Hypaque gradient purification of the mononuclear cells. The results of HLA typing of lymphocytes from unclotted and clotted blood were identical.     

Response of Primed LD Typing Cells to Homozygous Typing Cells

At least two different methods using cellular responses have been described for defining the determinants of the HLA-D region: typing with HLA-D homozygous cells and primed LD typing. Primed LD typing cells were generated in one-haplotype-different combinations and grouped on the basis of two or more cells appearing to define the same HLA-D-region-determined PL antigen. Such cells were restimulated with homozygous typing cells for several of the presently known HLA DW clusters. A very strong correlation was noted: PLT cells defining the antigen PL1 were restimulated with homozygous typing cells for DW3, those PLT cells defining the antigen PL2 were restimulated by homozygous typing cells for DW2, and those defining PL5 were restimulated by homozygous typing cells for DW1.     

Two new HLA Cw* alleles,Cw*0105 and Cw*1405, detected by sequence based typing

During recent years, the view of the relative importance of the HLA Cw locus has undergone substantial change. From being an HLA locus with both limited polymorphism and biological significance there are now more than a hundred different alleles known and the biological importance of HLA Cw, both as a transplantation antigen and as a receptor for NK cells, is well established. Sequence based typing has been shown to be a powerful tool, especially for HLA Cw typing. Here we describe two new HLA Cw* alleles found during routine typing of potential bone marrow donors and hematological patients. The HLA Cw*0105 differs from Cw*0102 at positions 361 and 368 in exon 3 leading to a Trp to Arg and Cys to Ser substitution, respectively. HLA Cw*1405 differs from Cw*14021 by a single nucleotide substitution at position 368. This mutation results in an amino acid substitution of Phe for Tyr.     

Serological detection and molecular localization of allelic HLA-DP supertypic epitopes

A DP serological allospecificity was identified using 125I-labeled preparations of HLA class II molecules isolated from cells of HLA homozygous typing cell lines, SLE (DRw6, DQw1, DPw3) and WT46 (DRw6, DQw1, DPw2), and depleted of DR molecules by absorption with an anti-DR monoclonal antibody. The specificity, provisionally called WT, was carried by class II molecules possessing the characteristics of DP molecules on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and detected primarily in DPw1, DPw3 and DPw5 cells and exceptionally in some DPw2 cells including WT46 and DPw4 cells on a large panel of DP-pretyped B cell lines mostly derived from the 10th International Histocompatibility Workshop B cell reference panel. It was apparently allelic to another DP serological specificity BUT previously defined on DP molecules isolated from cells of DPw2+ HLA deletion mutant cell line LCL 721.82. On the same cell panel; the BUT specificity was negative in all DPw1, DPw3 and DPw5 cells, and positive in all DPw2 and DPw4 cells and also in DPw2B and DPw4B cells except the cells typed WT+. This DP association pattern was similar to that of the known allelic sequences, GGPM and DEAV, in DP beta F segment, one of the six variable segments in the second exon of DP beta gene. Thus, genomic DNA from 22 B cell lines pretyped for BUT and WT specificities were enzymatically amplified for the second exon of DP beta gene by the use of locus-specific oligonucleotide primers and hybridized with 32P-labeled oligonucleotide probes corresponding to the F segment sequence variations. This oligonucleotide typing showed perfect one-to-one correlation with the BUT and WT serological typing. The typing also revealed that WT46 cells, although typed DPw2, have the DEAV sequence common to DPw1, DPw3 and DPw5.     

A one-step monoclonal antibody typing procedure that simplifies HLA class I and class II typing

Abstract: We have developed monoclonal antibodies to most HLA specificities, making it possible for us to devise a simple, rapid, one-step micro-cytotoxicity test. The test is performed by adding 1 μl of cells to 1 μl of antibody-complement mixture predotted on the microtest tray. The reactions are read following a 1-hour incubation period (30 minutes in some instances). The analysis of reactions seen on testing 105 class I antibodies and 50 class II antibodies is shown. A comparison of typing by the standard NIH method and the new one-step procedure showed a > 96% concordance in the 500 T cells and 200 B cells we examined. Class I and class II typing could be performed using B cells, thus obviating the need to isolate both T and B cells for HLA typing.     

