Tissue typing the HLA-A locus from genomic DNA by sequence-specific PCR: comparison of HLA genotype and surface expression on colorectal tumor cell lines

HLA Class I Analysis Provides Insight Into the Genetic and Epigenetic Background of Immune Evasion in Colorectal Cancer With High Microsatellite Instability

BACKGROUND & AIMS

A detailed understanding of antitumor immunity is essential for optimal cancer immune therapy. Although defective mutations in the B2M and HLA-ABC genes, which encode molecules essential for antigen presentation, have been reported in several studies, the effects of these defects on tumor immunity have not been quantitatively evaluated.

METHODS

Mutations in HLA-ABC genes were analyzed in 114 microsatellite instability-high colorectal cancers using a long-read sequencer. The data were further analyzed in combination with whole-exome sequencing, transcriptome sequencing, DNA methylation array, and immunohistochemistry data.

RESULTS

We detected 101 truncating mutations in 57 tumors (50%) and loss of 61 alleles in 21 tumors (18%). Based on the integrated analysis that enabled the immunologic subclassification of microsatellite instability-high colorectal cancers, we identified a subtype of tumors in which lymphocyte infiltration was reduced, partly due to reduced expression of HLA-ABC genes in the absence of apparent genetic alterations. Survival time of patients with such tumors was shorter than in patients with other tumor types. Paradoxically, tumor mutation burden was highest in the subtype, suggesting that the immunogenic effect of accumulating mutations was counterbalanced by mutations that weakened immunoreactivity. Various genetic and epigenetic alterations, including frameshift mutations in RFX5 and promoter methylation of PSMB8 and HLA-A, converged on reduced expression of HLA-ABC genes.

CONCLUSIONS

Our detailed immunogenomic analysis provides information that will facilitate the improvement and development of cancer immunotherapy.

Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy

Anti-PD-1 therapy is used as a front-line treatment for many cancers, but mechanistic insight into this therapy resistance is still lacking. Here we generate a humanized (Hu)-mouse melanoma model by injecting fetal liver-derived CD34⁺ cells and implanting autologous thymus in immune-deficient NOD-scid IL2Rγ^null (NSG) mice. Reconstituted Hu-mice are challenged with HLA-matched melanomas and treated with anti-PD-1, which results in restricted tumor growth but not complete regression. Tumor RNA-seq, multiplexed imaging and immunohistology staining show high expression of chemokines, as well as recruitment of FOXP3⁺ Treg and mast cells, in selective tumor regions. Reduced HLA-class I expression and CD8⁺/Granz B⁺ T cells homeostasis are observed in tumor regions where FOXP3⁺ Treg and mast cells co-localize, with such features associated with resistance to anti-PD-1 treatment. Combining anti-PD-1 with sunitinib or imatinib results in the depletion of mast cells and complete regression of tumors. Our results thus implicate mast cell depletion for improving the efficacy of anti-PD-1 therapy.

Immune checkpoint therapies (ICT) are promising for treating various cancers, but response rates vary. Here the authors show, in mouse models, that tumor-infiltrating mast cells colocalize with regulatory T cells, coincide with local reduction of MHC-I and CD8 T cells, and is associated with resistance to ICT, which can be reversed by c-kit inhibitor treatment.

MHC Class I Regulation: The Origin Perspective

Viral-derived elements and non-coding RNAs that build up “junk DNA” allow for flexible and context-dependent gene expression. They are extremely dense in the MHC region, accounting for flexible expression of the MHC I, II, and III genes and adjusting the level of immune response to the environmental stimuli. This review brings forward the viral-mediated aspects of the origin and evolution of adaptive immunity and aims to link this perspective with the MHC class I regulation. The complex regulatory network behind MHC expression is largely controlled by virus-derived elements, both as binding sites for immune transcription factors and as sources of regulatory non-coding RNAs. These regulatory RNAs are imbalanced in cancer and associate with different tumor types, making them promising targets for diagnostic and therapeutic interventions.

A density-watershed algorithm (DWA) method for robust, accurate and automatic classification of dual-fluorescence and four-cluster droplet digital PCR data

Droplet digital PCR (ddPCR) is a single-molecule amplification technology with broad applications in precision medicine and clinical diagnosis. Dual-fluorescence and four-cluster ddPCR (two/four-ddPCR) assay is an effective way to quantify copy numbers. Currently, two/four-ddPCR data are usually classified with manual thresholds. For clinical applications, automatic and accurate methods are required to avoid subjectivity in diagnosis. Although there are some automatic classification algorithms, their accuracy and robustness still need to be improved to meet the needs of clinical diagnosis. Therefore, a new method is in high demand to automatically classify two/four-ddPCR data in an accurate and robust way. Here, a novel density-watershed algorithm (DWA) method was developed for the accurate, automatic and unsupervised classification of two/four-ddPCR data. First, data gridding was applied to a scatter plot of the fluorescence signal intensity to calculate data densities. Based on the data densities, the watershed algorithm was used to divide the gridded scatter plot into isolated regions automatically. Next, an optimal cluster pattern was determined based on these isolated regions, and excess regions were merged. Finally, the two/four-ddPCR data were classified based on the merged regions, and DNA template copy numbers were calculated accordingly. Using the DWA method for the quantification of both wild types and mutants of epidermal growth factor receptor (EGFR) L858R and T790M, the classification results were highly consistent with expectations, and significantly better than commonly-used automatic algorithms for now. The computed template copy numbers scaled proportionally to the relative concentration of input templates (r2 > 0.998) in four orders of magnitude with a good reproducibility, and achieved a limit of detection over 40 times lower than the commonly-used automatic algorithms. Furthermore, the DWA method was validated on 254 clinical DNA samples derived from frozen tissues, formalin-fixed paraffin-embedded tissues and peripheral blood. In most cases, the DWA method derived accurate and valid classification results. This highly effective DWA method may be widely used for automatically classifying two/four-ddPCR data, and it will greatly promote the application of ddPCR in clinical diagnosis.

MHC/HLA Class I Loss in Cancer Cells

In this chapter I describe Tumour Immune Escape mechanisms associated with MHC/HLA class I loss in human and experimental tumours. Different altered HLA class-I phenotypes can be observed that are produced by different molecular mechanisms. Experimental and histological evidences are summarized indicating that at the early stages of tumour development there is an enormous variety of tumour clones with different MHC class I expression patterns. This phase is followed by a strong T cell mediated immune-selection of MHC/HLA class-I negative tumour cells in the primary tumour lesion. This transition period results in a formation of a tumour composed only of HLA-class I negative cells. An updated description of this process observed in a large variety of human tumors is included. In the second section I focus on MHC/HLA class I alterations observed in mouse and human metastases, and describe the generation of different tumor cell clones with altered MHC class I phenotypes, which could be similar or different from the original tumor clone. The biological and immunological relevance of these observations is discussed. Finally, the interesting phenomenon of metastatic dormancy is analyzed in association with a particular MHC class I negative tumor phenotype.

