Deep Panning: Steps towards Probing the IgOme

Background

Polyclonal serum consists of vast collections of antibodies, products of differentiated B-cells. The spectrum of antibody specificities is dynamic and varies with age, physiology, and exposure to pathological insults. The complete repertoire of antibody specificities in blood, the IgOme, is therefore an extraordinarily rich source of information–a molecular record of previous encounters as well as a status report of current immune activity. The ability to profile antibody specificities of polyclonal serum at exceptionally high resolution has been an important and serious challenge which can now be overcome.

Methodology/Principal Findings

Here we illustrate the application of Deep Panning, a method that combines the flexibility of combinatorial phage display of random peptides with the power of high-throughput deep sequencing. Deep Panning is first applied to evaluate the quality and diversity of naïve random peptide libraries. The production of very large data sets, hundreds of thousands of peptides, has revealed unexpected properties of combinatorial random peptide libraries and indicates correctives to ensure the quality of the libraries generated. Next, Deep Panning is used to analyze a model monoclonal antibody in addition to allowing one to follow the dynamics of biopanning and peptide selection. Finally Deep Panning is applied to profile polyclonal sera derived from HIV infected individuals.

Conclusions/Significance

The ability to generate and characterize hundreds of thousands of affinity-selected peptides creates an effective means towards the interrogation of the IgOme and understanding of the humoral response to disease. Deep Panning should open the door to new possibilities for serological diagnostics, vaccine design and the discovery of the correlates of immunity to emerging infectious agents.     

Idiotypy of antibodies against human serum albumin in immunized rabbit serum, which are directed against different regions of this antigen

Idiotypy has been studied in rabbit antibodies against human serum albumin. Antibodies which are directed against three different regions of serum albumin have similar idiotypic specificities. The molecular distribution of idiotypic determinants may be different in antibodies with specificity for different determinants as revealed for example by their precipitability or non precipitability by the same anti-idiotypic antibodies. The anti-albumin antibodies which are not precipitable by the anti-idiotypic antibodies, though they do combine with them, become precipitable after being mildly polymerized. Similar idiotypic specificities may be found in antibodies to serum albumin and in immunoglobulins apparently devoid of anti-serum albumin antibody function.     

Specificities of human heterophile Hanganutziu and Deicher (HD) antibodies to glycosphingolipids and a glycoprotein

The specificities of five heterophile Hanganutziu and Deicher (HD) antibody-containing sera from four different cancer patients and one other diseased patients were compared. Three glycosphingolipids and one glycoprotein antigens and their chemically modified derivatives were used. The antibodies of all whole sera showed similar specificities. IgG and IgM antibody fractions of each serum were separated. Although antibodies of the same class showed similar specificities, differences were detected between the specificities of IgG and IgM. IgG antibody specificities were dependent on the hydrophobic (ceramide) group while IgM antibodies were directed more to the terminal sialic acid moiety of the glycosphingolipid antigens. The results suggested that a similar population of IgG-producing lymphocytes is stimulated in patients. Due to the similarities in specificities of HD antibodies, the results of this study will facilitate the future isolation of either IgG or IgM antibody-producing lymphocyte(s) from a patient with HD antibodies and the establishment of a monoclonal antibody through hybridization with a human myeloma cell line.     

Purification and properties of antibodies having specificity for the carbohydrate moieties of synthetic glycoconjugates

Three types of antibodies having specificity for carbohydrate moieties of glycoconjugate antigens have been isolated from the sera of rabbits immunized with vaccines of β-d-glucosyl-bovine serum albumin, β-d-galactosyl-bovine serum albumin, or β-lactosyl-bovine serum albumin. The antibodies were isolated by affinity chromatography on adsorbents bearing appropriate carbohydrate ligands. The antibody types are specific for the β-d-glucosyl, β-d-galactosyl, or β-lactosyl groups of the synthetic glycoconjugates. The specificities have been established by data on hapten-inhibition, agar-diffusion, periodate-oxidation, and affinity-chromatography experiments. Each antibody type is of the IgG class of immunoglobulins and is of uniform molecular size, with molecular weight of 1.5 × 10⁵. Data from gel-isoelectrofocusing experiments showed that each preparation of antibodies, although specific for identical determinant groups of the same antigen, nevertheless consisted of a set of different proteins. The anti-d-glucose antibodies consisted of five proteins, the anti-d-galactose antibodies of eleven proteins, and the anti-lactose antibodies of seventeen proteins. The suggestion has been made earlier that the members of such a set of antibodies, in which each member is induced by the same determinant group of an antigen and each member combines with this group in the precipitin reaction, be called isoantibodies.     

The production of high affinity monoclonal antibodies to progesterone

Using different immunisation regimens and the antigens 6β-hydroxyprogesterone hemisuccinate and 11α-hydroxyprogesterone hemisuccinate conjugated to bovine serum albumin, we have produced 35 monoclonal antibodies against progesterone with a wide range of specificities and affinities (K_a = 8 × 10⁷−3 × 10¹⁰ M⁻¹). The 10 antibodies raised against the 6β-antigen showed no advantage in terms of specificity when compared with those raised against the 11α-antigen. The four antibodies with the best binding characteristics were all derived from fusion experiments performed after long (5 booster injections) immunisation with the 11α-antigen. Although the specificities of these monoclonal antibodies were similar to those of a high affinity rabbit antiserum raised against the same antigen, a measurable improvement in sensitivity was obtained when one of these four antibodies was used for radioimmunoassay.     

