Molecular definition of an elusive third HLA-A9 molecule: HLA-A9.3

The HLA-A9 family has been characterized as possessing two well defined specificities; HLA-A23 and A24. Serological studies have suggested the presence of a third member of this family HLA-A9.3, however there is doubt surrounding the existence of this specificity. HLA-A23, A24, and the putative A9.3 proteins were analyzed biochemically by immunoprecipitation and isoelectric focusing. Both HLA-A24 and A9.3 have identical isoelectric points whereas A23 is different. We have sequenced cDNA encoding HLA-A23, A24, and A9.3. From the observed protein sequences, we found A9.3 to differ from A24 by two amino acid substitutions located in the ₂ helix of the class I molecule. These substitutions are expected to significantly change the shape of the peptide binding cleft.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M64740 (HLA-A ^*2402); M64741 (HLA-A ^*2403); M64742 (HLA-A ^*2301). Address correspondence and offprint requests to: P. Parham.     

Structural analysis of HLA-A2.4 functional variant KNE. Implications for the mapping of HLA-A2-specific T-cell epitopes

HLA-A2 antigens are divided into four subtypes, designated A2.1 to A2.4, by the use of cytolytic T lymphocytes (CTL). The A2.4 subtype consists of a functionally heterogeneous group of variants that are not recognized by A2.1-, A2.2-, or A2.3-specific CTL lines while it is indistinguishable from A2.1 by isoelectric focusing. The structure of an A2.4 variant expressed on donor KNE has been established by comparative peptide mapping with A2.1 and radiochemical sequencing. It was found to differ from A2.1 by a single amino acid change of Cys to Tyr at position 99. This position is only moderately polymorphic and has not previously been found to vary in any other HLA or H-2 variants. The nature of the change is compatible with its generation by one-point mutation from A2.1. The only other previously characterized A2.4 variant, CLA, differs from A2.1 by a single amino acid replacement at position 9. Both residues 9 and 99 are located in homologous positions within the 1 and 2 domains, respectively. The results shown contribute to the molecular interpretation of the heterogeneity of CTL recognition within the HLA-A2.4 group of antigens.Abbreviations used in this paper CTL cytotoxic T lymphocytes - HPLC high performance liquid chromatography     

Molecular characterization of HLA-A28*, a novel HLA product,and its relationship to HLA-A28 and HLA-A2

The HLA-A28^* molecule expressed by the B-cell line IDF is serologically distinct and intermediate between HLA-A28 and HLA-A2. Comparative tryptic peptide mapping of biosynthetically labeled HLA-A28^*, A28, and A2 molecules showed that HLA-A28^* is also chemically distinct. Reverse-phase high pressure liquid chromatographic analysis of tryptic peptides labeled with ³H-arginine and ³H-lysine revealed that A28^*. A28, and A2 share 65% of their tryptic peptides. Multiple differences were observed between A28^* and both A28 and A2. No peptides unique to A28^* were detected and 25 peptides were shared with both A28 and A2. These results show that A28^* is a novel HLA product that is closely related to A28 and A2. Tryptic peptide map comparisons of these molecules labeled separately with 11 amino acids confirm these results. The data suggest that HLA-A28 ^* may have arisen from a genetic exchange event involving HLA-A28 and -A2. These data are consistent with the hypothesis that A28^* is identical with A28 in the first extracellular domain ( ₁) and identical with A2 in the second domain ( ₂).Abbreviations used in this paper EDTA ethylenediaminetetraacetic acid - HPLC high-pressure liquid chromatography - MHC major histocompatibility complex - NP40 Nonidet P40 - PMSF phenylmethylsulphonylfluoride - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis - TPCK L(tosylamido-2-phenyl) ethyl chloromethyl ketone - Tris tris (hydroxymethyl)-aminomethane - A alanine - C cysteine - D aspartic acid - E glutamic acid - G glycine - H histidine - K lysine - L leucine - M methionine - N asparagine - Q glutamine - R arginine - S serine - T threonine - V valine - W tryptophan - Y tyrosine     

DNA sequence of HLA-A11: Remarkable homology with HLA-A3 allows identification of residues involved in epitopes recognized by antibodies and T cells