HLA typing by sequence-specific primers

HLA typing by sequence-specific primers (PCR-SSP) is a commonly used technique in HLA typing in which multiple pairs of cis-located allele-specific primers are used to determine the alleles present in a given DNA sample. Although the technique is around two decades old, it still offers a relatively straight forward way of typing and has the benefit of using commonly available laboratory equipment. Here we describe the background of the PCR-SSP, how to design and validate reactions, and common problems that arise.

HLA typing by SSO and SSP methods

Human leukocyte antigen (HLA) typing, utilising the sequence-specific oligonucleotide (SSO) and sequence-specific primer (SSP) technologies, has been in routine use in many tissue typing laboratories worldwide for more than 20 years since the development of the polymerase chain reaction. Both methods are very useful for clinical and research purposes and can provide generic (low resolution) to allelic (high resolution) typing results. This chapter provides an overview of the SSO and SSP methods in relation to HLA typing.

High-throughput high-resolution class I HLA genotyping in East Africa

HLA, the most genetically diverse loci in the human genome, play a crucial role in host-pathogen interaction by mediating innate and adaptive cellular immune responses. A vast number of infectious diseases affect East Africa, including HIV/AIDS, malaria, and tuberculosis, but the HLA genetic diversity in this region remains incompletely described. This is a major obstacle for the design and evaluation of preventive vaccines. Available HLA typing techniques, that provide the 4-digit level resolution needed to interpret immune responses, lack sufficient throughput for large immunoepidemiological studies. Here we present a novel HLA typing assay bridging the gap between high resolution and high throughput. The assay is based on real-time PCR using sequence-specific primers (SSP) and can genotype carriers of the 49 most common East African class I HLA-A, -B, and -C alleles, at the 4-digit level. Using a validation panel of 175 samples from Kampala, Uganda, previously defined by sequence-based typing, the new assay performed with 100% sensitivity and specificity. The assay was also implemented to define the HLA genetic complexity of a previously uncharacterized Tanzanian population, demonstrating its inclusion in the major East African genetic cluster. The availability of genotyping tools with this capacity will be extremely useful in the identification of correlates of immune protection and the evaluation of candidate vaccine efficacy.

Detection of circulating tumour cells in peripheral blood with an automated scanning fluorescence microscope

We have developed an automated, highly sensitive and specific method for identifying and enumerating circulating tumour cells (CTCs) in the blood. Blood samples from 10 prostate, 25 colorectal and 4 ovarian cancer patients were analysed. Eleven healthy donors and seven men with elevated serum prostate-specific antigen (PSA) levels but no evidence of malignancy served as controls. Spiking experiments with cancer cell lines were performed to estimate recovery yield. Isolation was performed either by density gradient centrifugation or by filtration, and the CTCs were labelled with monoclonal antibodies against cytokeratins 7/8 and either AUA1 (against EpCam) or anti-PSA. The slides were analysed with the Ikoniscope® robotic fluorescence microscope imaging system. Spiking experiments showed that less than one epithelial cell per millilitre of blood could be detected, and that fluorescence in situ hybridisation (FISH) could identify chromosomal abnormalities in these cells. No positive cells were detected in the 11 healthy control samples. Circulating tumour cells were detected in 23 out of 25 colorectal, 10 out of 10 prostate and 4 out of 4 ovarian cancer patients. Five samples (three colorectal and two ovarian) were analysed by FISH for chromosomes 7 and 8 combined and all had significantly more than four dots per cell. We have demonstrated an Ikoniscope® based relatively simple and rapid procedure for the clear-cut identification of CTCs. The method has considerable promise for screening, early detection of recurrence and evaluation of treatment response for a wide variety of carcinomas.

Cell growth, global phosphotyrosine elevation, and c-Met phosphorylation through Src family kinases in colorectal cancer cells

The heterogeneity of cancer cell signaling is a significant obstacle for the effective development and clinical use of molecularly targeted therapies. As a contribution to a better understanding of the diversity of signaling activities in colorectal cancers (CRCs), we have analyzed the activity of Src family kinases (SFKs), which are implicated in human cancer development, in 64 CRC cell lines. A striking diversity of SFK activity was observed within this panel. Importantly, all CRC lines tested depend on SFK activity for their growth. In addition, SFK activity levels strongly correlated with global levels of tyrosine-phosphorylated (pTyr) proteins in CRC lines. SFK inhibition substantially reduced these pTyr levels, suggesting that SFKs may function as signal integration points and master controllers for the pTyr protein status in CRC lines. The majority of analyzed CRC lines with high-SFK activity express activated c-Met (pYpY1234/1235), a receptor tyrosine kinase contributing to the regulation of cell proliferation, migration, and invasion. Inhibition of SFKs reduced c-Met phosphorylation in most cases, indicating a reversed signal flow from SFK to c-Met. We conclude that SFK activity is important for the growth of CRC lines, although only low activity levels are required. If this also is true for CRC patients, tumors with low-SFK activity may be particularly sensitive to SFK inhibitors, and such patients should be targeted in clinical trials testing SFK inhibitors.

Sequence-specific primed PCR (PCR-SSP) typing of HLA Class I and Class II alleles

For donor selection in hematopoetic stem cell transplantation, two-digit sequencespecific oligonucleotide (SSO) typing may be sufficient in the related sibling transplant setting. However, SSO typing is not sensitive enough to differentiate between the alleles that share the same cis-trans linkeage sequence casettes. In unrelated donor selection, PCR using sequence-specific primers, a flexible and widely used method known to cause less ambiguious results, may be preferable. However, this technique is limited by the number of the samples that can be processed at one time and also by the number of the primer mixes that can be utilized.

Loss or down-regulation of HLA class I expression at the allelic level in freshly isolated leukemic blasts

Loss or down-regulation of human leukocyte antigen (HLA) class I expression has been demonstrated in a variety of solid tumors. To date, such altered HLA expression has not been studied extensively in freshly isolated leukemic blasts. If it occurs, leukemic cells could escape T-cell surveillance as a consequence. Genotypes of nine leukemic cell lines were determined using a polymerase chain reaction for HLA classes I and II. Cells were also examined for HLA beta2-microglobulin, and allele-specific HLA protein expression using flow cytometry. Next, 44 samples of freshly isolated leukemic blasts from 43 patients with malignant hematological diseases were examined for allele-specific HLA expression using flow cytometry. Microsatellite analysis was performed to determine heterozygosity in the HLA region on chromosome 6. Genotype analysis for HLA class I together with microsatellite analysis demonstrated loss of HLA haplotype in HL-60 cells. No loss of HLA haplotype was observed in 44 samples of freshly isolated leukemic blasts. As reported previously, flow cytometric analysis rarely demonstrated loss or down-regulation of HLA expression at initial diagnosis (3/39; 7.7%); however, this was evident in two of five cases in relapse (40.0%), which contrasts with previous reports. In one patient with acute leukemia, HLA-A2 cell surface expression was present at initial diagnosis, lost at relapse, and completely restored after 48 h of culture in the presence of interferon-gamma. These results suggest loss of allele-specific HLA expression may be involved in the pathogenesis of relapse in patients with leukemia. The findings should be valuable in designing new strategies for clinical immunotherapy.

