Infant and adult human B cell responses to rotavirus share common immunodominant variable gene repertoires

Ab repertoires exhibit marked restrictions during fetal life characterized by biases of variable gene usage and lack of junctional diversity. We tested the hypothesis that Ab repertoire restriction contributes to the observed poor quality of specific Ab responses made by infants to viral infections. We analyzed the molecular determinants of B cell responses in humans to two Ags of rotavirus (RV), a common and clinically important infection of human infants. We sequenced Ab H and L chain V region genes (V(H) and V(L)) of clones expanded from single B cells responding to RV virus protein 6 or virus protein 7. We found that adults exhibited a distinct bias in use of gene segments in the V(H)1 and V(H)4 families, for example, V(H)1-46, V(H)4-31, and V(H)4-61. This gene segment bias differed markedly from the V(H)3 dominant bias seen in randomly selected adult B cells. Recombinant Abs incorporating any of those three immunodominant V(H) segments bound to RV-infected cells and also to purified RV particles. The RV-specific B cell repertoires of infants aged 2-11 mo and those of adults were highly related when compared by V(H), D, J(H), V(L), and J(L) segment selection, extent of junctional diversity, and mean H chain complementarity determining region 3 length. These data suggest that residual fetal bias of the B cell repertoire is not a limiting determinant of the quality of Ab responses to viruses of infants beyond the neonatal period.     

Ricin B chain and discoidin I share a common primitive protein fold

The galactoside-binding B chain of the cytotoxic protein ricin is apparently derived from a conservative exon-sized 40-residue peptide which is repeated four times in the molecule. A very similar peptide can also be seen in the amino acid sequence of the slime mold lectin discoidin I, which itself appears to be the product of a gene duplication. There is presently no chemical or structural evidence concerning the function of this peptide region. Nevertheless, the size of this unit, its prominence in the structure of ricin B chain, and its apparent conservation in carbohydrate-binding proteins from widely divergent organisms suggest that it may represent an extremely ancient galactoside-binding exon unit.     

Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts

An EST database has been generated for coffee based on sequences from approximately 47,000 cDNA clones derived from five different stages/tissues, with a special focus on developing seeds. When computationally assembled, these sequences correspond to 13,175 unigenes, which were analyzed with respect to functional annotation, expression profile and evolution. Compared with Arabidopsis, the coffee unigenes encode a higher proportion of proteins related to protein modification/turnover and metabolism-an observation that may explain the high diversity of metabolites found in coffee and related species. Several gene families were found to be either expanded or unique to coffee when compared with Arabidopsis. A high proportion of these families encode proteins assigned to functions related to disease resistance. Such families may have expanded and evolved rapidly under the intense pathogen pressure experienced by a tropical, perennial species like coffee. Finally, the coffee gene repertoire was compared with that of Arabidopsis and Solanaceous species (e.g. tomato). Unlike Arabidopsis, tomato has a nearly perfect gene-for-gene match with coffee. These results are consistent with the facts that coffee and tomato have a similar genome size, chromosome karyotype (tomato, n=12; coffee n=11) and chromosome architecture. Moreover, both belong to the Asterid I clade of dicot plant families. Thus, the biology of coffee (family Rubiacaeae) and tomato (family Solanaceae) may be united into one common network of shared discoveries, resources and information.     

The analysis of clonal expansions in normal and autoimmune B cell repertoires

Clones are the fundamental building blocks of immune repertoires. The number of different clones relates to the diversity of the repertoire, whereas their size and sequence diversity are linked to selective pressures. Selective pressures act both between clones and within different sequence variants of a clone. Understanding how clonal selection shapes the immune repertoire is one of the most basic questions in all of immunology. But how are individual clones defined? Here we discuss different approaches for defining clones, starting with how antibodies are diversified during different stages of B cell development. Next, we discuss how clones are defined using different experimental methods. We focus on high-throughput sequencing datasets, and the computational challenges and opportunities that these data have for mining the antibody repertoire landscape. We discuss methods that visualize sequence variants within the same clone and allow us to consider collections of shared mutations to determine which sequences share a common ancestry. Finally, we comment on features of frequently encountered expanded B cell clones that may be of particular interest in the setting of autoimmunity and other chronic conditions.     

