The molecular evolution of the immune response

Effects of skeletal unloading on the bone marrow antibody repertoire of tetanus toxoid and/or CpG treated C57BL/6J mice

Spaceflight is known to impact the immune system in multiple ways. However, its effect on the antibody repertoire, especially in response to challenge, has not been well characterized. The development of the repertoire has multiple steps that could be affected by spaceflight, including V-(D-)J-gene segment rearrangement and the selection of complementarity determining regions (CDRs); specifically, CDR3, responsible for much of the diversity in the repertoire. We used skeletal unloading with the antiorthostatic suspension (AOS) model to simulate some of the physiological effects associated with spaceflight. Animals ± AOS were challenged with tetanus toxoid (TT) and/or CpG, an adjuvant. Two weeks after challenge, bone marrow was collected and sequenced using the Illumina MiSeq 2 × 300 platform. The resulting antibody repertoire was characterized, including V-, D- (heavy only), and J-gene segment usage, constant region usage, CDR3 length, and V(D)J combinations. We detected changes in gene-segment usage in response to AOS, TT, and CpG treatment in both the heavy and light chains. Additionally, changes were seen in the class-switched VH-gene repertoire. Alterations were also detected in V/J pairing for both the heavy and light chains, and changes in CDR3 length. We also detected lower levels of CDR3 AA overlap than detected in the splenic repertoire. These results demonstrate that AOS, TT, and CpG alter the bone marrow antibody repertoire however, it is still unclear from the data whether there is a loss of host antigen-specific responsiveness because of the change in gene use.

Effects of skeletal unloading on the antibody repertoire of tetanus toxoid and/or CpG treated C57BL/6J mice

Spaceflight affects the immune system, but the effects on the antibody repertoire, responsible for humoral immunity, has not been well explored. In particular, the complex gene assembly and expression process; including mutations, might make this process vulnerable. Complementarity determining region 3 (CDR3), composed of parts of the V-(D-)J-gene segments, is very important for antigen binding and can be used as an important measure of variability. Skeletal unloading, and the physiological effects of it, parallel many impacts of space flight. Therefore, we explored the impact of skeletal unloading using the antiorthostatic suspension (AOS) model. Animals were experimentally challenged with tetanus toxoid (TT) and/or the adjuvant CpG. Blood was analyzed for anti-TT antibody and corticosterone concentrations. Whole spleen tissue was prepared for repertoire characterization. AOS animals showed higher levels of corticosterone levels, but AOS alone did not affect anti-TT serum antibody levels. Administration of CpG significantly increased the circulating anti-TT antibody concentrations. AOS did alter constant gene usage resulting in higher levels of IgM and lower levels of IgG. CpG also altered constant gene region usage increasing usage of IgA. Significant changes could be detected in multiple V-, D-, and J-gene segments in both the heavy and light chains in response to AOS, TT, and CpG treatments. Analysis of class-switched only transcripts revealed a different pattern of V-gene segment usage than detected in the whole repertoire and also showed significant alterations in gene segment usage after challenge. Alterations in V/J pairing were also detected in response to challenge. CDR3 amino acid sequence overlaps were similar among treatment groups, though the addition of CpG lowered overlap in the heavy chain. We isolated 3,045 whole repertoire and 98 potentially TT-specific CDR3 sequences for the heavy chain and 569 for the light chain. Our results demonstrate that AOS alters the repertoire response to challenge with TT and/or CpG.

The amino acid residue at position 95 and the third CDR region in the H chain determine the ceiling affinity and the maturation pathway of an anti-(4-hydroxy-3-nitrophenyl)acetyl antibody

Two groups of anti-(4-hydroxy-3-nitrophenyl)acetyl (NP) Abs each possessing a different amino acid, Tyr or Gly, at position 95, appeared respectively at early and late stages of immunization. The early Abs predominantly harbored Tyr95 and were referred to as the Tyr95 type. These had ∼100-fold lower ceiling affinity than the late Abs harboring Gly95, which were referred to as the Gly95 type. We found that in order to raise affinity, the Tyr95 type utilized a mutation at position 33 in V(H), while the Gly95 type used multiple mutations in both V(H) and V(L), and that the effect of the mutations was reciprocal; the former mutation had a positive effect on Tyr95 type Abs but a negative effect on Gly95 type Abs, and vice versa. The reciprocal effect of these mutations on affinity enabled us to assess the type of Abs prepared by introducing 20 different amino acids at position 95. We found that Abs harboring Lys95, Arg95, Pro95, and Tyr95 belonged to the Tyr95 type and those with Ala95 and Gly95, to the Gly95 type. Since this dependency on the amino acid at position 95 was observed in H chains whose third CDR (CDR 3H) consisted of 9 amino acids and not 11, the CDR 3H region was also considered to play an important role in determining the maturation pathway and the magnitude of the ceiling affinity.

Antigenic repeat structures in proteins of Plasmodium falciparum

The majority of malaria antigens that have been cloned contain short sequence repeats which encode antigenic epitopes that are naturally immunogenic. Synthetic peptides have been used to show that natural antibody responses to a strain-specific Plasmodium falciparum S antigen are largely directed against epitopes encoded in an 11-amino acid sequence that is repeated approximately 100 times in the molecule. A 16-amino acid peptide conjugated to bovine serum albumin induced antibodies specific for the S antigen of the homologous isolate. Synthetic peptides have also been used to confirm the natural immunogenicity of epitopes encoded within two blocks of related repeats in the Ring-infected Erythrocyte Surface Antigen (RESA). A 16-amino acid peptide, comprising four repeats of the tetrameric sequence EENV, induced antibodies reactive with the native molecule. Detailed analyses of these anti-peptide antisera indicate that short sequence repeats express more than one epitope, some of which may cross-react with other repeat structures.