MHC Class I Antigens and Immune Surveillance in Transformed Cells

MHC class I antigens play a crucial role in the interaction of tumor cells with the host immune system, in particular, in the presentation of peptides as tumor-associated antigens to cytotoxic lymphocytes (CTLs) and in the regulation of cytolytic activity of natural killer (NK) cells. In this review we discuss the role of MHC class I antigens in the recognition and elimination of transformed cells and in the generation of tumor immune escape routes when MHC class I losses occur in tumors. The different altered MHC class I phenotypes and their distribution in different human tumors are the main topic of this review. In addition, molecular defects that underlie MHC alterations in transformed cells are also described in detail. Future research directions in this field are also discussed, including the laboratory analysis of tumor MHC class I-negative variants and the possible restoration of MHC class I expression.

Tumor infiltrating lymphocytes in seminoma lesions comprise clonally expanded cytotoxic T cells

Seminoma lesions are characterized by a brisk inflammatory infiltrate containing both CD4 and CD8 T cells, which is of prognostic significance. However, whether seminoma cells express the HLA molecules required for classical T-cell recognition remains controversial. In the present study, we conducted a molecular, phenotypical and functional characterization of tumor infiltrating lymphocytes (TILs) from seminoma lesions. T-cell receptor clonotype mapping demonstrated the presence of clonally expanded T cells in the majority of the lesions. The cytotoxic capacity of TILs was indicated by expression of CD107a, which is a recently described surrogate marker for cytolytic activity. Indeed, the frequency of CD107a positive cells was substantially higher in TILs when compared to peripheral blood mononuclear cells. Moreover, fluorescence activated cell sorting of CD107a positive TILs allowed comparison of the clonotypic T-cell receptor fingerprint and demonstrated the ability of expanded clones to express this cytotoxic marker, suggesting cytotoxic activity at the tumor site. The cytotoxicity was confirmed by in situ granzyme B expression. Furthermore, by staining with multimeric HLA-peptide complexes, we could demonstrate the presence of Mage-3 specific T cells among TILs. In summary, specific and functional T-cell responses are operative in seminoma, indicating that the inflammatory infiltrate is indeed involved in the immunological control of the tumor.

Longitudinal studies of clonally expanded CD8 T cells reveal a repertoire shrinkage predicting mortality and an increased number of dysfunctional cytomegalovirus-specific T cells in the very elderly

The age-associated decrease in functionality of the human immune system is thought to have a negative impact on the capacity to provide protection against infection, in turn leading to increased incidence of mortality. In a previous longitudinal study of octogenarians, we identified an immune risk phenotype (IRP) in the very elderly defined by an inverted CD4/CD8 ratio, which was associated with increased mortality and persistent CMV infection. In this study, we analyzed the CD8 clonal composition of nonagenarians and middle-aged individuals. An increased number of CD8 T cell clones was observed in the nonagenarians, and was associated with CMV-seropositivity. Surprisingly, CMV-seropositive nonagenarians with the IRP had a significantly lower number of clones compared with non-IRP individuals. The decrease in clone numbers in IRP individuals was associated with shorter survival time. MHC/peptide multimer staining indicated that the frequency of CMV-specific T cells was higher in nonagenarians than in the middle-aged, but the ratio of functionally intact cells was significantly lower. The lowest ratio of functional CMV-specific T cells was found in an IRP individual. A thorough longitudinal analysis of the CMV-specific T cells in nonagenarians showed a stable pattern with respect to frequency, phenotype, and clonal composition. We hypothesize that the number of different CD8 T cell clonal expansions increases as the individual ages, possibly, as a compensatory mechanism to control latent infections, e.g., CMV, but eventually a point is reached where clonal exhaustion leads to shrinkage of the CD8 clonal repertoire, associated with decreased survival.

Distribution of breakpoints on chromosome 18 in breast, colorectal, and pancreatic carcinoma cell lines

Chromosome 18 is frequently rearranged in carcinomas. We explored the distribution of breakpoints affecting chromosome 18 by mapping 56 breakpoints in 26 carcinoma cell lines by fluorescence in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) and band paints. The distribution of breaks among 18 intervals of chromosome 18 was significantly nonrandom. The interval spanning the centromere contained the greatest number of breaks and had the highest average copy number of any interval. There was a high density of breaks close to the centromere as well as actually within the centromere. A cluster of breaks encompassing SMAD4 was associated with the minimum average copy number, consistent with SMAD4 being a tumor suppressor gene. There may be another cluster of breaks around 18q12. We offer two interpretations of the concentration of breaks near the centromere. It may reflect selection for an oncogene near the centromere, or there may be an underlying bias of breakage toward the centromere. We show that the latter is predicted by a simple model that invokes random breakage following anchorage of some random point on the chromosome, or selection of breaks proximal to one of several tumor suppressor genes.

Expression profiling of colon cancer cell lines and colon biopsies: towards a screening system for potential cancer-preventive compounds

Interest in mechanisms of colon cancer prevention by food compounds is strong and research in this area is often performed with cultured colon cancer cells. In order to assess utility for screening of potential cancer-preventive (food) compounds, expression profiles of 14 human cell lines derived from colonic tissue were measured using cDNA microarrays with 4000 genes and compared with expression profiles in biopsies of human colon tumours and normal tissue. Differences and similarities in the gene expression profiles of the cell lines were analysed by clustering and principal component analysis (PCA). Cytoskeleton genes and immune response genes are two functional classes of genes that contributed to the differences between the cell lines. A subset of 72 colon cancer-specific genes was identified by comparing expression profiles in human colon biopsies of tumour tissue and normal tissue. A separation of the cell lines based on the tumour stage of the original adenocarcinoma was observed after PCA of expression data of the subset of colon cancer-specific genes in the cell lines. The results of this study may be useful in the ongoing research into mechanisms of cancer prevention by dietary components.

A mutated HLA-A*0101 allele in the colorectal cell line HCA-7

The colorectal cell line HCA-7 expresses surface human leucocyte antigen-A*0201 (HLA-A*0201), but lacks expression of HLA-A*0101 whilst the normal B-cell line (EVA-1224), derived from the same individual, expresses both surface HLA-A1 and HLA-A2. Amplification refractory mutation system-polymerase chain reaction analysis, using sequence-specific primers, suggested that HCA-7 has a mutation in a 7 base pair (bp) cytosine repeat sequence located at the beginning of Exon 4 (bp 621-627). Cloning and sequencing revealed HCA-7 to have eight cytosine residues in this repeat sequence. In contrast, EVA-1224 contained only 7 cytosines. Analysis of the mRNA for HLA-A*010 using reverse trancriptase-polymerase chain reaction (RT-PCR), with an allele-specific 5' primer in exon 2 (bp 253-271) and a series of 3' primers in exons 3, 4 and 7 and in the 3'untranslated region, revealed that HCA-7 contained a shortened message terminating in the region of the exon 3/4 boundary. The insertion of an extra cytosine in this region, which is only two bases from the exon 3/4 splice site, is presumed to lead to a splicing defect between exons 3 and 4 resulting in the lack of expression of a functional HLA-A*0101 product. HCA-7 is mismatch repair (MMR) defective due to lack of expression of hMLH1 resulting from hypermethylation of the promoter region. The consequential increase in errors in single-nucleotide repeat stretches of DNA can account for the HLA-A*0101 mutation. This has probably then been selected for in the tumour to enable escape from immune attack against an HLA-A*0101-restricted tumour-specific determinant that has also arisen as a result of the tumour being MMR defective.