A new approach to HLA typing designed for solid organ transplantation: epityping and its application to the HLA‐A locus

HLA‐specific antibodies bind discrete clusters of amino acids called epitopes, but serological assignment of antibody specificities makes no reference to this. As HLA typing for solid organ transplantation is provided at only medium (serologically equivalent) resolution, this means that recipient HLA antibodies to donor HLA epitopes may not be identified. We have designed a novel and rapid HLA‐A epitope typing method (epityping) using a two‐stage PCR‐SSP‐based method to detect the HLA‐A locus epitopes described by El Awar et al. 2007, Transplantation, 84 , 532. The initial PCR step utilizes HLA‐A locus‐specific primers; the product is cleaned using the QIAquick Spin Purification procedure. The purified product is tested using our in‐house epitope‐specific primer panel, the results being visualized using gel electrophoresis. Twenty two UCLA DNA Exchange samples were epityped, blinded to the HLA type. Of the 75 primer pairs, the mean correlation coefficient was 0.95 with each sample giving 67 or more correct primer results. In all cases, it was possible to derive the first field classic HLA type from the epityping results. These results indicate that a method for identification of HLA epitopes which is comparable in time, cost and technical expertise to current HLA typing methods is achievable. Redesigning HLA typing to correlate with what the antibody binds should minimize inappropriate organ allocation. We suggest that epityping provides a more effective method than standard HLA typing for solid organ transplantation.     

Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing

We report the development of a general methodology to genotype HLA class I and class II loci. A Whole Genome Amplification (WGA) step was used as a sample sparing methodology. HLA typing data could be obtained with as few as 300 cells, underlining the usefulness of the methodology for studies for which limited cells are available. The next generation sequencing platform was validated using a panel of cell lines from the International Histocompatibility Working Group (IHWG) for HLA-A, -B, and -C. Concordance with the known, previously determined HLA types was 99%. We next developed a panel of primers to allow HLA typing of alpha and beta chains of the HLA DQ and DP loci and the beta chain of the DRB1 locus. For the beta chain genes, we employed a novel strategy using primers in the intron regions surrounding exon 2, and the introns surrounding exons 3 through 4 (DRB1) or 5 (DQB1 and DPB1). Concordance with previously determined HLA Class II types was also 99%. To increase throughput and decrease cost, we developed strategies combining multiple loci from each donor. Multiplexing of 96 samples per run resulted in increases in throughput of approximately 8-fold. The pipeline developed for this analysis (HLATyphon) is available for download at https://github.com/LJI-Bioinformatics/HLATyphon.     

The impact of transfused blood products on deceased donor HLA typing

Accurate deceased donor HLA typing assumes that the blood sample tested contains only DNA from the organ donor. Prior to procurement, many organ donors are transfused at least one unit of red blood cells (RBC). Non-organ donor DNA acquired from transfusions may result in incorrect and/or ambiguous HLA typing. To address this question, we investigated the impact of RBC transfusion on organ donor HLA typing by using different in vitro transfusion models: leukoreduced (LR) and non-LR RBCs. Various quantities of LR and non-LR RBCs were added to normal peripheral blood and HLA typing was performed by real time PCR. Our results show that HLA typing of deceased donors can be impacted dependent upon the type and quantity of transfused RBCs. Importantly, if LR RBCs are given, HLA typing is unlikely to be affected, precluding the need to delay typing and obtain an alternative source of donor DNA.     

Comparison of HLA-A antigen typing by serology with two polymerase chain reaction based DNA typing methods: implications for proficiency testing

Serology has been routinely used for class I HLA typing for the selection of donors for allotransplantation. However, serology is not adequate for the assignment of all class I specificities especially when testing non-Caucasians subjects and it is necessary to adopt new strategies for routine testing. At the present time the extent of incorrect serologic HLA-A assignments in clinical testing is not known. The polymerase chain reaction (PCR) based techniques have become useful standard clinical typing methods of HLA class II alleles but most laboratories still use serology for class I typing. In this report we have compared two PCR based techniques, PCR amplification with sequencespecific primers (PCR-SSP) and PCR amplification and subsequent hybridization with sequence-specific oligonucleotide probes (PCR-SSOP), for the assignment of HLA-A specificities in 56 blood samples from patients and families serologically typed for HLA-A. This side-by-side comparison of PCR methods showed 100% correlation between them. However, serology showed 7.1% misassignments and, in an additional panel of 19 cells where serology produced equivocal results, the PCR-SSP and SSOP methods identified the correct HLA-A specificity. Our results emphasize the need to complement routine serologic testing of HLA specificities with a small number of primers designed to test HLA-A34, A36, A43, A66, A74 and A80, that are not detected with high precision by serology. We concluded that the PCR-SSP and -SSOP methods can be used in routine HLA-A typing of patients and donors for transplantation with a greater precision than serology.     

