HLA-Cw allele analysis by PCR-restriction fragment length polymorphism: study of known and additional alleles

Characterization of a novel allele, HLA-B*15:228

B*15:228 differs from B*15:01:01:01 at three nucleotides in exon 4.

Molecular diversity of the HLA-C gene identified in a caucasian population

A DNA typing procedure, based on a two stage polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) typing strategy, has been developed and applied to DNA from 1000 healthy individuals from the Northern Ireland region. The two-stage procedure involves human leukocyte antigen (HLA-C) identification through the use of a medium resolution PCR-SSOP system, followed by four secondary group specific PCR-SSOP systems, to enable allele resolution. The PCR-SSOP systems were designed for the identification of HLA-Cw alleles with possible discrimination within exons 2 and 3 of the HLA-C gene, i.e., HLA-Cw*01-Cw*16. PCR-SSP tests were designed for the resolution of HLA-Cw*17 and -Cw*18 alleles. The systems can also be used independently of each other if selective allele resolution is required. HLA-Cw allele frequencies occurring within the Northern Ireland population have been compiled, along with estimations of HLA-B/Cw haplotype frequencies.

A commented dictionary of techniques for genotyping

Several tools, differing in their technical and practical parameters, are available for the detection of point mutations as well as small deletions and insertions. In this article, a dictionary featuring over fifty methods for detection of mutation is presented. The distinguishing principle for each method is briefly explained. Sorting of and discussion on the methods give the reader a brief introduction to the field of genotyping.

Octapeptide but not nonapeptide from HIV-1 p24gag protein upregulates cell surface HLA-C expression

OBJECTIVES

The HLA-Cw3 molecule has been reported to present peptides derived from HIV-1 p24gag protein to a cytotoxic T lymphocyte clone. We have shown previously that the synthetic octapeptide 145-152 derived from the p24gag sequence upregulated cell surface HLA-C expression on HLA-Cw*0303+ cells. Here, we examined the question of whether the nonapeptide 144-152 also exerts a similar effect.

METHODS

The HLA-Cw*0303+ B-LCL PAJ and control HLA-Cw3-negative cells B-LCL HAJ and T-LCL 500/C9 were used. HLA expression on peptide-pulsed and non-pulsed cells was evaluated using specific antibodies and flow cytofluorimetry. Binding of dansylated peptides onto different cell lines was measured spectrofluorimetrically.

RESULTS

The HIV-1 p24gag octapeptide upregulated cell surface HLA-C on PAJ (Cw*0303+) cells, whereas the nonapeptide did not. HLA-A2 expression was not affected by these peptides. Specificity of the effect of octapeptide was confirmed by the lack of HLA-C upregulation on HLA-Cw3- cells and by lower binding of dansylated peptide to the HLA-Cw3- cells HAJ and 500/C9.

CONCLUSIONS

The above results indicate that HLA-Cw*0303 preferentially binds the octapeptide rather than the nonapeptide derived from HIV-1 p24gag protein.

A reliable and efficient high resolution typing method for HLA-C using sequence-based typing

Serological typing of HLA-C has been poor and almost half of its alleles are serologically undetectable blanks in most populations. Therefore, DNA typing techniques have been used to identify and type for the HLA-C gene. Sequence-based typing (SBT) has proven a major typing strategy for highly polymorphic HLA genes. The technique enables direct identification of all sequence motifs without the need to continuously adjust primers. Here we describe a reliable solid-phase SBT strategy for HLA-C which can be used to distinguish all currently known HLA-C alleles without prior knowledge gained by low resolution typing. Exons 2 and 3 were amplified and sequenced and if necessary sequences of exons 1 and 5 were determined. A total of 257 individuals were typed for HLA-C using this protocol and 30 of the 42 known HLA-C alleles were detected. All heterozygous combinations found in this study were unambiguously discriminated. One hundred and forty-four individuals from the Dutch population were typed randomly. In this group Cw*0701 and *0702 were the most frequently detected alleles. Of the serological Cw blank alleles Cw*1203 was found to have the highest frequency (16%). From the total group 212 individuals were typed serologically and 106 were retyped with 97 selected antisera to further compare serological and molecular defined phenotypes. Discrepancies between serological typing and SBT are mainly attributable to the serologically Cw blank alleles Cw*12-18. The high resolution SBT protocol described will be a valuable tool for the identification of HLA-C alleles and the determination of the role of HLA-C in marrow and organ transplantation.