The human class I alleles HLA-A11 and HLA-A3 have a well-documented history of serological cross-reactivity. This cross-reactivity suggests that they are closely related, a suggestion which is supported by the fact that the HLA-A11 and HLA-A3 genes are distinguished from all other A-locus genes by a restriction fragment length polymorphism observed in Bam HI digests. To examine the extent of sequence homology between HLA-A11 and HLA-A3, we have cloned the HLA-A11 gene and sequenced the coding regions (exons). The results reveal that HLA-A11 and HLA-A3 display the highest degree of homology reported for any pair of serologically defined class I alleles. Only nine base differences resulting in six amino acid differences were observed in exons 2–8. One of the amino acid substitutions is in the 1 domain and the other five are in the 2 domain. Comparison of this sequence with that of other human class I molecules implicates Gln₆₂ as a critical residue involved in HLA-A11 – HLA-A3 serological cross-reactivity. In addition, the amino acid sequence allowed us to successfully predict cross-reactive recognition of HLA-A11 by cytotoxic T lymphocytes specific for a rare subtype of HLA-A3, HLA-A3.2. This result provides further support for the importance of the 2 domain residues 152 and 156 in forming determinants on class I molecules that are recognized by cytotoxic T lymphocytes.Abbreviations used in this paper CTL cytotoxic T lymphocyte - PBL peripheral blood lymphocyte - PHA phytohemagglutinin     

An HLA-A2 population variant with structural polymorphism in the α3 region

The HLA-A2 antigen expressed by donor OZB can be distinguished from the main HLA-A2.1 subtype by isoelectric focusing - it is one charge unit more acidic — and by some alloreactive T-cell clones but not by cytolytic T lymphocyte lines. The structure of variant OZB has been examined by comparative peptide mapping with A2.1 and radiochemical sequence analysis. The two molecules were found to differ in a single tryptic peptide from the 0 region, spanning residues 220–243. The amino acid sequence of this peptide from variant OZB revealed that there was only one amino acid change of Glu instead of Ala at position 236, a hitherto invariant residue in class I HLA antigens. All previously characterized HLA or H-2 natural variants have structural changes restricted to the 1 and/or 2 domains. Thus, variant OZB is unique in that (1) it has one amino acid change in 3 and (2) it has no changes in l and 2. The only detected substitution of this variant may be accounted for by a single base change at the DNA level, suggesting that it might have resulted from a point mutation in the A2.1 gene. The structural features of variant OZB open a novel way to examine the influence of polymorphism in 3 on cytolytic T-cell recognition of naturally occurring class I antigens.Abbreviations CTL cytolytic T lymphocytes - HPLC high performance liquid chromatography - IEF isoelectric focusing - MHC major histocompatibility complex     

Identification of a single nucleotide change in a mutant gene for hypoxanthine-guanine phosphoribosyltransferase (HPRTAnn Arbor)

Summary HPRT_{Ann Arbor} is a variant of hypoxanthine (guanine) phosphoribosyl-transferase (HPRT: EC 2.4.2.8), which was identified in two brothers with hyperuricemia and nephrolithiasis. In previous studies, this mutant enzyme was characterized by an increased K_m for both substrates, a normal V_max, a decreased intracellular concentration of enzyme protein, a normal subunit molecular weight and an acidic isoelectric point under native isoelectric focusing conditions. We have cloned a full-length cDNA for HPRT_{Ann Arbor} and determined its complete nucleotide sequence. A single nucleotide change (TG) at nucleotide position 396 has been identified. This transversion predicts an amino acid substitution from isoleucine (ATT) to methionine (ATG) in codon 132, which is located within the putative 5-phosphoribosyl-1-pyrophosphate (PRPP)-binding site of HPRT.     