HLA Haplotype Validator for quality assessments of HLA typing

HLA alleles are observed in specific haplotypes, due to Linkage Disequilibrium (LD) between particular alleles. Haplotype frequencies for alleles in strong LD have been established for specific ethnic groups and racial categories.Application of high-resolution HLA typing using Next Generation Sequencing (NGS) is becoming a common practice in research and clinical laboratory settings.HLA typing errors using NGS occasionally occur due to allelic sequence imbalance or misalignment. Manual inspection of HLA genotypes is labor intensive and requires an in-depth knowledge of HLA alleles and haplotypes.We developed the “HLA Haplotype Validator (HLAHapV)” software, which inspects an HLA genotype for both the presence of common and well-documented alleles and observed haplotypes. The software also reports warnings when rare alleles, or alleles that do not belong to recognized haplotypes, are found.The software validates observable haplotypes in genotype data, providing increased confidence regarding the accuracy of the HLA typing, and thus reducing the effort involved in correcting potential HLA typing errors. The HLAHapV software is a powerful tool for quality control of HLA genotypes prior to the application of downstream analyses.We demonstrate the use of the HLAHapV software for identifying unusual haplotypes, which can lead to finding potential HLA typing errors.     

Statistical methods for studying homozygous typing cells of unknown specificity

A situation can arise in D typing in which the HLA (A,B,C,D, or DR) specificities of the responders are known and the specificities of the HTC's are unknown. The powerful and direct method of detecting association between the unknown stimulator (HTC) and any given HLA specificity is by comparing the observed double normalized values (DNV's) of individuals known to be positive for the specificity with DNV's of negative individuals. This can be done by comparing the two groups with a Kolmogorov-Smirnov test (K-S test), an established statistical procedure for evaluating correlation between continuous variables, such as the DNV, and discrete variables (such as presence of D type). The application of the K-S test will generate as a “cutoff” value the point that maximizes the average of the frequencies of correct assignments in D positives and D negatives. We also propose an alternative method of computing the “r” value. We have analyzed 49 HTC's from the 8th International Workshop and present the association observed with the D and DR specificties.     

A double determinant immunoassay for HLA class I typing using serum as an antigen source

We have applied a double determinant immunoassay (DDIA) to HLA-A2,A28, and B13 typing, using serum as an antigen source. The results obtained show a correlation of 96% (B13) and 89.1% (A2,A28) with the results obtained by conventional HLA typing. Furthermore, the results obtained were highly reproducible, since testing of 18 sera on two occasions gave concordant results with all samples tested. The variation in the content of HLA-A2 antigens in sera taken at different times from a given donor was less than 5%. A sevenfold variation was found in the serum level of HLA-A2,A28 antigens: the highest level was found in the sera from HLA-A2,A28 donors and in decreasing order in HLA-A2 homozygous, HLA-A28 homozygous, HLA-A2 heterozygous, and HLA-A28 heterozygous donors. The results of this study indicate that the DDIA is a sensitive, simple, and reproducible procedure for HLA class I typing. The DDIA offers the following advantages in comparison with the conventional lymphocytotoxic assay: it provides information not only about the expression of a given alloantigen, but also about its level; it does not require viable cells, thus facilitating retrospective studies and typing of leucopenic patients; it eliminates variability of results caused by abnormal susceptibility of target cells to complement-dependent lysis.     

Preimplantation HLA typing: Practical tool for stem cell transplantation treatment of congenital disorders

It is well known that to achieve an acceptable engraftment and survival in stem cell therapy, an human leukocyte antigens (HLA) identical stem cell transplant is strongly required. However, the availability of the HLA matched donors even among family members is extremely limited, so preimplantation HLA typing provides an attractive practical tool of stem cell therapy for children requiring HLA matched stem cell transplantation. The present experience of preimplantation genetic diagnosis (PGD) for HLA typing of over one thousand cases shows that PGD provides the at-risk couples with the option to establish an unaffected pregnancy, which may benefit the affected member of the family with hemoglobinopathies, immunodeficiencies and other congenital or acquired bone marrow failures. Despite ethical issues involved in preimplantation HLA typing, the data presented below show an extremely high attractiveness of this option for the couples with affected children requiring HLA compatible stem cell transplantation.     