Resource competition determines selection of B cell repertoires

Previous experiments with mouse chimeras demonstrated that cellular competition for antigen-specific survival signals plays a crucial role in the maintenance of the naive B cell repertoire. Transgenic (Tg) B cell populations in these chimeras have a shortened lifespan and poor competitive abilities as compared to more diverse non-Tg populations in the same mice. We develop a mathematical model to investigate the mechanism of B cell competition. The model allows for various B cell clones, generated in the bone marrow, to go into the peripheral circulation, where they compete specifically for various ligands providing survival signals. In the model we also find the observed poor competitive abilities of the Tg repertoire. Investigating the nature of the competition in the model, we find that most of the competition is "intraspecific" occurring largely within the clone of truly Tg B cells, and within the repertoire of leaky Tg and non-Tg B cells. This is confirmed by analysing a simplified version of the model, which only allows for intraspecific competition, and resembles a simple ecological model with density-dependent death. The fact that our model accounts for the data, casts doubt on a previous interpretation of the same data arguing that more diverse repertoires outcompete repertoires of lower diversity. Here, we conclude that most of the data can be explained with intraspecific competition, and formulate an experimental prediction that allows one to distinguish between the previous interpretation of inter-specific competition between repertoires, and the current interpretation of intraspecific competition.     

Epitope-specific human influenza antibody repertoires diversify by B cell intraclonal sequence divergence and interclonal convergence

We generated from a single blood sample five independent human mAbs that recognized the Sa antigenic site on the head of influenza hemagglutinin and exhibited inhibitory activity against a broad panel of H1N1 strains. All five Abs used the V(H)3-7 and J(H)6 gene segments, but at least four independent clones were identified by junctional analysis. High-throughput sequence analysis of circulating B cells revealed that each of the independent clones were members of complex phylogenetic lineages that had diversified widely using a pattern of progressive diversification through somatic mutation. Unexpectedly, B cells encoding multiple diverging lineages of these clones, including many containing very few mutations in the Ab genes, persisted in the circulation. Conversely, we noted frequent instances of amino acid sequence convergence in the Ag combining sites exhibited by members of independent clones, suggesting a strong selection for optimal binding sites. We suggest that maintenance in circulation of a wide diversity of somatic variants of dominant clones may facilitate recognition of drift variant virus epitopes that occur in rapidly mutating virus Ags, such as influenza hemagglutinin. In fact, these Ab clones recognize an epitope that acquired three glycosylation sites mediating escape from previously isolated human Abs.     

Hemorrhage in mice produces alterations in B cell repertoires

Multiple organ system failure secondary to infection is the major cause of late deaths after trauma and hemorrhage. The production by B cells of antibodies directed against bacterial antigens is an important component of host defenses. In order to determine the effects of hemorrhage on B cell function, we examined hemorrhage-induced alterations in available (clonal precursors) and actual (plasma cells) B cell repertoires in the course of an immune response toward bacterial antigens. Hemorrhage produced greater than twofold decreases in the absolute frequency and number of clonal precursors specific for the bacterial antigens dextran, levan, and pneumococcal polysaccharide type II. After blood loss, there were decreases in absolute frequency, but not in numbers, of clonal precursors capable of producing antibodies against the nonbacterial antigens ovalbumin and mouse transferrin. Immunization with the bacterial antigen levan within 24 hr of hemorrhage resulted in approximately 50% fewer levan-specific plasma cells than that seen in normal, unhemorrhaged mice. These results demonstrate that hemorrhage produces marked alterations in B cell repertoires, which may contribute to postinjury abnormalities in host defenses.     

