Complete amino acid sequence of pooled papain-solubilized HLA-A, -B, and -C antigens: relatedness to immunoglobulins and internal homologies

A DNA methylation network interaction measure, and detection of network oncomarkers

Epigenetic processes–including DNA methylation–are increasingly seen as having a fundamental role in chronic diseases like cancer. DNA methylation patterns offer a route to develop prognostic measures based directly on DNA measurements, rather than less-stable RNA measurements. A novel DNA methylation-based measure of the co-ordinated interactive behaviour of genes is developed, in a network context. It is shown that this measure reflects well the co-regulatory behaviour linked to gene expression (at the mRNA level) over the same network interactions. This measure, defined for pairs of genes in a single patient/sample, associates with overall survival outcome independent of known prognostic clinical features, in several independent data sets relating to different cancer types. In total, more than half a billion CpGs in over 1600 samples, taken from nine different cancer entities, are analysed. It is found that groups of gene-pair interactions which associate significantly with survival identify statistically significant subnetwork modules. Many of these subnetwork modules are shown to be biologically relevant by strong correlation with pre-defined gene sets, such as immune function, wound healing, mitochondrial function and MAP-kinase signalling. In particular, the wound healing module corresponds to an increase in co-ordinated interactive behaviour between genes for worse prognosis, and the immune module corresponds to a decrease in co-ordinated interactive behaviour between genes for worse prognosis. This measure has great potential for defining DNA-based cancer biomarkers. Such biomarkers could naturally be developed further, by drawing on the rapidly expanding knowledge base of network science.

New family of exon-shuffled recombinant genes reveals extensive interdomain interactions in class I histocompatibility antigens and identifies residues involved

The specificities of an extensive panel of anti-H-2Dd monoclonal antibodies, which had been previously characterized using exon-shuffled H-2Dd/H-2Ld molecules and a number of anti-H-2DP antibodies, were examined using H-2Dd/H-2DP recombinants. The use of this new family of recombinant antigens revealed extensive interaction between the membrane-distal (N and Cl) domains of class I molecules. 20 out of 48 mAbs recognize complex epitopes formed by the interaction of these two domains. These antibodies exhibit a number of distinct patterns of crossreactivity with other class I proteins, revealing the presence of multiple epitopes within the region of domain interaction. Comparison of the data presented here with those from previous work allowed the identification of a small number of residues in the Cl domain that participate in the generation of complex epitopes involving both the N and Cl domains. The results are discussed in terms of the structural information available for these two domains.

Intracellular transport blockade caused by disruption of the disulfide bridge in the third external domain of major histocompatibility complex class I antigen

The third external domain of major histocompatibility class I antigens has a highly conserved disulfide bridge between cysteine-203 and cysteine-259. To elucidate the functional significance of this disulfide bridge, we have produced a mutant H-2Ld gene by site-directed mutagenesis in which the codon for cysteine-203 is changed to a codon for serine, which is unable to form a disulfide bridge. The mutant H-2Ld gene was introduced into mouse L cells and its expression has been studied. No measurable expression of the H-2Ld antigen was detected on the cell surface of the transformants by antibody-binding assays. However, a large quantity of the mutant H-2Ld antigen was found in the cytoplasm of the transformants as observed by immunoprecipitation of metabolically labeled lysate and by immunocytochemistry of membrane-permeabilized cells, using an antibody specific for the first external domain of the H-2Ld antigen. The mutant antigen was glycosylated and associated, at least in part, with beta 2-microglobulin. Subcellular fractionation experiments indicated that the transport of the antigen was blocked between the endoplasmic reticulum and the plasma membrane. It is concluded that structural integrity of the third external domain is a prerequisite for intracellular transport of class I antigens. On the basis of these findings we suggest that the domain structure containing the disulfide bridge serves as a signal structure necessary for receptor-mediated intracellular transport and that this requirement is the evolutionary basis for high conservation of similar structures present throughout the immunoglobulin supergene family.