Interferon-gamma is produced by CD8 T cells in response to HLA-A24-restricted hepatitis C virus epitopes after sustained virus loss

Differences in cytotoxic T lymphocyte activity in hepatitis C virus infection may account for the outcome of interferon monotherapy. To investigate this hypothesis, we analysed the response of peripheral CD8(+) T cells that recognized epitopes presented by HLA-A*2402. We synthesized HLA/beta2-microglobulin/peptide complexes using two epitopes. Production of interferon-gamma by CD8(+) T cells in response to plastic-bound monomeric HLA/peptide complex was observed frequently in sustained virus responders (SVR) (n = 13) against all the peptides, NS31296-1304 (the percentage of responding patients, 61.5%) and core 129-137 (53.8%), while no interferon-gamma production was observed in non-responders (NR) (n = 13) for any of the peptides. Tetramer-staining showed the presence of CD8(+) T cells specific for all the peptides except NS31296-1304 in two SVR at the end of interferon monotherapy, although hardly any such cells were found in four NR. Specific killing was observed against peptides NS31296-1304 (3/4) and core 129-137 (1/4) in sustained responders but none in non-responders. These results suggest that the responses of cytotoxic T lymphocytes (CTLs) were induced during interferon therapy in these patients and that interferon-gamma production by CD8(+) T lymphocytes against HCV NS31296-1304 and core 129-137 are well maintained in patients with SVR compared with those with NR. These findings emphasize the importance of the CD8(+) T cell response in controlling HCV infection.

Involvement of the chaperone tapasin in HLA-B44 allelic losses in colorectal tumors

Tumors can exhibit selective allelic losses of HLA class I antigens as part of altered HLA phenotypes. In colorectal tumors, the HLA class I allele most frequently lost is HLA-B44, although the precise mechanism responsible for this loss has not been described to date. From a total of 95 colorectal cryopreserved tumor samples, we selected (by immunohistochemical staining) 13 tumors with HLA-B44-negative expression. Loss of heterozygosity at 6p21.3 was demonstrated to be the cause of the negative expression in 4 cases. In the remaining 9 cases, structural analyses of microdissected tissue samples of the 3 subtypes of HLA-B44 loss in these tumors (B*4402, B*4403 and B*4405) did not reveal any mutations. However, all 3 subtypes of HLA-B44 presented in this study shared a common characteristic: the presence of an aspartic amino acid residue at position 114 in the HLA class I heavy chain. This residue has been described as determining tapasin dependence for the surface expression of these alleles and therefore for antigen presentation. We studied tapasin transcription by RT-PCR in these tumors and found tapasin downregulation in all 9 tumors samples with the HLA-B44-negative phenotype. In contrast, tapasin was normally transcribed in HLA-B44-positive colorectal tumors samples, as well as in 3 HLA-B44-negative laryngeal carcinomas and 1 bladder tumor. Defective tapasin transcription seems to be an alteration responsible for the absence of HLA-B44 expression in colorectal tumors, thus contributing to the generation of tumor immune escape phenotypes.

Low frequency of HLA haplotype loss associated with loss of heterozygocity in chromosome region 6p21 in clear renal cell carcinomas

HLA class I loss or downregulation is a widespread mechanism used by tumor cells to avoid tumor recognition by cytotoxic T lymphocytes favoring tumor immune escape. Multiple molecular mechanisms are responsible for these altered HLA class I tumor phenotypes. It has been described in different epithelial tumors that loss of heterozygosity (LOH) at chromosome region 6p21.3 is a frequent mechanism that leads to HLA haplotype loss, ranging between 40 and 50%, depending on the tumor entity analyzed. Here we have tested the frequency of LOH at 6p21 chromosome region in Renal Cell Carcinomas (RCC) of the clear cell and chromophobe subtype. A low frequency of HLA haplotype loss (6.6%) was found in clear cell RCC. These data significantly differ from those reported in other epithelial tumors. In contrast, in RCC of chromophobe subtype this frequency was 10 times higher (3 out of 5 cases analyzed). These results indicate that LOH at 6p21.3 is not a frequent mechanism that leads to HLA class I abnormalities in clear cell RCC. In addition, the chromophobe RCC subtypes differ not only in histopathological criteria but also in the frequency of LOH-mediating HLA class I alterations. These results might help to understand the significantly different biological behavior of both RCC subtypes.

Identification of HLA a*0201 glioblastoma multiforme cell lines for immunotherapy by PCR-SSP and DNA sequencing

Most tumor specific antigens characterized to date are restricted by HLA a*0201, which is the major HLA subtype in many ethnic groups. Cancer cells that express tumor antigens in association with the HLA a*0201 subtype have been shown to be responsive to various immunotherapies. We therefore sought to identify glioma cell lines that also express this HLA subtype and determine whether they had the molecular properties needed for tumor-peptide presentation. The HLA a*0201 allele was identified with PCR using sequence-specific primers followed by DNA sequencing. With this method, we screened 15 glioma cell lines to determine if they were of the HLA a*0201 genotype. Glioma cell lines that express the HLA a*0201 subtype were further studied for the expression of MHC class I and beta-2-microglobulin (beta2m) molecules by flow cytometry, and peptide presentation molecules TAP-1, TAP-2, and tapasin by RT-PCR. We identified six out of fifteen cell lines that were of the HLA a*0201 subtype. These cell lines are U87, T98, U373, U138, CRL2365 and UMN-4. All these six cell lines exhibited high levels of MHC class I and beta2m molecules. In addition, these cell lines all expressed molecules required for peptide presentation as shown by the presence of peptide presentation-related molecules TAP-1, TAP-2 and tapasin. The identification of glioma cell lines that express the HLA a*0201 subtype along with the necessary molecules for peptide-presentation will enable their use in developing new immunotherapeutic approaches for treating brain tumors. The method used to identify HLA a*0201 glioma cells is rapid and inexpensive, and suitable for screening tumor cells.