Hemorrhage in mice produces alterations in intestinal B cell repertoires

Abnormalities in immune response play a major role in the increased susceptibility to infection after hemorrhage and trauma. Infections occurring after injury often originate in the intestine. In order to determine the effects of hemorrhage on intestinal B cell function, we examined hemorrhage-induced alterations in available (clonal precursors) and actual (plasma cells) B cell repertoires among intestinal lamina propria and Peyer's patch cells. Hemorrhage resulted in complete suppression of the increase in levan-specific lamina propria and Peyer's patch plasma cell numbers following oral immunization with this bacterial polysaccharide antigen. The absolute frequency of clonal precursors specific for levan among lamina propria B cells decreased by more than twofold following hemorrhage. These results demonstrate that hemorrhage produces marked alterations in intestinal B cell repertoires, which may contribute to postinjury abnormalities in host defenses.     

Hemorrhage in mice produces alterations in pulmonary B cell repertoires

Nosocomial pneumonia occurs frequently after hemorrhage and trauma and contributes to the increased incidence of morbidity and mortality after severe injury. The production of secretory antibodies by mucosally associated B cells is an important component of pulmonary host defense mechanisms. To determine the effects of hemorrhage on pulmonary B cell function, we examined hemorrhage induced alterations in pulmonary B cell repertoires. There were no changes in the relative distribution of T or B cells among intraparenchymal pulmonary lymphocytes after blood loss. Hemorrhage induced decreases of between 5- and 10-fold in the frequencies and numbers of pulmonary B cell clonal precursors specific for the bacterial Ag levan and Pseudomonas aeruginosa polysaccharide. These decreases in numbers and frequencies of bacterial Ag-specific pulmonary B cell clonal precursors were present between 3 and 10 days after blood loss. Similar decreases in numbers and frequencies were found among pulmonary clonal precursors specific for the autoantigen mouse transferrin, but not for the autoantigen dsDNA or the external antigens OVA and keyhole limpet hemocyanin. These results demonstrate that hemorrhage produces marked alterations in pulmonary B cell repertoires, which may contribute to postinjury abnormalities in host defenses.     

Cadherin cell adhesion molecules with distinct binding specificities share a common structure.

Ca2+-dependent cell--cell adhesion molecules, termed cadherins, are divided into subclasses with distinct tissue distributions and distinct cell-binding specificities. To elucidate the biochemical relationship of these subclasses, we compared the pattern of tryptic cleavage and the partial amino acid sequence of mouse liver E-cadherin with those of chicken brain N-cadherin. Although these two cadherins are distinct in their cell-binding and immunological specificities, they showed an identical mol. wt and a similar tryptic cleavage pattern. We isolated tryptic fragments of E- and N-cadherin, and determined the sequences of nine amino acid residues of their amino terminus. The results showed that sequences of amino acids from the amino terminus to the 7th residues are identical in these two cadherins. We thus suggest that cadherins with distinct specificities have a common genic origin.     

Cleavage stage mouse embryos share a common cell adhesion system with teratocarcinoma cells

We examined similarities in adhesive properties of mouse cleaving embryos at one- to eight-cell stages and of teratocarcinoma cells by aggregation studies. Teratocarcinoma cells and fibroblastic cells have a Ca²⁺-dependent cell-cell adhesion site (CDS), which is resistant to trypsin in the presence of Ca²⁺ but sensitive in the absence of Ca²⁺. When several embryos treated with trypsin in the presence of Ca²⁺ (TC) were kept in contact with each other, they fused into a single aggregate in the medium with Ca²⁺ but not without Ca²⁺. Embryos treated with trypsin in the absence of Ca²⁺ (TE) did not show such Ca²⁺-dependent aggregation. Aggregation of TC-treated embryos was inhibited by Fab fragments of antibody raised against TC-treated teratocarcinoma F9 cells. The aggregation-inhibitory effect of the Fab was removed by absorption with TC-treated teratocarcinoma cells, but not with TE-treated teratocarcinoma cells. This effect was not removed by absorption with fibroblasts and some other tissue cells. TC-treated embryos adhered to TC-treated teratocarcinoma cells, but not to TC-treated fibroblastic cells. These results suggest that early mouse embryos share a common CDS molecule with teratocarcinoma cells but not with fibroblastic cells.     