Serological and partial molecular characterization of a Thy-1 homolog in tunicates

The occurrence of a Thy-1 homolog in the tissues of the advanced invertebrate group of tunicates has been investigated by using two monoclonal antibodies specific to rodent Thy-1.1 determinants and a heterologous anti-rat Thy-1 antiserum. In cellular and soluble-phase radioimmunoassays for Thy-1 using intact hemocytes, tissue extracts and hemolymph, membrane-bound and soluble Thy-1.1 cross-reacting determinants have been detected. Immunoprecipitation experiments with hemocyte deoxycholate extracts and hemolymph, labeled with 125I by lactoperoxidase/chloramine T and with NaB3H4 by galactose oxidase, established the association of the Thy-1.1 cross-reacting determinants with a single glycoprotein of apparent m.w. estimated at 27 000 in hemocytes and 22 500 in hemolymph by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The significance of this finding is discussed in relation to the phylogenetic emergence of the Thy-1 molecule during evolution.

HLA and disease

This review describes the greater portion of a large number of new studies on HLA and disease association which has appeared in the literature since 1979. The majority of these are concerned with the association of certain diseases with class II major histocompatibility complex antigens. The possible biologic significance of these associations in terms of their probable etiology appears to be the prevailing theme. Current thinking regarding certain heritable diseases is described. It seems that although much has been done to resolve the genetics of insulin-dependent diabetes mellitus, other diseases such a multiple sclerosis still remain a mystery. Doubtlessly, much will be gained from DNA cloning and sequencing studies proposed for the future. A great deal of new information has been obtained relative to HLA itself. New loci have been postulated in the HLA-D/DR region through the use of powerful immunochemical procedures made possibly by the advent of modern technological advances. The impact of these developments on our understanding of the function of the MHC in man and its possible relationship to disease are discussed.

Domain structures and molecular evolution of class I and class II major histocompatibility gene complex (MHC) products deduced from amino acid and nucleotide sequence homologies

Domain structures of class I and class II MHC products were analyzed from a viewpoint of amino acid and nucleotide sequence homologies. Alignment statistics revealed that class I (transplantation) antigen H chains consist of four mutually homologous domains, and that class II (HLA-DR) antigen beta and alpha chains are both composed of three mutually homologous ones. The N-terminal three and two domains of class I and class II (both beta and alpha) gene products, respectively, all of which being approximately 90 residues long, were concluded to be homologous to beta2-microglobulin (beta2M). The membrane-embedded C-terminal shorter domains of these MHC products were also found to be homologous to one another and to the third domain of class I H chains. Class I H chains were found to be more closely related to class II alpha chains than to class II beta chains. Based on these findings, an exon duplication history from a common ancestral gene encoding a beta2M-like primodial protein of one-domain-length up to the contemporary MHC products was proposed.

Specific association of repetitive DNA sequences with major histocompatibility genes

The DNA sequence organization of a 17.8-kilobase segment of porcine DNA, containing a functional major histocompatibility (MHC) gene, has been studied. The DNA flanking the MHC gene contains at least 10 distinct repetitive DNA sequence elements, each of which occurs only once within the 17.8-kilobase DNA segment. Their reiteration frequencies in the genome range from 10(2) to 10(4). The genomic organization of seven of these sequence elements has been examined; all are interspersed with other, unrelated DNA sequences. These seven repeated sequences are not generally associated in the genome. However, they appear to be nonrandomly linked in MHC-associated regions of the genome: at least two additional DNA segments containing MHC-homologous DNA also contain sequences homologous to DNA fragments bearing the seven different repeats. Of the seven sequences, four can be detected in splenic total RNA. These results suggest that these repeated elements are specifically associated with the MHC locus.

Specific association of repetitive DNA sequences with major histocompatibility genes

The DNA sequence organization of a 17.8-kilobase segment of porcine DNA, containing a functional major histocompatibility (MHC) gene, has been studied. The DNA flanking the MHC gene contains at least 10 distinct repetitive DNA sequence elements, each of which occurs only once within the 17.8-kilobase DNA segment. Their reiteration frequencies in the genome range from 10(2) to 10(4). The genomic organization of seven of these sequence elements has been examined; all are interspersed with other, unrelated DNA sequences. These seven repeated sequences are not generally associated in the genome. However, they appear to be nonrandomly linked in MHC-associated regions of the genome: at least two additional DNA segments containing MHC-homologous DNA also contain sequences homologous to DNA fragments bearing the seven different repeats. Of the seven sequences, four can be detected in splenic total RNA. These results suggest that these repeated elements are specifically associated with the MHC locus.