Induction of T lymphocytes specific to human gastric cancer using HLA-A matched allogeneic gastric tumor cells

Tumor-specific cytotoxic T lymphocytes (CTLs) from patients with early-stage tumors are usually more efficient at attacking tumor cells than CTLs from the progressing tumor stages. The authors investigated the antitumor activity of CTLs from gastric cancer patents and healthy donors. In this study, peripheral blood lymphocytes (PBLs) from gastric cancer patients and healthy donors were stimulated with HLA-A matched allogeneic gastric cancer cells such as KATO-3, MKN45, and SGC7901. Three different populations of lymphocyte, p5-CTL-KATO, h4-CTL-MKN45, and h4-CTL-KATO, were induced and expanded. Flow cytometry analyses showed that 85.2% to 97.8% of these cells were CD3-positive and 45.5% to 51.2% were CD8-positive. The induced CTLs efficiently kill HLA-A2 or HLA-A24 gastric cancer cells through CTL-mediated cytotoxicity. However, no effects were observed for other cancer cells or HLA-A2 negative gastric cancer cells. The specific cytotoxicity of the induced CTLs was further confirmed by cold-target inhibition and monoclonal antibody blockage. These results suggest that CTL-mediated cytotoxicity specific for tumor cells can be produced by stimulating PBLs from healthy donors using HLA-A matched tumor cells, which will lead to the development of new immunotherapeutic strategies to kill cancer cells.

Reduced incidence of GVHD without increase in relapse with low-dose rabbit ATG in the preparative regimen for unrelated bone marrow transplants in CML

SUMMARY

Antithymocyte globulin (ATG) treatment prevents graft failure and results in a low incidence of GVHD, but an increased risk of relapse could be expected as a consequence of reduced GVHD. From September 1995 to June 2001, 28 consecutive chronic myeloid leukemia (CML) patients underwent unrelated bone marrow transplants: 21 were in chronic phase (CP) and seven in advanced phase (AP). Median age was 35.5 years (range 20-50). HLA typing was based on high-resolution molecular techniques; in eight cases there were one or more allele mismatches. The preparative regimen consisted of TBI, EDX 120 mg/kg and rabbit ATG 15 mg/kg. All patients engrafted and no rejection occurred. Acute GVHD grade III-IV occurred in six patients (21%). Chronic GVHD occurred in 10 (40%) and it was extensive in one. Four out of seven patients transplanted in AP had a hematological relapse. Of 21 in CP, there was one cytogenetic and one molecular relapse: these two patients are now in complete remission with imatinib mesylate. With a median follow-up of 45.7 months, the 5-year survival is 76.2% for those transplanted in CP. These data demonstrate that transplants performed in CP, with low-dose ATG, are associated with a good outcome, low incidence of GVHD and no increase of relapse.

Loss of single HLA class I allospecificities in melanoma cells due to selective genomic abbreviations

Expression of human leucocyte antigen (HLA) Class I molecules is essential for the recognition of malignant melanoma (MM) cells by CD8(+) T lymphocytes. A complete or partial loss of HLA Class I molecules is a potent strategy for MM cells to escape from immunosurveillance. In 2 out of 55 melanoma cell cultures we identified a complete phenotypic loss of HLA allospecificities. Both patients have been treated unsuccessfully with HLA-A2 peptides. To identify the reasons underlying the loss of single HLA-A allospecificities, we searched for genomic alterations at the locus for HLA Class I alpha-chain on chromosome 6 in melanoma cell cultures established from 2 selected patients with MM in advanced stage. This deficiency was associated with alterations of HLA-A2 gene sequences as determined by polymerase chain reaction-sequence specific primers (PCR-SSP). Karyotyping revealed a chromosomal loss in Patient 1, whereas melanoma cell cultures established from Patient 2 displayed 2 copies of chromosome 6. Loss of heterozygosity (LOH) using markers located around position 6p21 was detected in both cases. By applying group-specific primer-mixes spanning the 5'-flanking region of the HLA-A2 gene locus the relevant region was amplified by PCR and subsequent sequencing allowed alignment with the known HLA Class I reference sequences. Functional assays using HLA-A2-restricted cytotoxic T-cell clones were performed in HLA-A2 deficient MM cultures and revealed a drastically reduced susceptibility to CTL lysis in HLA-A2 negative cells. We could document the occurrence of selective HLA-A2 deficiencies in cultured advanced-stage melanoma metastases and identify their molecular causes as genomic alterations within the HLA-A gene locus.

Human leukocyte antigens and prognosis in patients with head and neck cancer: results of a prospective follow-up study

BACKGROUND

Prognostic information is essential for optimal treatment of patients with head and neck cancer. We studied the relationship of class I and class II human leukocyte antigens (HLA) on prognosis in patients with head and neck cancer.

METHODS

HLA-A, -B, -C and -DR antigens were determined in 209 patients with squamous cell carcinoma of the oral cavity, oropharynx, hypopharynx, or larynx. The patients were subjected to follow-up investigations for a period of 5 years.

RESULTS

Five-year survival rates in relation to tumor stage varied between 86% for stage I tumors and 28% for stage IV tumors (P <.0001, log-rank trend test). The EBA-A11 antigen showed a significant negative correlation with survival. While the 5-year survival of 124 HELA-A11-negative patients was 58%, none of the 17 HLA-A11-positive patients survived 5 years (P = .0002). A significant negative correlation with survival was also observed for HLA-DR6. While the 5-year survival rate of 106 HLA-DR6-negative patients was 60%, it was only 40% in 35 HLA-DR6-positive patients (P = .0313).

CONCLUSIONS

If the findings of our study can be confirmed, HLA-A11 and HLA-DR6 might become clinically important supplemental prognostic markers in head and neck cancer.

Impaired surface antigen presentation in tumors: implications for T cell-based immunotherapy

The identification of tumor-associated antigens has suggested new possibilities for cancer therapy. However, multiple mechanisms may contribute to the ability of tumor to escape antitumor immune responses. Tumor antigen heterogeneity, modulation of HLA expression and immune suppressive mechanisms may occur at any time during tumor cell progression, and can affect the outcome of therapeutic immune intervention. In particular, the appearance of altered HLA class I phenotypes during tumor development may have important biological and medical implications due to the role of these molecules in T and NK cell functions. Exhaustive tumor tissue studies are necessary before deciding whether a particular patient is suitable for inclusion in T cell-based immunotherapy protocols.

A graft-versus-colonic cancer effect of allogeneic stem cell transplantation

Allogeneic stem cell transplantation (ASCT) has proved to have an important immune-mediated anti-tumour effect in patients with haematologic malignancies. There is also evidence of such an effect in patients with malignant tumours. We studied this effect of ASCT in a patient with colorectal cancer. A 77-year-old man having a primarily resected colonic cancer with disseminated lymph node involvement received ASCT from his HLA-identical sibling as the only treatment. Mixed haematopoietic chimerism was monitored using PCR-amplification of variable number tandem repeats and tumour size, assessed by repeated CT scans. Recipient leucocytes were gradually replaced by donor cells for 1 month. Continuous resolution of lymph node metastases was seen together with clinical graft-versus-host disease (GVHD). The patient died of pneumonia and cardiac insufficiency 4 months after transplantation. At autopsy, most of the metastases were necrotic, with few remaining tumour cells. Clinical and histopathological postmortem results showed a graft-versus-colorectal cancer effect.