Analysis of the functional epitopes on different HLA-A2 molecules

Recent studies show that the serologically defined HLA-A2 molecule can be subdivided according to functional and biochemical characteristics. By the use of various HLA-A2-specific cytotoxic T lymphocytes (CTLs) and isoelectric focusing, the serologically homogeneous HLA-A2 molecule can be divided into four subtypes. The polymorphism of the serologically defined HLA-A2 molecule has also been demonstrated by the use of HLA-A2-restricted CTLs. This study was designed to analyze the functional epitopes on different HLA-A2 molecules with special regard to the recognition patterns of different types of HLA-A2-restricted CTLs directed against minor histocompatibility (minor H) antigens. Fifteen so-called HLA-A2 variants belonging to distinct HLA-A2 subtypes were tested as target cells in the cell-mediated lympholysis (CML) assay against (1) HLA-A2-restricted antiminor H-Y CTLs, (2) HLA-A2 and -B7-restricted antiminor H-Y CTLs, and (3) HLA-A2, -Bw62 and -B27-restricted antiminor HA CTLs. We found that those three CTLs recognized only one of those HLA-A2 variants. Furthermore, positive reactions by the antiminor H CTLs were only observed on those variant cells which carried, in addition to the HLA-A2 variant, either another normal HLA-A2 molecule or another required restricting class I molecule necessary for associative recognition. These results indicate that the absence of HLA-A2 normal allotypic target determinant(s) leads to the loss of epitope(s) necessary for recognition of minor H-Y and minor HA transplantation antigens by HLA-restricted CTLs. We can conclude from the present study that HLA-A2-restricted antiminor H CTLs use, in general, the same epitope (or cluster of epitopes) for cellular recognition as alloimmune HLA-A2-specific CTLs.     

Molecular analysis of an HLA-A2 functional variant CLA defined by cytolytic T lymphocytes

By using cytolytic T lymphocytes (CTL), the HLA-A2 serologic specificity may be divided into at least four subtypes designated as A2.1 to A2.4. The HLA-A2.4 antigen expressed by donor CLA is not recognized by allogeneic CTL specific for either A2.1, A2.2, or A2.3, but is indistinguishable from HLA-A2.1 by H-Y-specific, HLA-A2-restricted CTL and by isoelectric focusing. The structure of this HLA-A2.4 antigen was compared with the known structure of the main A2.1 subtype expressed on JY cells to establish the molecular basis for the immunologic differences between the two antigens. Comparative peptide mapping and radiochemical sequence analysis were used to establish that they differed by a single amino acid change: Phe at position 9 in HLA-A2.1 was replaced by Tyr in HLA-A2.4 from donor CLA. This position displays the highest variability score among all polymorphic residues of the class I HLA antigens. But its participation in the specific determinants recognized by CTL has not been previously established, because no other known HLA variant or H-2 mutant has been found to vary at this position. In addition, HLA-A2.4 from CLA is the only HLA-A2 subtype antigen that is identical to A2.1 in the segment spanning residues 147 to 157, a region in which all three A2.1, A2.2, and A2.3 antigens are different.     

Three new rare variants of α1-Antitrypsin

Summary Three new rare genetic variants of the serum protein ₁-antitrypsin (₁-protease inhibitor) have been identified in a Caucasian population. The new alleles in the PI system are PI ^*EFRA, PT^*PCAS, and PI ^*XALB. When compared with the normal type M by isoelectric focusing in polyacrylamide, Efranklin (EFRA) is anodal, and Pcastoria (PCAS) and Xalban (XALB) are cathodal. These variants have been compared with previously described variants by isoelectric focusing and by electrophoresis in agarose and acid starch gels. All three variant alleles appear to be associated with normal amounts of ₁-antitrypsin, assayed both by functional and immunological methods.This work was supported by a grant from the Medical Research Council of Canada     

Definition of four HLA-A2 subtypes by CML typing and biochemical analysis

The population of HLA-A2-positive individuals, currently considered serologically homogeneous, can be divided into three subtypes on the basis of antigen recognition by various HLA-A2-specific cytotoxic T lymphocytes (CTLs). When these three types of HLA-A2 antigens were analyzed biochemically, they were found to be distinct. Isoelectric focusing (IEF) of HLA antigens digested with neuraminidase (NANAse) suggested that the difference(s) reside in the polypeptide backbone of the HLA-A2 heavy chain. Biochemical analysis distinguishes three distinct categories of HLA-A2 antigens: (1) a major subtype, designated HLA-A2.I, (2) a minor subtype, designated HLA-A2.II, possessing a more basic isoelectric point (IEP) and (3) a minor HLA-A2 subtype more acidic in its IEP than HLA-A2.I, designated HLA-A2.III. A fourth HLA-A2 subtype could be defined by discordance between cell-mediated lympholysis (CML) typing and biochemical analysis. The latter HLA-A2 antigen was defined as a variant by CTL, but was biochemically indistinguishable from the major subtype HLA-A2.I.     