Three-dimensional analyses of the binding of synthetic chemotactic and opioid peptides in the Mcg light chain dimer

Synthetic peptides with chemotactic or opioid activity were bound to crystals of a light chain dimer and their three-dimensional structures and modes of binding were determined by X-ray analysis. The chemotactic series consisted of di- and tripeptides initiated with N-formylmethionine or N-formylnorleucine residues. Opioid peptides included the enkephalins and casomorphins ranging in length from four to seven residues. The binding region of the protein proved to be malleable in adjusting to the surface contours of the peptides. Aromatic contact residues, as well as polypeptide segments of hypervariable loops, moved to improve the complementarity with the ligands. The peptides were even more flexible and tended to conform fairly closely to the space and geometry available for occupancy in the binding sites. Binding interactions were not confined to the interior of the cavity. In both the chemotactic and opioid series, the carboxyl tails of the peptides encroached upon the outer surfaces of the rim and contributed to the binding energies for the protein-ligand complexes. The peptide bond in N-formylmethionyltryptophan was found to be in the energetically unfavourable cis configuration. There was also evidence for less severe distortions in peptide bond geometry when N-formyltripeptides were bound to the dimer.

Selection of high affinity p-azophenyarsonate Fabs from heavy-chain CDR2 insertion libraries

The length of the heavy chain complementarity-determining region two (HCDR2) of the unmutated anti-p-azophenylarsonate (Ars) monoclonal antibody (36-65 mAb) was extended by three residues in order to test whether this insertion can provide additional contacts between the Ab and the antigen. Two libraries were generated using 36-65 heavy and light chain genes which were cloned as Fab in the phage-display vector pComb3. In the first library, three randomized amino acids were inserted between residues Gly 54 and Asn 55, which are the most solvent exposed residues in the HCDR2 loop. In the second library, in addition to the 3-mer randomized insertion, the flanking residues at positions 54 and 55 were also randomized to allow additional loop flexibility for binding to Ars. Solid-phase and solution phase affinity panning were used to select for clones that bind to Ars. Results indicate that diverse 3-mer HCDR2 insertions can be tolerated, and affinities 10-fold higher than germline encoded 36-65 Ab can be obtained. The sequence diversity of the insertion among the selected clones from both libraries suggests that the insertion increases contact between the Ab and the protein carrier rather than the hapten alone.

The structural basis of repertoire shift in an immune response to phosphocholine

The immune response to phosphocholine (PC)-protein is characterized by a shift in antibody repertoire as the response progresses. This change in expressed gene combinations is accompanied by a shift in fine specificity toward the carrier, resulting in high affinity to PC-protein. The somatically mutated memory hybridoma, M3C65, possesses high affinity for PC-protein and the phenyl-hapten analogue, p-nitrophenyl phosphocholine (NPPC). Affinity measurements using related PC-phenyl analogues, including peptides of varying lengths, demonstrate that carrier determinants contribute to binding affinity and that somatic mutations alter this recognition. The crystal structure of an M3C65-NPPC complex at 2.35-A resolution allows evaluation of the three light chain mutations that confer high-affinity binding to NPPC. Only one of the mutations involves a contact residue, whereas the other two have indirect effects on the shape of the combining site. Comparison of the M3C65 structure to that of T15, an antibody dominating the primary response, provides clear structural evidence for the role of carrier determinants in promoting repertoire shift. These two antibodies express unrelated variable region heavy and light chain genes and represent a classic example of the effect of repertoire shift on maturation of the immune response.

Structural Requirements for a Specificity Switch and for Maintenance of Affinity Using Mutational Analysis of a Phage-Displayed Anti-Arsonate Antibody of Fab Heavy Chain First Complementarity-Determining Region

We previously showed that a single mutation at heavy (H) position 35 of Abs specific for p-azophenylarsonate (Ars) resulted in acquisition of binding to the structurally related hapten p-azophenylsulfonate (Sulf). To explore the sequence and structural diversity of the H chain first complementarity-determining region (HCDR1) in modulating affinity and specificity, positions 30–36 in Ab 36–65 were randomly mutated and expressed as Fab in a bacteriophage display vector. Ab 36–65 is germline encoded, lacking somatic mutations. Following affinity selection on Sulf resins, 55 mutant Fab were isolated, revealing seven unique HCDR1 sequences containing different amino acids at position H:35. All Fab bound Sulf, but not Ars. Site-directed mutagenesis in a variety of HCDR1 sequence contexts indicates that H:35 is critical for hapten specificity, independent of the sequence of the remainder of HCDR1. At H:35, Asn is required for Ars specificity, consistent with the x-ray crystal structure of the somatically mutated anti-Ars Ab 36–71, while Sulf binding occurs with at least seven different H:35 residues. All Sulf-binding clones selected following phage display contained H:Gly33, observed previously for Ars-binding Abs that use the same germline VH sequence. Site-directed mutagenesis at H:33 indicates that Gly plays an essential structural role in HCDR1 for both Sulf- and Ars-specific Abs.

Harmful somatic mutations: lessons from the dark side

The ability of somatic mutation to modify the course of an immune response is well documented. However, emphasis has been placed almost exclusively on the ability of somatic mutation to improve the functional characteristics of representative antibodies. The harmful effects of somatic mutation, its dark side, have been far less well characterized. Yet evidence suggests that the number of B cells directed to wastage pathways as a result of harmful somatic mutation probably far exceeds the number of cells whose antibodies have been improved. Here we review our recent findings in understanding the structural and functional consequences of V-region mutation.

Memory B cells are biased towards terminal differentiation: a strategy that may prevent repertoire freezing

Isolation of large numbers of surface IgD+CD38- naive and surface IgD-CD38- memory B cells allowed us to study the intrinsic differences between these two populations. Upon in vitro culture with IL-2 and IL-10, human CD40-activated memory B cells undergo terminal differentiation into plasma cells more readily than do naive B cells, as they give rise to five- to eightfold more plasma cells and three- to fourfold more secreted immunoglobulins. By contrast, naive B cells give rise to a larger number of nondifferentiated B blasts. Saturating concentrations of CD40 ligand, which fully inhibit naive B cell differentiation, only partially affect that of memory B cells. The propensity of memory B cells to undergo terminal plasma cell differentiation may explain the extensive extra follicular plasma cell reaction and the limited germinal center reaction observed in vivo after secondary immunizations, which contrast with primary responses in carrier-primed animals. This unique feature of memory B cells may confer two important capacities to the immune system: (a) the rapid generation of a large number of effector cells to efficiently eliminate the pathogens; and (b) the prevention of the overexpansion and chronic accumulation of one particular memory B cell clone that would freeze the available peripheral repertoire.