Unfavorable prognosis of patients with non-small cell lung carcinoma associated with HLA-A2

BACKGROUND

HLA class I molecules present antigenic peptides to cytotoxic T lymphocytes and, thus, play an important role in immune surveillance. Since 1970s there have been many reports of an increased frequency of one or more HLA haplotype in association with autoimmune disease, and malignancy. We studied types of HLA class I antigens in 204 resected non-small cell lung carcinoma (NSCLC) patients and also examined its correlation with clinicopathologic features and prognosis.

METHOD

Serological typing for HLA class I antigens was performed using a microcytotoxicity test. The disease-free survival curves were calculated by the Kaplan-Meier method and then compared using the Logrank test. Multivariate analysis was carried out by Cox's proportional hazard method.

RESULTS

The difference in disease-free survival time between the HLA-A2 present group and A2 absent group was significant (P = 0.040). The 3-year disease-free survival rate of all patients was 44% in HLA-A2 present group and 66% in A2 absent group. When a comparison was made within the group with stage I, expression of HLA-A2 was the only independent factor that affected survival time by multivariate analysis (P = 0.0457).

CONCLUSIONS

Expression of HLA-A2 was considered as one of the unfavorable prognostic factors in NSCLC patients. Our results suggested expression of HLA-A2 in NSCLC patients was one of the mechanisms of escape from immune surveillance.

Low-intensity conditioning is sufficient to ensure engraftment in matched unrelated bone marrow transplantation

OBJECTIVE

Matched unrelated bone marrow transplantation (BMT) for patients with hematological malignancies is associated with a high incidence of transplant-related complications due to high doses of chemoradiotherapy administered pre-BMT to ensure engraftment. The aim of this study was to investigate the feasibility of low-intensity conditioning for BMT from matched unrelated donors.

MATERIALS AND METHODS

Sixteen patients with hematologic malignancies underwent non-T-cell-depleted BMT following a low-intensity conditioning regimen consisting of fludarabine monophosphate 30 mg/m(2)/day for 6 days, busulfan 4 mg/kg/day for 2 days, anti-T lymphocyte globulin 10 mg/kg/day for 4 days. Seven of the patients suffered from chronic myelogenous leukemia, four from acute lymphoblastic leukemia, four from acute myelogenous leukemia, and one from Ki-1 non-Hodgkin's lymphoma. Three of the patients had secondary leukemia and two were post-autologous BMT (ABMT). All patients were transplanted from fully matched unrelated donors.

RESULTS

Fifteen of the 16 patients had 100% donor chimerism; no graft rejection was observed. None of the patients developed >Grade II veno-occlusive disease, sepsis, multiorgan failure, or renal or pulmonary toxicity. Four patients died posttransplant; one of thrombocytopenia and severe hemorrhagic cystitis, one of central nervous system toxicity, one of Grade IV graft-vs-host disease, and one following relapse (9 months post-BMT). Survival and disease-free survival at 36 months are 75% (95% confidence interval 46-90%) and 60% (95% confidence interval 30-80%), respectively.

CONCLUSION

These results indicate that low-intensity conditioning is sufficient to ensure stable engraftment of bone marrow grafts in a matched unrelated setting.

Alkaline-mediated differential interaction (AMDI): a simple automatable single-nucleotide polymorphism assay

The key requirements for high-throughput single-nucleotide polymorphism (SNP) typing of DNA samples in large-scale disease case-control studies are automatability, simplicity, and robustness, coupled with minimal cost. In this paper we describe a fluorescence technique for the detection of SNPs that have been amplified by using the amplification refractory mutation system (ARMS)-PCR procedure. Its performance was evaluated using 32 sequence-specific primer mixes to assign the HLA-DRB alleles to 80 lymphoblastoid cell line DNAs chosen from our database for their diversity. All had been typed previously by alternative methods, either direct sequencing or gel electrophoresis. We believe the detection system that we call AMDI (alkaline-mediated differential interaction) satisfies the above criteria and is suitable for general high-throughput SNP typing.

Sequences of cytotoxic T-lymphocyte epitopes in the Epstein-Barr virus (EBV) nuclear antigen-3B gene in a Japanese population with or without EBV-positive lymphoid malignancies

Latent infection antigens of EBV, including EBV nuclear antigens (EBNAs) and latent membrane proteins, are expressed in latently infected and immortalized B cells but work as target antigens for host cytotoxic T-lymphocyte (CTL) responses in an HLA class I-restricted manner. Among these latent antigens, the immunodominant CTL epitopes in EBNA3B (EBNA3B 399-408 and EBNA3B 416-424) are well characterized. Mutations and strain differences in these sequences, compared to the prototype A sequence, reduce CTL responses to latently infected B cells. These EBNA3B CTL epitopes in the normal Japanese population and in 2 lymphoid neoplasias, pyothorax-associated lymphoma (PAL) and nasal natural killer-cell lymphoma, were directly sequenced by PCR. Most EBV in peripheral blood leukocytes (PBLs) from healthy Japanese donors exhibited the prototype A sequence, with mutations in approximately 20% (3/16). The sequence of EBNA3B CTL epitopes in lymphoma tissue was obtained in 6 PAL cases, and 5 exhibited mutations or strain differences compared to the prototype A sequence. Furthermore, the EBNA3B sequence in PAL tissue was different from that in PBLs of the same patient or 1 of the sequences found in PBLs. However, the EBNA3B gene in nasal lymphoma tissues exhibited predominantly the prototype A sequence. Because PAL cells expressed EBNA3B mRNA, detected by RT-PCR, but nasal lymphoma cells did not, mutations and strain differences of the sequences of EBNA3B CTL epitopes were specific findings in EBNA3B-positive lymphomas.

A PCR-SSP method to specifically select HLA-A*0201 individuals for immunotherapeutic studies

HLA-A*0201 is an important restriction element for peptide presentation to T cells in disease and cancer. Mutation studies and analyses using cytotoxic T lymphocytes have shown the functional relevance of subtype-specific differences in HLA-A2 molecules for peptide binding and T-cell receptor recognition. Therefore, many immunotherapeutic studies need to accurately select HLA-A*0201-positive individuals. We designed an easy, robust approach based on the polymerase chain reaction using sequence-specific primers (PCR-SSP) to specifically distinguish A*0201-positive individuals from other HLA-A2 subtypes described to date. The first step includes reactions that give information whether the sample donor is HLA-A2 and, if so, whether the individual is homozygous or heterozygous for HLA-A2. Further, it is determined whether the sample has an HLA-A*0209 or an HLA-A*0201 sequence at the corresponding position in exon 4. Samples that may contain an HLA-A*0201 allele according to the results of this first step are subtyped in a second step nested PCR. Here the strategy is focussed on the discrimination of HLA-A*0201 from the other subtypes by considering divergent nucleotide positions in two ways. One SSP combination amplifies the HLA-A*0201 sequence while a corresponding SSP combination specifically amplifies the subtype or group of subtypes differing from HLA-A*0201 at this position. Thus, at relevant polymorphic nucleotide positions the HLA-A*0201 sequence is both directly and indirectly confirmed. This strategy strongly enhances the reliability of the subtyping and allows better verification of HLA-A*0201-positive patient selection for clinical studies.