Identification and functional perspective of a novel HLA-A allele: A*0279

A novel HLA-A allele, HLA-A*0279, was identified using PCR-SSP and PCR-SBT methods. It is inheritable. HLA-A*0279 differs from HLA-A*020601 by a single nucleotide at position 497 in exon 3, leading to an amino acid change from Threonine to Isoleucine at the alpha2 helix of HLA molecule. To investigate whether the altered amino acid residue could affect its peptide-binding repertoire, we compared the predicted crystal structure of HLA-A*020601 and HLA-A*0279 by Swiss-PdbViewer software analysis. We found that the crystal structure of the two molecules is very similar except for a difference in the number of hydrogen bonds they can possibly form, which in turn could affect their structural stability. To test whether HLA-A*0279 has the ability to cross-present A*0201 - restricted peptides to T cells, the full lenght cDNA of HLA-A*0201, -A* 020601 and -A*0279 were respectively transfected into COS-7 cells, which were then used as targets in IFN-gamma release Elispot assay. A*2079 was found to be able to present A*0201- restricted peptides to and induce the response of CTL, thus it can be classified as member of the HLA-A2 functional supertype family. This finding would benefit the design of peptide vaccines to be applied in broader populations.The nucleotide sequence data reported in this paper have been submitted to the Genbank nucleotide sequence database and have been assigned the accession numbers AY856830 and HWS10002813.The name HLA-A*0279 was officially assigned by the World Health Organization Nomenclature Committee in January 2005.     

The eighth component of human complement: molecular basis of C8A (C81) polymorphism

Using an exon-specific polymerase chain reaction (PCR) followed by direct DNA sequence analysis we have analyzed the polymorphism of the -chain of the eighth component of human complement (C8) at the DNA level. We found that two common alleles, C8A^*A and C8A^*B, are characterized by the substitution of a single amino acid (Gln to Lys), which is caused by a point mutation of a single nucleotide (C to A) in exon 3 at position 187 of the mature C8 cDNA sequence. Based on this mutation, an allele-specific PCR was designed detecting the two alleles of C8A. We applied this method to type the C8A polymorphism using DNA samples from a Chinese Han population. The comparison with the data of protein typing of the same samples proved that the described method is efficient and reliable for the identification of C8A genotypes and may be valuable for further application in population studies and forensic science.     

Two subtypes of HLA-B51 differing by substitution at position 171 of the α2 helix

Newly defined antigens of the B5, B35 cross-reacting group have been found in Japanese and North American Indians. Nucleotide sequencing of the alleles encoding the Japanese B5.35 antigen and the variant B5 antigen from the Piman Indians show them to be identical. This new allele, B ^* 5102, differs from B ^* 5101 by a single nucleotide substitution that changes residue 171 from histidine to tyrosine. Residue 171, which is part of the ₂ helix, is believed to contribute directly to peptide interaction in the A pocket of the binding groove and is either histidine or tyrosine in all HLA-A, B, C heavy chains. Tyrosine 171 is shared by B ^* 5102, B ^* 3501, B ^* 3502, and B ^* 5301 and must be responsible for the serological cross-reactivities of these molecules not shared with B ^* 5101. Stimulation of lymphocytes from a B ^* 5101 positive donor with B ^* 5102 positive cells failed to generate cytotoxic T cells with specificity for the difference between these molecules. However, one out of five clones of cytotoxic T cells raised against B ^* 5101 failed to lyse targets expressing B ^* 5102. Substitution of histidine for tyrosine at residue 171 affected recognition of HLA-B35-restricted human minor histocompatibility antigen-specific T cell clones.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M68964.     