Correlation between immune maturation and idiotypic network recognition

The maturation of T-dependent humoral immune responses is mediated by somatic mutations. Antigen selection is one mechanism for the activation of B cell clones which express antibodies with progressively increased affinity and which are derived as somatic variants from germ-line-encoded genes. However, the emergence of B cell clones secreting rather low-affinity antibodies and the shift to alternative germ-line V region gene combinations during secondary and tertiary responses cannot be explained by antigen selection. It has been considered that idiotypic suppression may favor this clonal shift. Such an involvement would require that idiotypic recognition in the syngeneic host must be highly restricted to private idiotopes of each clone sequentially activated during immune maturation. To test this possibility, we produced 19 syngeneic anti-idiotypic antibodies to the germ-line-encoded major Ox1 idiotype (IgM-IdOx1 H11.5) of the anti-2-phenyl-oxazolone (phOx) immune response in BALB/c mice. The fine specificity of these anti-IdOx1 was tested with a set of anti-phOx monoclonal antibodies, representing the first steps of maturation. About half of the anti-IdOx1 showed almost no reactivity with the IdOx1 after the switch to IgG and none of the anti-IdOx1 reacted with anti-phOx antibodies which carried a glycine or histidine instead of arginine as the middle amino acid of the D region. These observations suggest a strong correlation between immune maturation and the idiotypic network. A model is presented in which idiotypic suppression may function as a driving force for diversification and maturation of the antigen-induced immune response.

Normal human IgD+IgM- germinal center B cells can express up to 80 mutations in the variable region of their IgD transcripts

Somatic hypermutation in immunoglobulin variable region genes occurs within germinal centers. Here, we describe a subset of germinal center dark zone centroblasts that express only sIgD and have accumulated up to 80 mutations per heavy chain variable region (IgVH delta gene). Over half of the hypermutated IgVH delta sequences were found to be clonally related. This level of mutation is not observed in either IgVH gamma transcripts from the same sample or IgVH delta transcripts from peripheral blood, suggesting that these cells neither undergo isotype switch nor mature into circulating memory B cells. Optimal growth of these cells in vitro depends on CD40 ligand, T cell cytokines, and a fibroblast stroma, a combination possibly mimicking the dark zone microenvironment. Our hypothesis is that these cells may be sequestered within germinal centers, where their somatic mutation machinery is triggered. The isolation of these hypermutated B cells may represent a critical step for studying both the biology and biochemistry of somatic hypermutation.

Follicular dendritic cells and germinal centers

Follicular dendritic cells (FDCs) are stromal cells unique to primary and secondary lymphoid follicles. Recirculating resting B cells migrate through the FDC networks, whereas antigen-activated B cells undergo clonal expansion within the FDC networks in a T cell-dependent fashion, thereby generating germinal centers. Here, B cells undergo somatic mutation, positive and negative selection, isotype switching and differentiation into high-affinity plasma cells and memory B cells. Since the discovery of FDCs by electron microscopy as long-term antigen-retaining cells 30 years ago isolation of FDCs and generation of FDC-like cells lines and of FDC-specific monoclonal antibodies have been achieved. FDCs express all three types of complement receptors as well as Ig-Fc receptors, through which antigen-antibody immune complexes are retained. However, the mechanism that prevents FDCs from internalizing the antigens and retaining them in native form for long periods of time remains obscure. Substantial evidence derived from cultures in vitro indicates that FDCs contribute directly to the survival and activation of peripheral B cells. The adhesion between FDCs and B cells is mediated by ICAM-1 (CD54)-LFA-1(CD11a) and VCAM-VLA-4. T cells may interact with FDCs in a CD40/CD40-ligand-dependent fashion. Whether FDCs originate from hematopoietic progenitors or from stromal elements is still a controversy. New evidence suggests the presence of two types of dendritic cells within human germinal centers: (i) the classic FDCs that express DRC-1, KiM4, and 7D6 antigens represent stromal cells; and (ii) the newly identified CD3-CD4-CD11c- germinal center dendritic cells (GCDC) represent hematopoietic cells that may be analogous to the antigen-transporting cells described in mice. Finally, FDCs appear to be involved in the growth of follicular lymphomas and in the pathogenesis of HIV infection.

Transient dominance of the early primary immune response by a highly conserved B-cell clone that is distinguished by its lack of memory, high threshold of activation, and a high affinity

We establish here that the very early primary response to the hapten phthalate (Xmp) is distinguished by a restricted heterogeneity with over 80% of the anti-Xmp antibodies expressing a single well-defined cross-reactive idiotype (CRIXmp-1) associated with a previously described highly conserved clonotype that is expressed by most inbred strains of mice and many outbred mouse populations as well. The characteristic early dominance of this one clonotype in the primary response is transient. While the CRIXmp-1 clonotype is present later in the primary and throughout the secondary response, it represents only a very small proportion of the total anti-Xmp antibody population at these times. The early dominance of the single clonotype is rapidly replaced by a heterogeneous population of antibodies. Differential activation thresholds for the primary response clonotype (CRIXmp-1) and secondary response clonotypes, and the failure of the dominant primary response clonotype to expand in the secondary response (i.e., absence of memory) suggest the presence of two distinct B-cell lineages.