Decreased HLA-A expression in prostate cancer is associated with normal allele dosage in the majority of cases

A comparison has been made of the phenotypic expression of MHC class I antigens with the corresponding HLA-A genotype in 15 cases of benign prostatic hyperplasia (BPH) and 34 cases of primary locally invasive prostatic carcinoma. Expression of class 1 protein, detected by immunocytochemistry, was partially or completely lost in approximately 90% of the tumours examined. Comparative genomic analysis of the beta2 microglobulin (beta2m) gene and 15 individual HLA-A haplotypes using a polymerase chain reaction (PCR)-based method demonstrated abnormal gene dosage in the minority of cases: homozygous deletion of the beta2m locus was detected in one case and HLA-A allele in two cases (HLA-A1 and HLA-A2, respectively), representing approximately 8% of the population studied. This first comparative study of gene dosage and expression of class 1 protein reported for prostate cancer reveals that deletion is not the cause of the partial or complete loss seen in the majority of cases. This raises the possibility, in the future, for novel selective immunomodulatory therapeutic strategies which stimulate a clinically significant re-expression of class 1 protein and associated cytotoxic T-cell response.

Complete sequence analysis of the A*1103 allele

Here we report the full-length sequence of a novel A*11 variant. The variant was identified by ARMS-PCR and serology, the sequence was confirmed by cloning and subsequent sequencing. This variant, A*1103, found in a family of oriental origin, resembles the A*1101 sequence in exon 2 but differs in exon 3 with regard to codons 151 and 152. The polymorphism's result in two amino acid substitutions (one conserved (His->Arg), one introducing a negative charge (Ala->Glu)) located in the alpha2 helical region. The arginine at amino acid position 151 is rare amongst Alocus alleles and is besides A*1103 only observed in A*29 variants, the glutamine at amino acid position 152 is shared with A*0301, A*25, *26, *34 variants and the A*02 subtypes A*0203, *0213 and *0226. In fact, the amino acid motif comprising codons 151 and 152 is unique to A*1103 among Alocus alleles, but is common to C-locus alleles.

Human leukocyte antigen class I gene mutations in cervical cancer

BACKGROUND

Various mechanisms contribute to the loss of human leukocyte antigen (HLA) class I expression that is frequently observed in cancers. Although some single allele losses have been ascribed to mutations in HLA class I genes, direct evidence for this phenomenon in vivo is still lacking. Thus, we investigated whether HLA class I gene mutations could account for the loss of allele-specific expression in cervical carcinomas.

METHODS

We used polymerase chain reaction-based techniques, including sequencing, oligonucleotide hybridization, and microsatellite analysis, to identify HLA class I gene defects in two tumor-derived cell lines and to confirm the presence of these defects in the original tumors.

RESULTS

In one tumor, in exon 2 of the HLA-B15 gene, a four-nucleotide insertion resulted in a stop codon in exon 3. In the other tumor, in two duplicated copies of the HLA-A24 gene, single-point mutations resulted in stop codons in exons 2 and 5.

CONCLUSIONS

To our knowledge, this is the first report of HLA class I gene mutations identified in primary tumors that lead to loss of allelic expression in tumor cells. Such tumor-specific mutations may permit the cell to escape HLA class I-restricted cytotoxic T-cell responses.

Chromosome loss is the most frequent mechanism contributing to HLA haplotype loss in human tumors

Loss of heterozygosity (LOH) in the short arm of chromosome 6 (6p) was detected in samples obtained from colon (13.8%), larynx (17.6%) and melanoma (15.3%) tumors. The parallel study of HLA-antigen expression in tumor tissues using locus- and polymorphic-specific antibodies in combination with LOH microsatellite analysis on 6p allowed us to establish that LOH in chromosome 6 is a representative phenomenon in most tumor cells present in a given tumor tissue. In most cases, specific HLA alleles had been lost in a predominant population of tumor cells, indicating that LOH is a non-irrelevant mutation that probably confers a selective advantage for survival of the mutant cell. We also demonstrate that LOH frequently occurred through chromosome loss rather than somatic recombination. LOH at all loci studied on the p and q arms of chromosome 6 was observed in at least 56.2% (9/17) cases. This HLA-associated microsatellite analysis was a useful tool for classifying tumors as LOH-positive or -negative, and therefore to consider a patient as a potential non-responder or responder in a vaccination trial.

HLA-A alleles of patients with pyothorax-associated lymphoma: anti-Epstein-Barr virus (EBV) host immune responses during the development of EBV latent antigen-positive lymphomas

Pyothorax-associated lymphoma (PAL) is an Epstein-Barr virus (EBV) latent antigen-positive lymphoma resembling EBV-transformed lymphoblastoid cell lines (LCLs) and develops in non-immunocompromised patients. Thus, deficient anti-viral-antigen immune responses might be involved in the development of PAL. As MHC class I-restricted cytotoxic T lymphocytes (CTLs) are the major constituent of anti-viral immune responses, the HLA allele type and its expression may affect the development of PAL. Flow-cytometric analyses of PAL cell lines and LCLs using the W6/32 monoclonal antibody revealed that expression of HLA class I varied among cell lines. Although one PAL cell line, OPL-2, exhibited low expression, an LCL and another PAL cell line, OPL-1, strongly expressed HLA class I. Among the EBV latent infection genes, EBV nuclear antigens 2, 3, 4 and 6 and latent membrane proteins can induce efficient CTL responses in combination with HLA-A2 or -A11. HLA-A alleles of PAL patients were determined using low-resolution PCR-based typing with HLA-A locus sequence-specific primer combinations. The antigen frequencies of HLA-A2 and -A11 in PAL patients were not significantly different from those in the normal Japanese population. Although HLA class I antigen should be expressed during the course of lymphomagenesis, no HLA-A alleles influenced the development of overt PALs.

Nested Polymerase Chain Reaction With Sequence-Specific Primers Typing for HLA-A, -B, and -C Alleles: Detection of Microchimerism in DR-Matched Individuals

It is widely accepted that donor leukocytes survive within the recipient periphery after blood transfusion or solid organ transplantation. The significance of this microchimerism remains unclear, partially because of the insecurity of assays used to detect the donor-derived material. The techniques used to detect donor-derived DNA within recipient peripheral blood rely largely on major histocompatibility complex class II polymorphism. We and others have shown that the sensitivity of polymerase chain reaction with sequence-specific primers (PCR-SSP) typing for HLA class II alleles can be increased 100-fold by the addition of a primary amplification step (nested PCR-SSP). We have now extended this technique to encompass typing for HLA class I alleles, thereby adding flexibility to microchimerism testing by enabling testing of recipients HLA-DR matched with their donors. However, the high level of sensitivity achieved with the technique (1:100,000) leads to a concomitant decrease in the specificity that results in the amplification of unexpected products, a phenomenon we encountered in the development of our nested PCR-SSP typing system for HLA class II alleles. We describe here how it is possible to compensate for these anomalies by including multiple testing of a pretransfusion sample that acts as a specificity control, establishing a rigorous baseline for subsequent analysis.