The control of IgM expression in a murine B cell lymphoma

The regulation of IgM expression was studied in clones derived from a murine B lymphocyte cell line, WEHI279.1. During normal B cell development IgM heavy chain synthesis increases concomitantly with heightened IgM secretion and reduced cell-surface IgM. However, in these subclones, the levels of membrane-bound and secreted IgM were regulated independently of one another. The amount of IgM secreted by the cells was tightly coupled to the amount of heavy chain synthesis, suggesting that the major control of secretion is pretranslational. Surface IgM exhibited a more complex regulation, with both pre- and posttranslational components. Variation in the expression of both forms of IgM occurred at high frequency. Although IgM expression follows a unidirectional pathway in nontransformed cells, the variability in these tumor cells was reversible and cellautonomous. High levels of phenotypic variability may be important in the ability of transformed cells to escape the immune response.     

Globin-coupled sensors and protoglobins share a common signaling mechanism

The globin-coupled sensors (GCSs) and protoglobins (Pgbs) form one lineage of the globin superfamily. The GCSs are multidomain sensory proteins involved in aerotaxis or gene regulation, while the Pgbs are single-domain globins of yet unknown function. We postulate that the GCSs and Pgbs share a common signaling mechanism to modulate diverse physiological functions. To elucidate the signaling properties of individual globin domains, we constructed and expressed chimeric receptors in Escherichia coli. We demonstrate that all the chimeric receptors reversibly bind oxygen in vitro and trigger aerotactic responses in vivo. Thus, oxygen binding to the globin domains of diverse GCSs and Pgbs form a common signaling state that can trigger aerotactic responses.     

Protein farnesyltransferase and geranylgeranyltransferase share a common alpha subunit

Mammalian farnesyltransferase, which attaches a 15 carbon isoprenoid, farnesyl, to a cysteine in p21ras proteins, contains two subunits, alpha and beta. The beta subunit is known to bind p21ras proteins. We show here that the alpha subunit is shared with another prenyltransferase that attaches 20 carbon geranylgeranyl to Ras-related proteins. Farnesyltransferase and geranylgeranyltransferase have similar molecular weights on gel filtration, but are separated by ion exchange chromatography. Both enzymes are precipitated and immunoblotted by multiple antibodies directed against the alpha subunit of farnesyltransferase. The two transferases have different specificities for the protein acceptor; farnesyltransferase prefers methionine or serine at the COOH-terminus and geranylgeranyltransferase prefers leucine. The current data indicate that both prenyltransferases are heterodimers that share a common alpha subunit with different beta subunits.     

Acquisition and maturation of expressed B cell repertoires in normal and autoimmune mice

The expressed B cell repertoires of mice from 1 day to 5 mo of age were examined. The ELISA-spot assay was used to enumerate individual Ig-secreting splenic B cells and determine the proportion of these cells producing antibodies reactive with each of six autoantigens and two conventional Ag. Results indicate that i) neonatal B cells producing antibodies against specific members of the Ag panel arose in a temporally defined sequence, ii) antibodies produced by 1- to 5-wk-old mice appeared to be more cross-reactive than those produced by adult mice, iii) no bias toward autoantibody production was found in the neonatal repertoires of autoimmune-prone mice, and iv) as a whole, the pattern of repertoire development among diverse strains of mice was highly conserved, although individual mice varied considerably in the absolute number of B cells committed to the production of antibodies of a given specificity.     