Specificity variants in monoclonal antibodies reactive with peptide epitopes of the ring-infected erythrocyte surface antigen (RESA) of Plasmodium falciparum

It has been suggested that repeat sequence antigens of Plasmodium falciparum may serve the parasite in immune evasion by modifying the host antibody response and impairing the development of protective immunity. According to this proposal networks of cross-reactive, repeat sequence malarial antigens have the ability to stimulate a high proportion of all somatically mutated B cells with altered antibody specificity, and thus to hinder the normal process of antibody affinity maturation. To determine the rate at which immunoglobulin mutations produce new reactivities with repeat sequence antigens, hybridoma cell lines specific for the ring-infected erythrocyte surface antigen (RESA) were examined for the incidence of specificity variants that arose naturally or as a result of treatment with the chemical mutagen ethylmethane sulphonate (EMS). From one of the cell lines variants were readily isolated having reactivity towards a very closely related repeat sequence epitope within the same RESA antigen. However, the other hybridoma/antigen combinations revealed no variants. In general, mutations giving rise to antibodies with altered specificity for related repetitive antigens were not readily induced and only limited support of the hypothesis was obtained.

Molecular heterogeneity of auto-anti-idiotypic antibodies in MLR-lpr/lpr mice

The VH and V kappa gene families expressed by 20 monoclonal auto-anti-idiotypes (Ab2) derived from unmanipulated MLR-lpr/lpr mice were determined by Northern blotting. Complete variable region sequences of six Ab2, along with three additional V kappa-JH Ab2 sequences, were obtained. These auto-anti-idiotypes arose spontaneously in the animals, and they bound specifically to an idiotypic determinant (Id/r) on mAb 28/12, a monoclonal IgG2b MLR-lpr/lpr anti-small nuclear ribonucleoprotein antibody. The 16 Ab2 heavy chains belonged to 7 different VH gene families, and the 10 Ab2 light chains were derived from 8 V kappa families. The light chains of two Ab2 were approximately 99% identical; the remaining variable region sequences were highly heterogeneous. There was no correlation between primary amino acid sequence of either heavy or light chain and idiotypic properties of the auto-anti-idiotypes. Six Ab2 used VH or V kappa genes that are identical to known germ-line genes. A high proportion of the spontaneous auto-anti-idiotypes was shown to have autoantibody activity (anti-DNA, anti-ribonucleoprotein), or specific binding reactions with lipopolysaccharide of Salmonella RE, or both properties. The structural diversity of spontaneous MLR-lpr/lpr auto-anti-idiotypes differs sharply from the structural homogeneity reported for Ab2 induced in normal animals against syngeneic Ab1. Our results suggest that auto-anti-idiotypes might arise independently of an immunogenic stimulus from an Ab1.

Affinity repertoire of monoclonal antibodies obtained by primary or secondary in vitro immunization

The effect of the antigenic dose (1 ng-10 micrograms DNP-KLH/ml) on affinity constants of monoclonal antibodies produced by in vitro immunization was investigated. A statistically significant (p = 0.0000) trend could be demonstrated since the higher antigen concentration that was used during the five day culture the lower was the obtained Kass value. The range of affinities of the IgM monoclonal antibodies was similar to what was obtained from IgM antibodies produced by in vivo immunizations. However, the combination of a primary in vivo immunization followed by a secondary in vitro stimulation schedule resulted in an antigen dependent generation of high affinity isotype switch variants, exhibiting even higher affinities compared to monoclonal antibodies produced from only in vivo immunized animals. These results demonstrate that it is possible to elicit both an antigen-driven primary or secondary response in vitro.

On the skew distribution of immunoglobulins and the inverted protein-folding problem

The question of antibody specificity is discussed in the framework of the inverted protein-folding problem (i.e. the characterization of protein sequences with a common fold). A stochastic model of the immune response, patterned after a model for the distribution of words in natural languages is proposed. It is shown that the steady-state probability distribution of immunoglobulin variable-region frequencies is the Yule distribution.

Clonal repertoire analysis of murine B cells specific for repeat sequence antigens of Plasmodium falciparum

Clonal analysis of the murine B-cell repertoire has been used to investigate the possible role of tandem repeat sequence epitopes of Plasmodium falciparum in immune evasion. A limiting dilution culture system was used whereby murine spleen cells were stimulated with the B-cell mitogen lipopolysaccharide (LPS) in the presence of 3T3 fibroblast filler cells. One in three B cells were shown to produce clones secreting immunoglobulin measurable by an ELISA. The frequency of antibody forming cell precursors (AFCp) specific for the 3' repeat epitopes of the ring injected erythrocyte surface antigen (RESA) was estimated in non-primed mice and found to be low. However, an accurate frequency determination was not possible using this method since the detection of the few positive cultures was found to depend on the presence of more than one AFCp or its products. Limiting dilution analysis was used to assess the frequency and repertoire of splenic AFCp at various times after immunization with a synthetic peptide of the RESA 3' repeat epitope (8 x 4-mer), presented in various ways. There was no marked increase in LPS-responsive AFCp specific for this antigen at the level of either IgM or IgG secretion. This was in marked contrast to the antibody response in vivo, where moderate IgG antibody titres, normally indicative of a secondary response, were seen in the serum of the same mice used for AFCp assay. This discrepancy between serum titre and AFCp frequency following immunization was not apparent with a non-malarial antigen, keyhole limpet haemocyanin (KLH). It was concluded that the LPS-stimulated limiting dilution culture system was not registering RESA-specific memory AFCp. These results raise the possibility that the malarial antigens are deficient in memory B-cell generation, or that secondary responses to these determinants may arise from a distinct B-cell progenitor which is non-responsive to LPS in vitro.