Molecular analysis of HLA-B39 subtypes

Serological studies have suggested the presence of a new HLA-B39 subtype (B39.2) in the Japanese population. To identify the new HLA-B39 subtype and compare it with an other HLA-B39 subtype (B39.1), the genes encoding HLA-B39.1 (B ^* 39013) and B39.2 (B ^* 3902) have been cloned from Japanese. We have sequenced these genes and completed the sequence of HLA-B39.1 (B ^*39011 ) gene from a Caucasian that was partially sequenced. Comparison of the sequence data revealed that B ^* 3902 and B ^* 39013 differ by three nucleotide substitutions which result in a two amino acids change at residues 63 and 67, while one silent substitution at codon 312 is found between B ^* 39011 and B ^* 39013. These results suggest that B ^* 3902 has evolved from B ^* 39013 rather than B ^* 39011.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M94051 (HLA-B^*39013), M94052 (HLA-B^*39011), and M94053 (HLA-B^*3902).     

Genetic polymorphism of the complement C2 in Japanese

Summary Genetic polymorphism of the second component of human complement (C2) was investigated in 521 unrelated healthy adult Japanese using isoelectric focusing in polyacrylamide gel followed by a specific hemolytic overlay method. Besides the phenotypes reported previously (C, AC and BC), a relatively infrequent double-banded phenotype (tentatively named A'C) was observed. Moreover, a homozygous variant (A) and a heterozygous double variant (AB) were observed. The estimated frequencies for the common allele. C2 ² (=C2 ¹ ), and the variant alleles, C2 ^A , C2 ^B (=C2 ² ) and C2 ^A were 0.939, 0.034, 0.022, and 0.006, respectively.The results of further typing for HLA-A,-B,-C specificities indicated the presence of significant associations of C2 ^A with HLA-B15 and with A26, and of C2 ^B with HLA-Bw61. These findings support our previous observation that in Japanese there are allelic combinations showing linkage disequilibrium between C2 and HLA loci which are different from those in Caucasians, and that the C2 structural locus is more closely linked to HLA-B than to HLA-A.C2 hemolytic activities of each phenotypes were assayed. The mean activity of type AC sera was significantly higher than that of type C or type BC, while there were no differences in the activities among the types C, BC or A'C.Also presented are two pedigrees demonstrating the segregation of C2 with HLA alleles in which a homozygous C2A or C2B individual was observed.     

Molecular cloning and DNA sequence analysis of genes encoding cytotoxic T lymphocyte-defined HLA-A3 subtypes: the E1 subtype

Influenza-specific cytotoxic T cells restricted by HLA-A3 and allogeneic CTL specific for HLA-A3 recognize differences between serologically indistinguishable HLA-A3 antigens. Previous biochemical studies have indicated that such differential recognition can be explained by alterations in the primary structure of class I heavy chains. Characterization of these sequence differences may therefore identify portions of the class I molecule that form determinants recognized by CTL. In this study, we describe the cloning and sequencing of an HLA-A3 subtype from donor E1 (E1-A3). Cloning of the gene encoding E1-A3 was simplified by determining that a 15.5-kb BamHI fragment contains the complete gene and is characteristic of HLA-A3 and only one other class I gene (HLA-A11). Comparison of the E1-A3 sequence to that of a previously sequenced HLA-A3 gene for exons encoding extracellular class I domains revealed three nucleotide differences. All of these differences were located within a discrete region of exon 3 (encoding the alpha 2 domain) and result in a change of two amino acids, at positions 152 (Glu----Val) and 156 (Leu----Gln). This finding suggests that these amino acids are crucial for the information of a determinant recognized by CTL. Furthermore, the altered nucleotide sequence of E1-A3 is identical to the sequence of the HLA-Aw24 gene for codons 128 to 161. These observations of multiple clustered changes in the E1-A3 subtype (relative to the prototype sequence) and identity of the altered sequence with the sequence of another class I gene support the concept that gene conversion is a primary mechanism for the generation of class I polymorphism.     