HLA-C high resolution typing: analysis of exons 2 and 3 by sequence based typing and detection of polymorphisms in exons 1-5 by sequence specific primers

HLA-C high resolution sequence based typing developed in this study involves a unique DNA amplification encompassing exon 1 to intron 3 and four fluorescent sequencing reactions covering exon 2 and 3. Both dye primer and dye terminator sequencing techniques were performed and results compared. This approach allowed the identification of all of the 50 HLA-C allelic variants so far described, except for two allele pairs that are distinguished by non-coding nucleotide changes (Cw*12021 = 12022, Cw*15051 = 15052) and three allele pairs (Cw*0701 = 706, Cw*1701 = 1702 and Cw*1801 = 1802) that share the same nucleotide sequence in exon 2 and 3. For complete subtyping of these allelic variants, an amplification based on sequence specific primers (PCR-SSP) was used. No ambiguous heterozygous combinations of alleles were detected in our panel so far. HLA-C typing data obtained by this method were compared with data from serological and low resolution PCR-SSP typing, which had been performed previously on the samples sequenced.

A high-resolution genotyping method for HLA-C alleles and possible shared HLA-C-B haplotypes between Japanese and Caucasians

A genotyping system for HLA-Cw alleles using methods of PCR-single-strand conformation polymorphism (SSCP) and PCR-sequence-specific primers (SSP) was developed. Genomic DNA from 167 random healthy Japanese individuals were investigated to determine HLA-C allele frequencies and their associations with HLA-A and -B loci. Nine alleles were frequently detected: Cw*0102 (18.3%), Cw*0304 (12.0%), Cw*1202 (11.4%), Cw*0303 (10.5%), Cw*1403 (10.5%), Cw*0801 (10.2%), Cw*0702 (9.0%), Cw*1402 (6.0%) and Cw*0401 (5.1%). Several HLA-C-B haplotypes such as Cw*0303-B62, Cw*0304-B60, Cw*0501-B44, Cw*0602-B13, Cw*0602-B37, Cw*0702-B7, Cw*1202-B52, Cw*1402-B51 and Cw*1502-B51 were found to be shared by Japanese and Caucasians. With the PCR-SSCP method we could detect differences in each exon of HLA-C alleles, at a low cost and simply. This method is suitable for sequence-level matching with a relatively small number of samples.

Comparison of typing results by serology and polymerase chain reaction with sequence-specific primers for HLA-Cw in 650 individuals

HLA-Cw typing by standard serological techniques is associated with a high frequency of blanks, and reliable typing reagents for several of the Cw specificities are scarce. We evaluated the PCR-SSP technique for Cw typing in 370 kidney transplant patients and 280 healthy blood donors. Serological typing of all individuals was performed in our laboratory from 1995 to 1997 using commercially available tissue-typing trays. Comparison between serological and PCR-SSP typing revealed a discrepancy rate of 33.6% (n= 94) in blood donors and 32.4%) (n=120) in kidney recipients. Incorrect antigen assignments occurred only rarely (3.6% of the blood donors and 3.2% of the kidney recipients). The vast majority of discrepancies were due to antigens that were not detected serologically. In 26 individuals no Cw antigen was detected by serological typing, whereas PCR-SSP showed 1 allele in 13 and 2 alleles in the other 13 cases. Another 269 individuals were typed serologically with one blank (presumably homozygous). Of these, only 108 were confirmed to be homozygous, whereas an additional Cw allele was found in the remaining 161 cases using the SSP technique. Most of the "missed" specificities (86.5%) were those for which serological reagents were not available (HLA-Cw*12-*17). The most commonly "missed" specificity was HLA-Cw*1203, which occurred in 13.9% of the healthy blood donors. These results indicate that serological HLA-Cw typing is insufficient for examining the clinical importance of HLA-Cw matching in transplantation. Future studies based on molecular typing should allow the proper investigation of HLA-Cw matching in kidney and bone marrow transplantation.