Complete amino acid sequence of an HLA-DR antigen-like beta chain as predicted from the nucleotide sequence: similarities with immunoglobulins and HLA-A, -B, and -C antigens

The complete nucleotide sequence of an HLA-DR antigen-like beta-chain cDNA clone was determined. The 1,080 base pairs include the complete coding region and most of the untranslated portion. The predicted amino acid sequence has 229 residues. The beta chain contains two immunoglobulin-like disulfide loops and a 21-amino acid residue membrane-integrated segment. Ten amino acid residues reside on the cytoplasmic side of the plasma membrane. The single asparagine-linked carbohydrate moiety is attached to asparagine-19. The NH2-terminal 91 residues of the beta chain are homologous to the corresponding region of HLA-A, -B, and -C antigen heavy chains. Residues 92-192 of the beta chain display statistically significant homology to members of the immunoglobulin family, beta 2-microglobulin, and the immunoglobulin-like domain of HLA-A, -B, and -C antigen heavy chains. These data establish that the major histocompatibility antigens of class I and class II type and the constant regions of immunoglobulins are evolutionarily related.

Structure of crossreactive human histocompatibility antigens HLA-A28 and HLA-A2: possible implications for the generation of HLA polymorphism

The primary structure of two highly crossreactive human histocompatibility antigens, HLA-A28 and HLA-A2, has been determined to 96% and 90%, respectively, of the papain-solubilized molecules. Their sequences have been compared with the sequence of HLA-B7 and with each other in order to outline the sites of diversity. The overall homology between HLA-B7 and these HLA-A antigens is 86%. A large majority of the differences are located between residues 43 and 195. Within this area, substitutions cluster in at least three segments--residues 65-80, 105-116, and 177-194. HLA-A28 and HLA-A2 show 96% homology. Most of the differences fall within segments 65-74 and 107-116. These results strongly support the suggestion that residues in these segments are integral parts of the alloantigenic determinants of HLA-A28 and HLA-A2. It is further proposed that these three clusters may constitute major, albeit not exclusive, sites of antigenic diversity in human histocompatibility antigens. The nature of the differences among HLA-B7, HLA-A28, and HLA-A2 in the first variable segment suggests that gene conversion might play some role in the generation of HLA polymorphism.

Characterization of a porcine genomic clone encoding a major histocompatibility antigen: expression in mouse L cells

A porcine genomic clone encoding a major histocompatibility, (MHC) antigen was isolated by direct screening of a swine genomic library with a heterologous human MHC cDNA probe. Mouse L cells transformed with DNA from the clone stably express swine MHC antigen. Pig alloantisera specifically lyse transformant but not control cell lines in a complement-mediated cytotoxicity assay. Direct immunoprecipitation of radiolabeled cellular protein from transformed lines by pig alloantiserum results in the coprecipitation of swine MHC heavy chain and mouse beta 2-microglobulin, demonstrating the association of heterologous subunits of MHC antigens.

beta 2-Microglobulin and its relationship to the immune system

beta 2-Microglobulin has been isolated from several species, but only bovine beta 2-microglobulin, previously known as lactollin, has been crystallized. An improved method for its isolation from colostrum is described. The bovine homologue exhibits a concentration-dependent aggregation behavior. beta 2-Microglobulin is related to both immune and histocompatibility antigen systems. It exhibits homology with the constant domains of the immunoglobulin-G light and heavy chains and is an integral part of histocompatibility antigens bound to cell surface. beta 2-Microglobulin also occurs in the free state in various body fluids including milk and colostrum. The possible relationship of elevated free beta 2-microglobulin of pathological conditions is suggested for future research.