The biological effects of IgM hexamer formation

The inducible B cell lymphoma, CH12, and its in vitro adapted subclone, CH12-LBK, produce immunoglobulins of identical sequence, specificity and isotype, with equivalent affinities for the hapten trimethyl ammonium. However, the hemolytic efficiencies of the antibody secreted by the two cell lines are quite different. Antibody preparations from lipopolysaccharide-stimulated CH12 cells lyse erythrocytes six- to ten times more effectively than antibody preparations of the same concentration from CH12-LBK cells. Both cell lines secrete polymeric IgM, but while CH12-LBK cells secrete predominantly the canonical pentameric IgM, CH12 cells secrete a mixture of pentamers and hexamers. High-efficiency complement-dependent cytolysis is associated with hexameric IgM, which has a specific activity that is approximately twenty times higher than that of the pentameric form. J chain protein is found in the secreted IgM of both cell lines, but is associated only with the pentameric IgM and not with the hexameric form, nor with any intermediate polymers smaller than a pentamer. A deficit in, or the inaccessibility of, J chain protein appears to facilitate hexamer formation. These experiments confirm previously published data showing that J chain is not necessary either for assembly or secretion of polymeric IgM, and suggest instead that J chain may be important in regulating the lytic efficiency of polymeric IgM by controlling the IgM pentamer/hexamer ratio. The experiments further suggest a mechanism, in addition to isotype switching and somatic mutation, by which the biological efficiency of antibodies from a single clone of B cells can be regulated.

The efficiency of antibody affinity maturation: can the rate of B-cell division be limiting?

It has been known for many years that the affinity of antibodies for antigen increases with time during an immune response. It is now clear that two processes play fundamental roles in this affinity 'maturation' in the mouse - V gene somatic mutation and antigen affinity-based selection. Exactly how these two processes work in concert is not fully understood. In this article Tim Manser argues that models of affinity maturation based on the assumption that somatic mutation, antigen selection and B-cell division are interdependent may not explain the high efficiency of the process, and he suggests an alternative model.

Somatic mutation, affinity maturation and the antibody repertoire: a computer model

Somatic mutation has been implicated as a significant and possibly primary factor in the maturation of antibody affinity in the humoral immune response. B cells stimulated by antigen experience a hyper-mutation in the gene segments that code for the antigen-binding site of the antibody, creating antibody specificities that did not exist at the time of immunization. Although most of the mutations are likely to be disadvantageous, new specificities with a higher affinity for the antigen are sometimes created. These higher-affinity cells are preferentially selected for proliferation and eventual antibody secretion, resulting in a progressively higher average affinity over time. In this paper we present the results of an investigation of somatic mutation through the use of a computer model. At the basis of the model is a large repertoire of discrete antibodies and antigens, having three-dimensional structures, that exhibit properties similar to those of the real populations. The key factor is that the binding strength between any antibody/antigen pair can be calculated as a function of the complementarity of the (a) size, (b) shape and (c) functional groups that comprise the two structures. The created repertoires are imbedded in a dynamical system model of the immune response to directly evaluate the affect of somatic mutation on affinity maturation. We also present an expanded hypothesis of clonal selection and development to explain how the mutational restrictions imposed by the genetic code and the structure of the antibody repertoire, along with antigen concentration, affinity, and probabilistic factors may interact and contribute to the expansion of specific clones as the response develops over time.

The role of germline gene expression and somatic mutation in the generation of autoantibodies to DNA

Several distinctive features of anti-DNA autoantibodies have been identified by a detailed analysis of the available heavy and light chain sequences. They include unique VH gene segments that are not normally expressed in antibodies to external antigens, somatic mutations which may serve to change the antigenic specificity as well as to increase affinity, a less stringent choice of light chains, and a unique basic peptide in the heavy chain CDR3. It is proposed that in the majority of cases, the regulatory mechanism of self-tolerance in the healthy animal operates via VH gene expression to prevent the synthesis of potentially high affinity anti-DNA autoantibodies.

DNA antibody idiotypes: an analysis of their clinical connections and origins

Approximately thirty common DNA antibody idiotypes have been described on hybridoma derived or affinity purified DNA-binding antibodies. There are associations between some idiotypes and the clinical manifestations of systemic lupus erythematosus although none are sufficiently firm to be clinically useful in identifying subsets of SLE or in assessing disease activity in individual patients. The expression of these idiotypes is not confined to DNA antibodies in SLE. They may be found in the serum from patients with a range of autoimmune rheumatic disorders, infectious disease and blood dyscrasias. In most cases the antigen binding specificity of the antibody bearing the idiotype is unknown. The precise relationship between the various idiotypes is becoming better understood with increasing availability of genetic and structural data. DNA antibody idiotype manipulation may provide a potential new therapeutic modality in SLE.

The NK model of rugged fitness landscapes and its application to maturation of the immune response

Adaptive evolution is, to a large extent, a complex combinatorial optimization process. Such processes can be characterized as "uphill walks on rugged fitness landscapes". Concrete examples of fitness landscapes include the distribution of any specific functional property such as the capacity to catalyze a specific reaction, or bind a specific ligand, in "protein space". In particular, the property might be the affinity of all possible antibody molecules for a specific antigenic determinant. That affinity landscape presumably plays a critical role in maturation of the immune response. In this process, hypermutation and clonal selection act to select antibody V region mutant variants with successively higher affinity for the immunizing antigen. The actual statistical structure of affinity landscapes, although knowable, is currently unknown. Here, we analyze a class of mathematical models we call NK models. We show that these models capture significant features of the maturation of the immune response, which is currently thought to share features with general protein evolution. The NK models have the important property that, as the parameter K increases, the "ruggedness" of the NK landscape varies from a single peaked "Fujiyama" landscape to a multi-peaked "badlands" landscape. Walks to local optima on such landscapes become shorter as K increases. This fact allows us to choose a value of K that corresponds to the experimentally observed number of mutational "steps", 6-8, taken as an antibody sequence matures. If the mature antibody is taken to correspond to a local optimum in the model, tuning the model requires that K be about 40, implying that the functional contribution of each amino acid in the V region is affected by about 40 others. Given this value of K, the model then predicts several features of "antibody space" that are in qualitative agreement with experiment: (1) The fraction of fitter variants of an initial "roughed in" germ line antibody amplified by clonal selection is about 1-2%. (2) Mutations at some sites of the mature antibody hardly affect antibody function at all, but mutations at other sites dramatically decrease function. (3) The same "roughed in" antibody sequence can "walk" to many mature antibody sequences. (4) Many adaptive walks can end on the same local optimum. (5) Comparison of different mature sequences derived from the same initial V region shows evolutionary hot spots and parallel mutations. All these predictions are open to detailed testing by obtaining monoclonal antibodies early in the immune response and carrying out in vitro mutagenesis and adaptive hill climbing with respect to affinity for the immunizing antigen.