HLA class I-restricted and tumor-specific cytotoxic T lymphocytes from metastatic lymph nodes of esophageal cancers

This paper investigates the presence of HLA class I-restricted and tumor-specific cytotoxic T lymphocytes (CTL) in tumor sites of esophageal cancers. Five CTL lines were established from the metastatic lymph nodes or pleural effusion by incubation with interleukin-2 of tumor-infiltrating lymphocytes: cases 1 and 5, HLA-A26- and HLA-A33-restricted and squamous cell carcinoma (SCC)-specific CTL; case 2, HLA-Cw0102-restricted and esophageal SCC-specific CTL; case 3, HLA-A24- and HLA-A26-restricted CTL recognizing histologically different tumor cells; and case 4, HLA-A26-restricted and esophageal SCC-specific CTL. These results suggest the existence of HLA class I-restricted and tumor-specific CTL in metastatic esophageal SCC.

HLA class-I-restricted and tumor-specific CTL in tumor-infiltrating lymphocytes of patients with gastric cancer

Immune recognition of human cancers except melanoma is not well understood at either the cellular or the molecular level. We demonstrate in this study the existence of HLA class-I-restricted and tumor-specific CTL in IL-2-activated TIL (tumor-infiltrating lymphocytes) of all 4 gastric cancer patients tested. We established HLA A2-restricted and adenocarcinoma-specific CTL in 2 HLA A0201+ patients, and HLA A2402-restricted CTL recognizing both adenocarcinoma and squamous-cell carcinomas (SCC) in the 2 remaining HLA A2402+ patients. Further, HLA A3101-restricted and adenocarcinoma-specific CTL were established in 1 of the 2 HLA A2402+ patients who had HLA A3101 allele. HLA A2-, A2402- and A3101-restricted CD8+ CTL clones were established from these parental CTL lines. The 2 HLA A2-restricted CTL lines lysed 8 of 13 HLA A2+ adenocarcinoma cell lines established from different organs (stomach, colon, lung and breast) with different subtypes (HLA A0201, A0206 and A0207). The HLA A2-restricted CTL line recognized 9 and 6 different HPLC fractions of peptides eluted from the HLA A0201+ breast and HLA A0201+ colon adenocarcinoma cell lines, respectively. Allele-specific deletion of HLA A2 or A24 molecules was observed in some tumor lines that were not susceptible to lysis by the CTL lines. These results suggest that TIL of gastric cancer possess CTL recognizing different peptide antigens binding to different HLA-A alleles that are widely expressed on adenocarcinomas and also, to some extent, on SCC from different organs.

HLA-A locus-restricted and tumor-specific CTLs in tumor-infiltrating lymphocytes of patients with non-small cell lung cancer

HLA class I restriction and tumor specificity of cytotoxicity in the IL-2-activated tumor-infiltrating lymphocytes from 16 patients with non-small cell lung cancer were investigated. Six HLA class I-restricted and tumor-specific CTL lines were established: (i) HLA A2-restricted and adenocarcinoma-specific CTLs in three (two A0201+ and one A0206+) patients with adenocarcinoma, (ii) HLA A3101- and A3302-restricted and adenocarcinoma-specific CTLs in an HLA A3101/3302+ patient with adenocarcinoma, and (iii) HLA A3302-restricted CTLs and (iv) HLA A2402-restricted CTLs recognizing tumors with different types of histology in an HLA A3302+ patient with adenocarcinoma and an HLA A2402+ patient with squamous cell carcinoma (SCC), respectively. The three HLA A2-restricted CTL lines recognized 4, 4, or 6 of 15 HLA A2+ adenocarcinoma cell lines that originated from lung, stomach, colon, and breast with different subtypes (HLA A0201, A0206, and A0207), respectively. Furthermore, the CTLs of an HLA A0206+ patient recognized five different fractions of peptides eluted from an HLA A0201+ adenocarcinoma cell line. These results showed evidence of the existence of HLA class I-restricted and tumor-specific CTLs recognizing peptide antigens on HLA-A alleles of adenocarcinoma or SCC in tumor sites of a substantial number of patients with non-small cell lung cancer.