Cell surface properties of HLA antigens on Epstein-Barr virus-transformed cell lines

A number of monoclonal antibodies have been used to investigate the distributions and rates of lateral motion of the HLA-A,B, and-DR antigens on several Epstein--Barr virus-transformed B-cell lines. The lateral diffusion coefficients (D) of fluorescein conjugates of the monoclonal antibodies bound to the cell surface were determined by fluorescence recovery after pattern photobleaching. Ds of HLA-A and-B were found to be comparable and of the order of 10(-9) to 10(-10) cm2/sec for each of the seven monoclonal antibodies and four cell lines examined. The HLA antigens appear to be monomeric on the cell surface based on experiments using mixtures of arsanilic acid-conjugated and fluorescein-conjugated antibodies. Four monoclonal antibodies against DR antigens were examined. Two of these, Genox 3.53 and L243, labeled the cell surface uniformly and gave Ds comparable to those obtained for the HLA-A and -B antigens. The other two, DA2 and 2.06, rapidly patched on the cell surface and were immobile. The DA2, L243, and Genox 3.53 antibodies bound outside of the caps formed with the arsanilic acid-conjugated 2.06 antibody and a second-step rhodamine-conjugated rabbit anti-arsanilate antibody. This is consistent with recent biochemical evidence that there are multiple distinct antigens coded for by the HLA-DR region.

Evolutionary relationship between HLA-DR antigen beta-chains, HLA-A, B, C antigen subunits and immunoglobulin chains

cDNA for a beta-chain of HLA-DR antigens was cloned and the partial nucleotide sequence was determined. The data suggest that the beta-chain consists of approximately 230 amino acids, of which about 200 are exposed on the cell surface. The beta-chain appears to be composed of two exposed disulphide-containing domains. The arrangement of the disulphide loops suggests that the beta-chain is similar in structure to the HLA-A, B, C antigen subunits and the immunoglobulin chains. For the beta-chain domain closest to the membrane this similarity was verified at the level of primary structure. The partial amino acid sequence of the NH2-terminal domain did not display any apparent homology to HLA-A, B, C antigens and immunoglobulins. However, the similarity established here between the two types of major histocompatibility antigen subunits and the immunoglobulin chains suggests a common ancestral origin for at least some regions of these molecules.

Binding of beta 2-microglobulin by heterologous sera

Purified human, rat or guinea-pig beta 2-microglobulin (beta 2m) was mixed with sera from guinea-pig, rat, mouse, rabbit, horse, goat, cow, rhesus monkey or man. The mixtures were incubated at 37 degrees C for various lengths of time. When the sera were separated by gel-chromatography on Sephadex G-200, beta 2m was traced not only in 'free' form but also in fractions with higher molecular weights. Evidence is presented suggesting that heterologous beta 2m binds to beta 2m-containing molecules in sera by exchange with the homologous counterpart.

Comparison between the specificity of primary and secondary killer cells against alloantigens and hapten-modified syngeneic lymphoid cells

Cytotoxic responses of lymphoid cells from different mouse strains against syngeneic cells modified with the haptens fluorescein isothiocyanate and trinitrophenyl were investigated. Mic of the H-2k strain demonstrated strong primary in vitro hapten-specific cytotoxicity reactions, which were H-2 restricted and involved the Kk specificity. However, cells from H-2d and H-2b mice developed hapten-specific cytotoxic reactions that showed H-2 cross-reactivity. This cross-reactivity, with regard to the restriction element, was particularly evident with cells from mice that had been immunized in vivo. No cross-reaction was observed between the two haptens, and Dd target cell antigens. Similar cross-reactions were demonstrated in vitro experiments in which secondary in vitro responses were induced by stimulation with cross-reacting H-2 antigens. This finding was also investigated in allogeneic cytotoxicity. In vitro induced responses resulting in relatively weak specific cell-mediated lympholysis reactions were H-2 specific, whereas secondary in vitro responses demonstrated cross-reactivity between Dd and Db antigens. In these test systems, cross-stimulation was also demonstrated in secondary in vitro responses. These results are discussed in terms of similarities of T cell recognition of hapten-modified self antigens and of alloantigens.

On mechanisms of activation and restriction in T and B lymphocytes

The mechanism of MHC restriction is discussed with special reference to cytotoxic T lymphocytes reactive against hapten-modified self determinants. Effector cell specificity is considered to reflect the specificity of primary induction and recognition between T lymphocytes and immunogenic antigenic determinants. Mechanisms of activation and development of different specificity repertoires in T and in B cells are discussed, with special reference to those self determinants that direct specificity and serve as markers for self-nonself discrimination.