Immunogenetics of HLA null alleles: implications for blood stem cell transplantation

The transplantation of haematopoietic stem cells is a potentially curative therapy for a variety of haematological and non-haematological diseases. Matching of donor and recipient for human leucocyte antigens (HLA) is pivotal for the success of blood stem cell transplantation. HLA null alleles are characterized by the lack of a serologically detectable product. Because serological HLA diagnostics are increasingly replaced by DNA-based typing methods considering only small regions of the genes, null alleles may be misdiagnosed as normally expressed variants. The failure to identify an HLA null allele as a non-expressed variant in the stem cell transplantation setting may result in an HLA mismatch that is highly likely to stimulate allogeneic T cells and to trigger graft-vs-host disease. For some HLA null alleles, the translation into a truncated polypeptide chain seems possible, which thus might act as minor histocompatibility antigens. Because the prevalence of HLA null alleles may be around 0.3% or even higher, a screening strategy for HLA null alleles should, therefore, be implemented in the clinical laboratory. It may consist of the combination of serology and standard molecular typing techniques. As the standard molecular techniques are sometimes troublesome especially for characterizing the cytosine island at the 5' end of HLA class I exon 4 and need continuously be updated, an alternative approach may consist of sequencing all samples from genomic DNA for exons 2-3 or 4 (class I) or exon 2 (class II), including the adjacent intron splicing sites. This approach will detect 36/40 so far known non-expressed variants and has the potential to easily uncover novel variants, thus essentially minimizing the risk of overlooking these challenging variants.     

Molecular strategies to define HLA haplotype loss in microdissected tumor cells

Loss of heterozygosity (LOH) of chromosome 6p21 is an important mechanism that generates HLA haplotype loss in various human tumors. This mechanism produces non-reversible HLA-deficient tumor cells that can escape T cell immune responses in peptide-vaccinated cancer patients. However, the exact frequency of this mechanism is still unknown, because contaminating stroma in solid tumor tissues masks the tumor DNA obtained from solid samples. A microdissection technique was applied to 4-8 microm sections of cryopreserved tumor tissues from a group of colorectal and laryngeal carcinomas. Fifteen patients were analyzed for the presence of LOH associated with the beta(2)-microglobulin gene in chromosome 15, and five patients for LOH associated with HLA genes in chromosome 6. In two cases, autologous metastasis tissue samples were also available. The patients were selected for showing an altered HLA class I tumor phenotype as determined by immunohistological techniques. DNA was obtained from this microdissected material and amplified in order to detect the presence or absence of nine previously selected microsatellite markers. HLA sequence based typing (SBT) was also applied to these microdissected DNA samples to define the HLA genotype. Microdissection greatly improved the definition of LOH, with nearly 100% signal reduction in one of the alleles. In addition, this procedure allowed us to detect beta(2)-microglobulin LOH in tumors that expressed some HLA molecules. Our data indicate that this procedure can be successfully applied to microdissected samples from solid tumors, thus enhancing the power and sensitivity of LOH detection.     

Use of monocytes in HLA-A,B, C and DR typings

A simple method of improved serologic typing of monocytes for HLA-A, B, C and DR specificities is described. The method employs monocytes recovered from frozen samples of peripheral blood mononuclear cells; it chiefly involves pretreatment of monocytes with 0.01% iodoacetamide (IAA) prior to typing. The advantage of this method lies principally in the lowering of the background nonspecific cytotoxicities and false positive readings upon IAA addition to the monocyte preparations. Using this method monocytes can be typed for HLA-A, B, C determinants. Although the addition of IAA results in substantial typing improvements, we found the assignment of A, B, C specificities difficult due to the presence of extra positive reactions when monocytes were compared to T lymphocyte typings. probably due to the presence of DR or monocyte specific antibodies in the routinely used HLA antisera. This method proved to be most useful in DR typings where mono cytes in the presence of IAA were compared with autologous B cells in the absence of IAA. The differences in typings due to a decrease in false positive cytotoxic readings were significantly in favor of using IAA treated monocytes in DR typings (P < 0.0001). The use of IAA in the course of B cell or T cell typings bad no adverse consequences on either A, B, C or DR typings, respectively. Our results indicate a potential usefulness for the use of IAA in typing monocytes HLA determinants in general and for the DR determinants in particular.