Decreased influenza-specific B cell responses in rheumatoid arthritis patients treated with anti-tumor necrosis factor

Introduction

As a group, rheumatoid arthritis (RA) patients exhibit increased risk of infection, and those treated with anti-tumor necrosis factor (TNF) therapy are at further risk. This increased susceptibility may result from a compromised humoral immune response. Therefore, we asked if short-term effector (d5-d10) and memory (1 month or later) B cell responses to antigen were compromised in RA patients treated with anti-TNF therapy.

Methods

Peripheral blood samples were obtained from RA patients, including a subset treated with anti-TNF, and from healthy controls to examine influenza-specific responses following seasonal influenza vaccination. Serum antibody was measured by hemagglutination inhibition assay. The frequency of influenza vaccine-specific antibody secreting cells and memory B cells was measured by EliSpot. Plasmablast (CD19+IgD-CD27hiCD38hi) induction was measured by flow cytometry.

Results

Compared with healthy controls, RA patients treated with anti-TNF exhibited significantly decreased influenza-specific serum antibody and memory B cell responses throughout multiple years of the study. The short-term influenza-specific effector B cell response was also significantly decreased in RA patients treated with anti-TNF as compared with healthy controls, and correlated with decreased influenza-specific memory B cells and serum antibody present at one month following vaccination.

Conclusions

RA patients treated with anti-TNF exhibit a compromised immune response to influenza vaccine, consisting of impaired effector and consequently memory B cell and antibody responses. The results suggest that the increased incidence and severity of infection observed in this patient population could be a consequence of diminished antigen-responsiveness. Therefore, this patient population would likely benefit from repeat vaccination and from vaccines with enhanced immunogenicity.     

Structural basis of a conserved idiotope expressed by an autoreactive human B cell lymphoma. Evidence that a VH CDR3 mutation alters idiotypy and specificity

Our laboratory has previously investigated the relationship of autoimmune disease and B cell neoplasia in a patient with a diffuse, well differentiated splenic B cell lymphoma and associated autoimmune hemolysis due to an anti-Pr2 antibody. EBV-immortalized B cell clones, established from this lymphoma, were shown to secrete the same pathologic anti-Pr2 antibody. The antiidiotypic mAb, RI.1, defined a private Id (IdRI.1) of the anti-Pr2 antibody that was related to the Ag-binding site and was expressed by both the lymphoma and derived cell lines. This unique Id was expressed by the majority of splenic tumor B cells and also was conserved over a period of 4 yr. In this report, the structural basis of IdRI.1 expression was investigated by analysis of Id- variants isolated by flow microfluorimetry using RI.1. Six Id- cell lines that secrete IgM kappa but lack Pr2 specificity were generated from an Id+ cell line, LS2. These lines were shown to be related to LS2 and the lymphoma by karyotype and by restriction fragment analysis of Ig gene rearrangements. Shared and unshared nucleotide substitutions in the VH and VL regions of the six independent clones were used to construct a genealogic tree relating the Id- clonal members to a common Id+ precursor. The tree illustrates that the base changes occurred sequentially, suggesting that they were introduced by somatic point mutation. Only one VH CDR3 bp difference from the LS2 nucleic acid sequence is common to all Id- sequences, resulting in an amino acid substitution of cysteine 108 to tyrosine. Taken together, these findings suggest that both the expression of IdRI.1 and Ag binding are affected by a single mutation localized to the D region of the anti-Pr2 antibody.     

RNase MRP and RNase P share a common substrate.

RNase MRP is a site-specific ribonucleoprotein endoribonuclease that processes RNA from the mammalian mitochondrial displacement loop containing region. RNase P is a site-specific ribonucleoprotein endoribonuclease that processes pre-tRNAs to generate their mature 5'-ends. A similar structure for the RNase P and RNase MRP RNAs and a common cleavage mechanism for RNase MRP and RNase P enzymes have been proposed. Experiments with protein synthesis antibiotics have shown that both RNase MRP and RNase P are inhibited by puromycin. We also show that E. coli RNase P cleaves the RNase MRP substrate, mouse mitochondrial primer RNA, exactly at a site that is cleaved by RNase MRP.