Separation and comparison of human TL-like antigens and HLA(A, B, C) antigens expressed on cultured T cells

Beta 2-microglobulin-bound T-cell membrane components containing both human TL-like antigens and HLA(A, B, C) antigens were partially purified from Renex 30-solubilized membrane material of cells of a human T-cell-type leukemia cell line, HPB-ALL. The radioiodinated preparation was subjected to limited papain digestion; the HLA(A, B, C) antigens split, whereas a large portion of the human TL-like antigens remained intact. The antigen molecules were recovered by lentil-lectin affinity chromatography and separated by gel filtration on the basis of the induced difference in molecular size. The human TL-like-antigen preparation thus obtained was essentially free of HLA(A, B, C) antigens. The human TL-like antigens were immunospecifically precipitated and the component polypeptide, heavy and light, chains were separated by acid dissociation followed by gel filtration. The component chains were compared with the corresponding chains of HLA(A, B, C) antigens obtained similarly from the same HPB-ALL cells with respect to their fragmentation patterns on chemical or enzymatic cleavage. The results provided convincing evidence for the identity of the light chains of human TL-like antigens and HLA(A, B, C) antigens, and also evidence suggesting the presence of substantial differences in the fundamental structure of the heavy chains of human TL-like antigens and HLA(A, B, C) antigens.

Primary structure of murine major histocompatibility complex alloantigens: completion of the sequence of the amino-terminal 284 residues of H-2Kb

The primary structure of the COOH-terminal cyanogen bromide (CNBr) cleavage fragment Ic (CN-Ic) of the extracellular portion of the murine histocompatibility antigen H-2Kb has been completed. CN-Ic contains a site of papain cleavage which has been utilized for solubilizing H-2Kb by cleaving off the membrane integrating portion of the molecule. The amino acid sequence of CN-Ic has been determined by using peptides recovered after trypsin digestion of CN-Ic before and after blockage of lysine groups with citraconic anhydride. Overlapping sequences for the tryptic fragments were obtained by amino-terminal sequence analysis. The sequence of fragment CN-Ic, which spans residues 229-284 in H-2Kb, is as follows: Glu-Leu-Val-Glu-Thr-Arg-Pro-Ala-Gly-Asp-Gly-Thr-Phe-Gln-Lys-Trp-Ala-Ser-Val-Val-Pro-Leu-Gly-Lys-Glu-Gln-Tyr-Tyr-Thr-Cys-His-Val-Tyr-Gln-Gln-Gly-Leu-Pro-Gln-Pro-Leu-Thr-Leu-Arg-Trp-Asp-Glu-Pro-Pro-Ser-Thr-Val-Ser-Asn-Met. This amino acid sequence determination completes the primary structure of the amino terminal 284 residues of H-2Kb, that portion of this histocompatibility antigen which is external to the cell membrane and which contains antigenic determinants. It was also possible to identify Val-281 as a papain cleavage site within CN-Ic. The completed structure was analyzed solely by radiochemical methods. The structure obtained for H-2Kb is 71% homologous to the reported structure of HLA-B7, a human homologue.

An evaluation of the significance of amino acid sequence homologies in human histocompatibility antigens (HLA-A and HLA-B) with immunoglobulins and other proteins, using relatively short sequences

A computer search was carried out for homologies between HLA-A and HLA-B antigen sequences and the sequences of constant and variable regions of immunoglobulins and of all other sequenced proteins. Searches were made both with relatively short peptide sequences from the HLA antigens and with those longer peptide sequences which were available in 1978. Significant homology of HLA antigen sequences to immunoglobulin constant region sequences was found in two cases: (1) a short decapeptide sequence which includes the fourth cysteine residue of HLA-B7 and (2) an 89-amino-acid residue (Ac-2) C-terminal fragment of the papainsolubilized HLA-B7 molecule. The difficulty of establishing statistically significant sequence homology with relatively short peptide sequences is emphasized by computer-based comparisons of the decapeptide sequence with randomly generated peptide sequences. It is concluded that statistically significant homology with short sequences can be assured only when extraordinarily high degrees of homology are present and additional constraints are included in the matches, for example, matches at relatively rare amino acid residues such as Cys, His and Trp. The homology of the 89-amino-acid residue sequence to constant region sequences of immunoglobulins is as great as or greater than that of beta 2-microglobulin. These findings and the unique domain structure involving a disulphide loop of comparable size strongly favour a common evolutionary origin for this region of HLA-A and -B, beta 2-microglobulin and immunoglobulin constant regions.