In vivo induction of A/J anti-ARS responses with different ranges of affinities: correlation between affinity and CRIA idiotype dominance

The anti-ARS immune response of A/J mice is characterized by the reproducible and dominant selection of CRIA bearing antibodies. In this report, we have investigated the role of affinity for the antigen in the selection of antibody repertoire during an immune response. A/J anti-ARS responses with different ranges of affinities for arsonate were elicited by the injection of differently arsanylated carrier proteins. The selection of higher affinity A/J anti-ARS responses was shown to be associated with the induction of higher levels of CRIA bearing anti-ARS antibodies. A detailed idiotopic analysis also showed a more precocious selection of the CRIA "canonical combination" in the higher affinity anti-ARS responses. These results strongly suggest an important role for affinity and clonal selection in the dominant expression of the CRIA idiotype in the A/J anti-ARS response.

Preliminary crystallographic studies of the Fab fragment of an anti-azophenylarsonate antibody

Single crystals of the Fab fragment of a murine A/J anti-azophenylarsonate monoclonal antibody have been prepared by the vapor diffusion method. Antibody 3A7 uses the same combination of variable region gene segments (VK, JK, VH, JH) as do anti-azophenylarsonate antibodies bearing a predominant cross-reactive idiotype, but utilizes a different D gene segment. The crystals grow in the presence of beta-octylglucoside as tetragonal bipyramids in the space group of either P4(1)2(1)2 or P4(3)3(1)2 and with unit cell dimensions of a = b = 77.9 A, and c = 146.7 A. They diffract X-rays to better than 2.7 A resolution. Data up to 2.7 A resolution have been collected.

Characterization of the heavy and light chain immunoglobulin variable region genes used in a set of anti-digoxin antibodies

Five murine A/J hybridomas (the 35-20 group) produce anti-digoxin antibodies that have homologous heavy and light chain immunoglobulin variable regions (VH and VL), yet differ from each other in fine specificity and affinity for digoxin and related cardiac glycosides [Mudgett-Hunter et al. Molec. Immun. 22, 477-488 (1985)]. To determine the origin of the VH and VL genes used in this set of hybridomas, the rearranged VH and VL genes from one of the 35-20 group hybridomas, 40-140, were cloned. The expressed V region, the leader exon and the 5' transcription control regions were sequenced. VH40-140 is a member of the VH36-60 gene family and has greater than 90% homology with several members of that family. A VH40-140 hybridization probe detected two members of the VH36-60 gene family not previously described. The VL40-140 region, a member of the Vk9 subgroup, is nearly identical to the Vk region used by the myeloma T1. Southern analysis with several restriction endonucleases and hybridization probes indicated that the 35-20 group hybridomas each use the same heavy and light chain variable region gene segments in the assembly of their expressed antibody genes. Functional rearranged antibody genes were detected with JH and VH heavy chain probes and with Jk and Vk light chain probes. The availability of the clones of the one heavy and the one light chain variable region gene segment used by the 35-20 hybridoma group will facilitate the use of in vitro mutagenesis in studies of the structural basis of fine specificity in the digoxin antigen-antibody system.

Specificity of human anti-neurofilament autoantibodies

The specificities and isotypes of human antibodies that react with neurofilament (NF) proteins were examined by Western blot analysis. Two-thirds of the subjects tested had antibodies to the 200 kDa high molecular weight neurofilament protein (NF-H), and fewer had antibodies to the low and middle molecular weight neurofilament proteins (NF-L and NF-M respectively). Human autoantibodies bound to both native and dephosphorylated NF-H, but some antibodies bound to dephosphorylated NF-H only, indicating the presence of at least two target epitopes. They also recognized a fusion protein containing a segment of the NF-H protein produced by a cDNA clone in Escherichia coli, indicating that they bind to unmodified peptide epitopes. The anti-NF-H antibodies were mostly IgG, but were frequently complexed to IgA or IgM antibodies, possibly with rheumatoid factor or anti-idiotypic activity. These characteristics of anti-NF-H antibodies are most consistent with a secondary immune response that is antigen driven and T-cell dependent.

Properties of a system of public idiotypes of lupus autoantibodies

We can conclude from the properties of the Id-16/6 system that a relatively restricted group of B cell clones is activated in systemic lupus erythematosus. Whether this is a property of the immunogenic stimulus that causes the diseases (if indeed there is one), or whether the observations are due to an idiotypic network that favors the selection of Id-16/6-expressing B cells is not known. These alternatives are under investigation. Apart from these theoretical considerations, the high frequency of Id-16/6(+) autoantibodies, including pathogenic autoantibodies, in systemic lupus erythematosus may point to targets amenable to the specific therapy of the disease.

Genetic control of early antibody responses

By using a pair of strains that have similar VK haplotypes but different VH haplotypes (e.g. BALB/c and C57BL) it is possible to demonstrate VH-controlled genetic differences in antibodies. By using a pair that have similar VH haplotypes but different VK haplotypes (RF and BALB/c) it is possible to demonstrate VK-controlled genetic differences in antibodies. A plausible explanation for the high frequency of certain V-gene combinations in the primary response is a high affinity of the product without somatic mutations. The products of two such major primary response combinations (VHOx1/VKOX1(H3) and VH186.2/V lambda 1) have an affinity for the immunogen well above 10(6). One combination of V genes, VHOx1/VKOx1(H3) has a major role in the primary anti-phOx response of several mouse strains - the product is idiotype 260. C57BL/10 mice lack the VHOx1 and RF mice the VKOx1(H3) gene. They use the remaining partner of the pair for the response in combination with other genes, but the affinity of the product is lower than the affinity of id. 260. Concordantly, the frequency of these "half-idiotypes" is lower in the primary response than the frequency of the full combination (23% and 16% instead of 50%). When the product of a V-gene combination is very frequent in the primary response, the affinity for the immunogen must be high, but the reverse is not always true. The product of a combination can have an unusually high affinity but the frequency is low. The simplest explanation then is that the frequency of available virgin B cells is low. It can be low because of a low rearrangement frequency of one of the V genes, VH or VK. Another possibility is that only a small proportion of B cells that have the particular combination rearranged can be recruited to the response. We have discussed an example where strict heavy chain CDR3 requirements must strongly limit available B cells.