A new partially deficient variant in the phosphoglucomutase 1 system,PGM1*W31

Summary In a case of disputed paternity an inherited hyposynthetical variant of the PGM1^*1A gene was identified. This variant could not be detected by conventional electrophoresis on cellulose acetate membranes but clearly appeared on polyacrylamide gels after isoelectric focusing. The enzyme activity of this variant was about 25% of the normal PGM1^*1A protein. The variant was designated PGM1^*W31.     

Liver glutathione S-transferase polymorphism in Japanese and its pharmacogenetic importance

Summary A total of 168 autopsy liver extracts from Japanese individuals were examined for the glutathione S-transferase (GST) isozymes by means of starch gel electrophoresis. The gene frequencies of GST1^*1, GST1^*2, and GST1^*0 in Japanese were 0.252, 0.057, and 0.691, respectively. GST1^*3 was detected as a rare variant allele. The incidence of GST1 0 in 41 liver biopsy samples from patients suffering from various liver diseases was investigated using polyacrylamide gel isoelectric focusing. The GST1 0 phenotype was found more frequently in livers with hepatitis and carcinoma than in control livers. The isozymes coded by different GST loci were partially purified and characterized to study their biochemical properties. The apparent Km values with 1-chloro-2,4-dinitrobenzene (CDNB) as substrate for the isozymes at the GST1, GST2, GST3, and GST4 loci were 604, 1345, 776 and 591 M, respectively.     

Cloning and expression of the A2a adenosine receptor from guinea pig brain

A full-length complementary DNA (cDNA) clone encoding the guinea pig brain A₂ adenosine receptor has been isolated by polymerase chain reaction (PCR) and low-stringency-hybridization screening of a guinea pig brain cDNA library. This cDNA contains a long open reading frame encoding a 409-amino acid-residue protein which is highly homologous to the A₂ adenosine receptors previously cloned from other species. Hydrophobicity analysis of the deduced protein sequence reveals seven hydrophobic regions, characteristic of a member of the G-protein-coupled receptor superfamily. Radioligand binding assay and functional (GTPase and cAMP) assays of the receptor, transiently expressed in mammalian cells, demonstrate typical characteristics of the A₂ type adenosine receptor. The messenger RNA (mRNA) of this A₂ receptor is found in the brain, heart, kidney and spleen. Receptor autoradiography with [³H]CGS21680, a specific A₂ agonist, and in situ hybridization with A₂ cRNA probe in guinea pig brain indicate that the receptor is expressed exclusively in the caudate nucleus. The pharmacological profile and anatomical distribution of this receptor indicate that it is of the A_2a subtype. This work represents the first cloning of an A_2a receptor in a rodent species, offers a complete pharmacological characterization of the receptor and provides an anatomical comparison between binding profile and gene expression of the receptor.Abbreviations ADAC adenosine amine congener - BA N⁶-benzyladenosine - bp nucleotide base pair - cAMP cyclic adenosine 3,5-monophosphate - CCPA 2-chloro-N⁶-cyclopentyladenosine - CGS 21680 2-p-(2-carboxyethyl)phenethylamino-5-N-ethylcarboxamido adenosine hydrochloride - CHA N⁶-cyclohexyladenosine - CNS central nervous system - CPA N⁶-cyclohexyladenosine - CNS central nervous system - CPA N⁶-cyclopentyladenosine - CPX 8-cyclopentyl-1,3-dipropylxanthine - DME Dulbecco's modified Eagle's medium - DMPX 3,7-dimethyl-1-propargylxanthine - DPMX 1,3-dipropyl-7-methylxanthine - DPX 1,3-dipropyl-8-(2-amono-4-chlorophenyl)xanthine - FCS fetal calf serum - IBMX 3-isobutyl-1-methylxanthine - KHB Kreb-HEPES buffer - MECA 5-N-methylcarboxamidoadenosine - NECA 5-N-ethylcarboxamidoadenosine - D-PBS Dulbecco's phosphate buffered saline - PCR polymerase chain reaction - R-PIA R(–)-N⁶-(2-phenylisopropyl)adenosine - SSPE sodium chloride-sodium phosphate-EDTA buffer - TM transmembrane domain - XAC xanthine amine congener Special issue dedicated to Dr. Bernard W. Agranoff