Nested Polymerase Chain Reaction With Sequence-Specific Primers Typing for HLA-A, -B, and -C Alleles: Detection of Microchimerism in DR-Matched Individuals

It is widely accepted that donor leukocytes survive within the recipient periphery after blood transfusion or solid organ transplantation. The significance of this microchimerism remains unclear, partially because of the insecurity of assays used to detect the donor-derived material. The techniques used to detect donor-derived DNA within recipient peripheral blood rely largely on major histocompatibility complex class II polymorphism. We and others have shown that the sensitivity of polymerase chain reaction with sequence-specific primers (PCR-SSP) typing for HLA class II alleles can be increased 100-fold by the addition of a primary amplification step (nested PCR-SSP). We have now extended this technique to encompass typing for HLA class I alleles, thereby adding flexibility to microchimerism testing by enabling testing of recipients HLA-DR matched with their donors. However, the high level of sensitivity achieved with the technique (1:100,000) leads to a concomitant decrease in the specificity that results in the amplification of unexpected products, a phenomenon we encountered in the development of our nested PCR-SSP typing system for HLA class II alleles. We describe here how it is possible to compensate for these anomalies by including multiple testing of a pretransfusion sample that acts as a specificity control, establishing a rigorous baseline for subsequent analysis.

Selective histocompatibility leukocyte antigen (HLA)-A2 loss caused by aberrant pre-mRNA splicing in 624MEL28 melanoma cells

Histocompatibility leukocyte antigen (HLA)-A2 is used as a restricting element to present several melanoma-associated antigen (MAA)-derived peptides to cytotoxic T lymphocytes (CTLs). HLA-A2 antigen is selectively lost in primary melanoma lesions and more frequently in metastases. Only scanty information is available about the molecular mechanisms underlying this abnormality, in spite of its potentially negative impact on the clinical course of the disease and on the outcome of T cell-based immunotherapy. Therefore, in this study we have shown that the selective HLA-A2 antigen loss in melanoma cells 624MEL28 is caused by a splicing defect of HLA-A2 pre-mRNA because of a base substitution at the 5' splice donor site of intron 2 of the HLA-A2 gene. As a result, HLA-A2 transcripts are spliced to two aberrant forms, one with exon 2 skipping and the other with intron 2 retention. The latter is not translated because of an early premature stop codon in the retained intron. In contrast, the transcript with exon 2 skipping is translated to a truncated HLA-A2 heavy chain without the alpha(1) domain. Such a polypeptide is synthesized in vitro but is not detectable in cells, probably because of the low steady state level of the corresponding mRNA and the low translation efficiency. These results indicate that a single mutational event in an HLA class I gene is sufficient for loss of the corresponding allele. This may account, at least in part, for the high frequency of selective HLA class I allele loss in melanoma cells. Our conclusion emphasizes the need to implement active specific immunotherapy with a combination of peptides presented by various HLA class I alleles. This strategy may counteract the ability of melanoma cells with selective HLA class I allele loss to escape from immune recognition.

A null HLA-A*68 allele in a bone marrow donor

The authors describe an A*68 allele present at the molecular level but not expressed at the cell surface. This non expression results from the deletion of one nucleotide in exon 1, which causes a shift of the reading frame leading to an early non-sense codon in the same exon.

HLA class I antigen downregulation in human cancers: T-cell immunotherapy revives an old story

Human leukocyte antigen (HLA) class I molecule downregulation occurs frequently in many cancers, and this abnormality might adversely affect the clinical course of cancer and the outcome of T-cell-based immunotherapy. Mutations in the HLA class I genes themselves, abnormalities in their regulation and/or defects in HLA class I-dependent antigen processing can underlie HLA class I downregulation. These mutations modulate the susceptibility of tumor cells to in vitro lysis by cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. Immune selection of CTL- and NK-cell-resistant tumor cells might explain the rapid progression and poor prognosis of cancers that exhibit HLA class I downregulation. These findings provide compelling evidence that HLA class I downregulation represents a significant challenge for the successful application of T-cell-based immunotherapy of cancer.

Molecular typing for HLA class I using ARMS-PCR: further developments following the 12th International Histocompatibility Workshop

Molecular typing for HLA class I was introduced in the 12th International Histocompatibility Workshop. Following a pilot study using three methods, sequence specific oligotyping (SSO), reverse dot blot and amplification refractory mutation system (ARMS)-PCR, the ARMS-PCR method was selected for use. A great advantage of an ARMS-PCR method is that, unlike the other two methods, it can determine whether sequence motifs are in cis or in trans, as ARMS-PCR detects two cis located motifs per reaction using forward and reverse sequence specific primers. Resolution was designed to be low to medium level for HLA-A, -B and -C alleles. Two hundred and fifty class I kits and 83 HLA-A2 subtyping kits were distributed. The A2 subtyping kit used a two round nested PCR system to identify all of the A2 alleles known at the time. Typing results on control DNA samples distributed with both the kits showed a very satisfactory performance. Since the 12th Workshop, the kits have been developed with the addition of new primers and primer mixes to increase the resolution of the test.

Endothelial cell activation by sera containing HLA antibodies is mediated by interleukin-1

BACKGROUND

It has been suggested that antibodies which are associated with chronic pathological conditions such as chronic rejection and autoimmune diseases have the capacity to activate endothelial cells by induction and up-regulation of adhesion molecules. It has also been suggested that HLA antibodies formed by patients awaiting transplantation can activate endothelial cells. These antibodies include HLA and those that bind to endothelial cells.

METHODS

We have further investigated this phenomenon using monoclonal antibodies against HLA class I determinants and sera from aortic valve graft recipients, containing strong HLA antibodies. The effect of 24-hr incubation of antibodies/serum with human umbilical vein endothelial cells (HUVECs) on adhesion molecule expression was measured by flow cytometry.

RESULTS

HLA monoclonal antibodies had no effect on ICAM-1 expression on HUVECs. Five of 31 (16%) patients' sera caused strong up-regulation of adhesion molecules (ICAM-1, vascular cell adhesion molecule-1, and E-selectin) but this did not correlate with HLA specificity, IgG, or IgM binding to HUVECs. The activity, found in whole serum and IgG-depleted fractions was inhibited by neutralizing antibodies against interleukin (IL)-1beta and tumor necrosis factor-alpha. Examination of patient sera for presence of IL-1beta demonstrated high levels of IL-1beta in all five sera (range, 30 -500 U/ml) as well as in samples from an additional three patients.

CONCLUSION

The ability to activate endothelial cells detected in our patient sera was caused by cytokines and not antibody. Our observation that addition of cytokines to sera before separation into large and low molecular weight fractions demonstrated retention of cytokines in both fractions may be a confounding issue when investigating endothelial cell activation by patients' sera.