Restricted use of T cell receptor V genes in murine autoimmune encephalomyelitis raises possibilities for antibody therapy

Experimental allergic encephalomyelitis (EAE) is a paralytic autoimmune disease induced in susceptible animals by active immunization with myelin basic protein (MBP) or by passive transfer of MBP-specific T helper (TH) lymphocytes. We have analyzed the T cell receptor genes of 33 clonally distinct TH cells specific for a nonapeptide of MBP inducing EAE in B10.PL (H-2u) mice. All 33 TH cells used two alpha variable gene segments (V alpha 2.3, 61%; V alpha 4.2, 39%), the same alpha joining gene segment (J alpha 39), and two V beta and J beta gene segments (V beta 8.2-J beta 2.6, 79%; V beta 13-J beta 2.2, 21%). The anti-V beta 8 monoclonal antibody F23.1 was found to block completely recognition of the nonapeptide by V beta 8 TH cells in vitro and to reduce significantly the susceptibility of B10.PL mice to peptide-induced EAE.

Genetic control and fine specificity of the immune response to a synthetic peptide of influenza virus hemagglutinin

The immune response to a synthetic peptide, H3 HA1(305-328), representing the C'-terminal 24 amino acid residues of the HA1 chain of the hemagglutinin of the H3 subtype of influenza virus is controlled by genes in the I region of the major histocompatibility complex. Mice of the H-2d haplotype are high responders and produce antibody for several months after a single injection of peptide without carrier. Mice of the H-2b, H-2k, and H-2q haplotypes are low antibody responders. Investigation of recombinant and congenic mouse strains revealed that high responsiveness requires the genes that encode the I-Ed molecule. Immunoassays, involving direct binding to analogs of this peptide and inhibition by both these analogs and synthetic epitopes, were used to analyze the specificity of the polyclonal response. In BALB/c mice, the primary antibody response is directed principally against the antigenic site 314-LKLAT-318, whereas the secondary response after a boost is predominantly directed to a distinct site, 320-MRNVPEKQT-328. The T-cell response to the peptide H3 HA1(305-328), as measured by antigen-induced proliferation of primed T cells in vitro, is also I-Ed restricted in high-responder H-2d mice and is directed against an antigenic site that does not require the four C-terminal residues unique to the H3 influenza subtype. A different epitope appears to be recognized by T cells from CBA (H-2k) mice, which proliferate to a moderate extent on exposure to the peptide but, nevertheless, do not provide help for an antibody response.

Functional affinity of IgM rheumatoid factor in patients with rheumatoid arthritis and other autoimmune diseases

The functional affinity of IgM rheumatoid factors (RF) was measured in 31 patients with rheumatoid arthritis (RA), 24 with systemic lupus erythematosus (SLE), 13 with Sjögren's syndrome (SS), and in 13 seropositive healthy individuals. The functional affinity of IgM RF from patients with RA was significantly lower than in the other clinical groups studied. In addition, there was a significant inverse correlation between functional affinity and titre of IgM RF in all the groups. These results suggest that the usual mechanisms of affinity based selective pressure (somatic diversification and antigen selection) may operate differently for autoantibodies to serum antigens such as IgG.

Selection of amino acid sequences in the beta chain of the T cell antigen receptor

The induction of an immune response in mammals is initiated by specifically reactive T lymphocytes. The specificity of the reaction is mediated by a complex receptor, part of which is highly variable in sequence and analogous to immunoglobulin heavy- and light-chain variable domains. The functional specificity of the T cell antigen receptor is, however, markedly different from immunoglobulins in that it mediates cell-cell interactions via the simultaneous recognition of foreign antigens and major histocompatibility complex-encoded molecules expressed on the surface of various lymphoid and nonlymphoid cells. The relation between the structure of the receptor and its functional specificity was investigated by analyzing the primary sequences of the receptors expressed by a series of T lymphocyte clones specific for a model antigen, pigeon cytochrome c. Within this set of T lymphocyte clones there was a striking selection for amino acid sequences in the receptor beta-chain in the region analogous to the third complementarity-determining region of immunoglobulins. Thus, despite the functional differences between T cell antigen receptors and immunoglobulin molecules, analogous regions appear to be important in determining ligand specificity.

Topographic analysis with monoclonal anti-idiotopes: probing the functional anatomy of immunoglobulin variable domains

Attempts to correlate immunoglobulin variable domain functional properties with variable domain primary structure have been valuable, but these efforts have suggested that to more fully account for variable domain function in terms of structure will require knowledge of molecular relationships in three dimensions. In this review we describe generally applicable methods, using monoclonal anti-idiotopes, for the determination of spatial relationships of idiotopes relative to one another and relative to two orienting structural markers of variable domains: 1) the hapten-binding site and 2) the junction of the variable and constant domains. Using these methods it has been possible to construct an oriented idiotope map which spans the variable domain along an axis connecting the paratope and the variable domain-constant domain junction. In addition, it has been possible to correlate idiotope position with other properties of idiotope expression. This approach may contribute to the development of predictive principles of idiotope expression.