HLA-DRB4 genotyping by PCR-RFLP: diversity in the associations between HLA-DRB4 and DRB1 alleles

The serologically defined HLA-DR53 antigen is associated with HLA-DR4, -DR7, and -DR9 antigens, and these haplotypes contain two functional genes, DRB1 and DRB4, and two pseudogenes, DRB7 and DRB8. The DRB4 gene encodes the DR53 antigen, and has been officially recognized to contain three allelic variants (DRB4*0101, 0102, and 0103). In this study, we have established the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for DRB4 genotyping and analyzed genetic polymorphism of the DRB4 gene in Japanese population. DRB4*0101, DRB4*0102, and DRB4*0103 could be observed at the frequencies of 0.5%, 1.1% and 32.7%, respectively. The same DRB1 allele does not necessarily share an identical DRB4 allele. Further, a tight linkage disequilibrium was found between DRB4*0102 and DRB1*0401 in Japanese population, whereas DRB1*0401 was associated with DRB4*0101 or *0103 in Caucasian population. These findings reveal extensive diversity of the HLA-DRB1 and -DRB4 haplotypes and may have important implications for HLA-disease associations and donor selection in unrelated transplantation.

Identification of HLA-C alleles using PCR-single-strand-conformation polymorphism and direct sequencing

Alleles encoding HLA-C antigens in Japanese were identified by polymerase chain reaction followed by single strand conformation polymorphism (PCR-SSCP) and nucleotide sequencing analyses. The results showed that at least sixteen different alleles code for eight serologically detectable antigen groups and undetectable blanks. Cw1 was mainly encoded by Cw*0102, whereas two split antigens of Cw3, Cw9 and Cw10, were encoded by Cw*0303 and Cw*0304, respectively. Cw4 and Cw6 were encoded by Cw*0401 and Cw*0602, respectively. Seven alleles, Cw*0801, Cw*0803, Cw*1202, Cw*1203, Cw*1402, Cw*1403 and Cw*1502, were found to encode serological HLA-C "blanks" in Japanese. Moreover, errors in the published nucleotide sequences of Cw*0501 and Cw*1201 were corrected. Twenty-one HLA-C alleles were distinguished from each other by means of group-specific PCR amplification followed by the SSCP method developed in the present study. The system using genomic DNAs can be used effectively for identification of new HLA-C alleles.

Histocompatibility leukocyte antigen-A2402-restricted cytotoxic T lymphocytes recognizing adenocarcinoma in tumor-infiltrating lymphocytes of patients with colon cancer

To cast light on T cell-mediated specific immunity at the tumor site of colon cancer, we investigated whether interleukin-2 (IL-2)-activated tumor-infiltrating lymphocytes (TIL) from colon cancer show histocompatibility leukocyte antigen (HLA)-class I-restricted cytotoxicity against adenocarcinoma. IL 2-activated TIL from all four HLA-A24 patients examined lysed HLA-A2402+ adenocarcinomas, but not HLA-A2402- tumors. Those of two of the four cases also lysed HLA-A2402+ squamous cell carcinomas. CD8+ cytotoxic T lymphocyte (CTL) clones recognizing HLA-A2402+ adenocarcinomas were established from one CTL line. This CTL line produced IFN-gamma upon recognition of an HLA-A2402- adenocarcinoma transfected with HLA-A2402 cDNA. These results suggest the presence of HLA-A2402-restricted CTL recognizing adenocarcinoma at the tumor site of colon cancer. Furthermore, HLA-A31-restricted CTL activity was found in IL-2-activated TIL from one of two HLA-A31+ patients, suggesting the existence of HLA-class I-restricted CTL involving an allele other than A24.