Measurements of mutation rates in B lymphocytes

It is established that somatic mutation is an important source of antibody diversity in vivo. It is also established that Igh-V gene segments are hypermutable in vitro. This is not a completely satisfactory situation. While there is no reason to believe that Igh-V genes are not hypermutable in vivo as well, direct experimental evidence is lacking. Perhaps experiments with transgenic mice will soon fill this gap. It is not so clear how much higher than normal the rate of hypermutation is. As far as we are aware, there are no direct measurements of mutation rates per base pair per cell generation in mammals, certainly not for lymphocyte cell lines. For a variety of reasons, it is difficult to measure very low mutation rates. The general consensus is that the normal rate should be somewhere between 10(-10) and 10(-12) mutations per base pair per cell generation. Therefore, an experiment designed to directly determine a rate using the compartmentalization test would involve hundreds of cultures, each containing at least 10(9) cells. It is not a trivial problem to find one or a few mutants among so many cells. It is simple to study mutation to resistance to a drug, for example, ouabain or azaguanine, but, as we discussed, there are technical and conceptual pitfalls. The vast excess of dead cells influences the growth of a few mutant cells, particularly in lymphocyte cell lines. Even if this problem could be solved, the mutation rate so obtained would be "per gene(s)" and not "per base pair". The problems associated with cytotoxic agents can be avoided by immunofluorescence methods in conjunction with selective cloning or cell sorting. Using these techniques, we have carried out extensive experiments to determine whether the immunoglobulin mutator system acts, at least partially, on genetic elements other than those in or near the heavy chain variable region gene segment. For an opal termination codon in a heavy chain constant region gene segment, the rate of reversion was less than 10(-7) per base pair per cell generation. This upper limit was fixed by the high rate of small deletions at the heavy chain locus. For an allotype mutation at B2m, the gene encoding beta 2 microglobulin, the rate of mutation was less than 10(-8). This upper limit could be lowered by at least two orders of magnitude by using a high-speed cell sorter.

Timing, genetic requirements and functional consequences of somatic hypermutation during B-cell development

While somatic antibody mutants are rare in the preimmune repertoire and in primary immune responses, they dominate secondary and hyperimmune responses. We present evidence that somatic hypermutation is restricted to a particular pathway of B-cell differentiation in which distinct sets of B-cell clones are driven into the memory compartment. In accord with earlier results of McKean et al. (1984) and Rudikoff et al. (1984), somatic mutation occurs stepwise in the course of clonal expansion, before and after isotype switch, presumably at a rate close to 1 X 10(-3) per base pair per generation. At this rate, both selectable and unselectable mutations accumulate in the rearranged V region genes. The distribution of replacement mutations in the V regions shows that a fraction of the mutations in CDRs is positively selected whereas replacement mutations are counterselected in the FRs. By constructing an antibody mutant through site-specific mutagenesis we show that a point mutation in CDR1 of the heavy chain, found in most secondary anti-NP antibodies, is sufficient to increase NP binding affinity to the level typical for the secondary response. Somatic mutation may contribute to the immune repertoire in a more general sense than merely the diversification of a specific response. We have evidence that clones producing antibodies which no longer bind the immunizing antigen can be kept in the system and remain available for stimulation by a different antigen. Somatic mutations are 10 times less frequent in DJH loci than in either expressed or non-expressed rearranged VDJH or VJ loci. We therefore conclude that a V gene has to be brought into the proximity of the DJH segment in order to fully activate the hypermutational mechanism in these loci.

Studies on the somatic instability of immunoglobulin genes in vivo and in cultured cells

We have examined the molecular mechanism and impact of somatic diversification on the T15 heavy chain variable region gene in vivo and in vitro. Somatic point mutation appears to be responsible for the changes we have observed in both hybridomas from early and late in the immune response and in the S107 myeloma cell line in culture. By identifying S107 mutants with decreases in antigen binding, we have shown that a single point mutation can cause the loss of binding to the eliciting antigen and the acquisition of binding to another antigen. Furthermore, in this case a point mutation of the T15 heavy chain variable region gene caused the conversion of an important protective antibody to an autoantibody. While the S107 cell line frequently generates both constant and variable region mutants, hybridomas appear to have relatively stable variable region genes and unstable constant region genes which in some cases result in mutants with increased binding.

Evolution of antibody variable region structure during the immune response

The results reviewed above reveal that during the anti-Ars immune response of strain A mice a somatic process that results in the evolution of V region structure occurs. This process involves both the selection of V regions encoded by particular gene segment combinations as well as the selection of structural variants of these V regions produced by somatic mutation as the immune response progresses. As a result, both quantitative and qualitative changes in the V region population initially elicited by immunization take place. The structural and functional character of the immune V region repertoire appears to be largely determined by this process of "somatic evolution" occurring in the primary response.

Somatic diversification of the chicken immunoglobulin light chain gene is limited to the rearranged variable gene segment

Previous studies have shown that the chicken lambda immunoglobulin light chain gene undergoes a single rearrangement that results in functional VJ joining of the unique variable (V lambda 1) and joining (J lambda) coding regions. The immunologic repertoire of lambda genes is created through extensive sequence diversification within the rearranged locus during B cell development in the bursa of Fabricius. This sequence diversification was detected only at the rearranged V lambda 1 segment and not within the 5' leader sequence, the J lambda segment, or the unrearranged V lambda 1 segment. The selective diversification of the rearranged V lambda 1 segment was associated with unique DNAase I-hypersensitive sites on the rearranged allele. While probes for V lambda 1 sequences detect multiple homologous V lambda segments, probes for both the 5' leader and J lambda segments fail to detect homologous sequences. Taken together, these results suggest that a highly selective process, possibly gene conversion, operates during B cell ontogeny to generate diversity within the lambda gene.

A hyperconversion mechanism generates the chicken light chain preimmune repertoire

The chicken immunoglobulin light chain repertoire has been shown to be entirely derived from a single V lambda 1-J rearranged combination. The complete coding information of the lambda locus was determined: it comprises 25 V-hybridizing elements, all of which are pseudogenes, clustered in both orientations within 19 kb of DNA, starting 2.4 kb upstream of the V lambda 1 gene. Sequences of somatically rearranged V lambda 1 genes from embryonic and posthatching bursal cells show that diversification of light chain sequences occurs during ontogeny by a segmental gene conversion mechanism which takes place at a frequency of 0.05-0.1 per cell generation between the pseudogene pool and the unique rearranged functional V gene.