Serologic dissection of HLA-D specificities by the use of monoclonal antibodies

To study the gene products of the HLA complex, we produced two monoclonal antibodies, termed HU-18 and HU-23. They were active in complement-dependent cytotoxicity and detected B-cell alloantigens encoded by a locus (or loci) linked to HLA. When three types of HLA-DR4 homozygous B-cell lines with different HLA-D specificities were tested for reactivity with HU-18 and HU-23, they displayed distinct reaction patterns depending on the HLA-D specificities they possessed: EBV-Wa (HLA-DYT homozygous), negative for both HU-18 and HU-23; KT2 and KOB (HLA-DKT2 homozygous), positive only for HU-18; and ER (HLA-Dw4 homozygous), positive for both. These differential reaction patterns were further confirmed by testing against a panel of 17 HLA-DR4-positive peripheral blood lymphocytes with known HLA-D specificities. Thus, these monoclonal antibodies allow us to identify HLA-DYT, HLA-DKT2, and HLA-Dw4 solely by serologic methods. This is the first clearcut serologic identification of these three HLA-DR4-associated HLA-D specificities, which have been indistinguishable by conventional serology and identified only by cellular techniques. It is hoped that immunochemical investigations using HU-18 and HU-23 will advance our understanding of the HLA-D region on a molecular level.     

The human Ia system: Definition and characterization by xenogeneic antisera

The production of xenogeneic anti-Ia serum against Ia antigens in serum has been previously described in the mouse and we now describe the production of xenogeneic anti-human Ia antisera using similar methods. With an indirect resetting technique, Ia-like antibodies were shown to react with the majority of B cells (95%), a subpopulation of T cells, with carbonyl iron adherent cells, and with some E^–Ig^– null cells, but there was no reaction with red cells and platelets. These reactions were the same as those obtained with DRW antisera using cytotoxicity testing. In addition, antigens detected with xenogeneic antisera were also found in serum, where they were found to exist in a low molecular weight, dialyzable form. By the selective removal of different cell surface markers by cocapping, no association could be found with the specifities detected with the xenogeneic anti-Ia antisera and with surface Ig, ₂-microglobulin, or HLA-A and B specificities. Alloantibodies to DRW specificities (but not HLA-A, B specificities) were able to specifically block the binding of the rabbit anti-Ia antibodies to B cells, and reciprocal blocking of rabbit antisera by DRW antibodies was also observed. Several xenogenic antisera were produced by immunizing rabbits with the serum of different individuals. Each antiserum was shown to contain a number of different specificities, as they gave different reaction patterns with different individuals when testing was done both directly and by absorption. These xenogeneic anti-la sera also segregated in a family with HLA-A and B specificities. The detection of a polymorphic antigenic system segregating with the HLA complex, distinct from HLA-A and B specificities, and whose antigens occur predominantly on B cells is therefore described. Because of the similarity of the reactions of the xenogeneic antisera in man to those found in the mouse, and because of the close relationship to the DRW specificities, the system has been provisionally called the H.Ia system.Abbreviations used in this paper AET 2-aminoethyl isothiouronium bromide - ₂-M -2 microglobulin - BSA Bovine serum albumin - H.Ia Human Ia - HuRBC Human red blood cells - Ig Immunoglobulin - Ir Immune response - MHC Major histocompatibility complex - MLR Mixed lymphocyte reaction - NHS Normal human serum - NMS Normal mouse serum - PBL Peripheral blood lymphocytes - PBS Phosphate-buffered saline - RAHIg Rabbit anti-human immunoglobulin - RASIg Rabbit anti-sheep immunoglobulin - RFC Rosette-forming cells - SAHIg Sheep anti-human immunoglobulin - SARIy Sheep anti-rabbit immunoglobulin - SRBC Sheep red blood cells     

Presence of the fish pathogen Vibrio salmonicida in fish farm sediments

The persistence of the fish pathogen Vibrio salmonicida in fish farm sediments was studied by use of fluorescent-antibody techniques. The specificities of the monoclonal antibodies and polyclonal rabbit serum used in the study were tested against a number of Vibrio strains, including 4 isolates from intestinal tracts of healthy fish and 98 isolates from sediments. V. salmonicida was detected in sediment samples from diseased farms several months after an outbreak of the disease. The bacterium was also detected in a sediment sample from a disease-free fish farm. No V. salmonicida could be detected in sediments not influenced by fish farming. The number of positive samples was generally higher with application of rabbit serum as opposed to use of monoclonal antibodies, indicating that the rabbit serum may cross-react with other bacteria.     

Characterization of the Borna disease virus phosphoprotein, p23.

Borna disease virus infection is diagnosed by the presence of serum antibodies reactive with the major viral proteins, p40 and p23. Although p40 and p23 are unrelated in amino acid sequence structure, cross-reactive antibodies are described. Protein fragments and synthetic peptides were analyzed to characterize the specificities of antibodies to p23. Epitope mapping revealed eight continuous epitopes accessible on the surface of a predicted structural model for the monomeric and the disulfide-linked dimeric forms of p23. None of these epitopes was reactive with antibodies to p40. Cross-reactivity with monospecific sera and monoclonal antibodies to p40 was found for one discontinuous epitope located at the amino terminus of p23.     

Presence of the fish pathogen Vibrio salmonicida in fish farm sediments.

The persistence of the fish pathogen Vibrio salmonicida in fish farm sediments was studied by use of fluorescent-antibody techniques. The specificities of the monoclonal antibodies and polyclonal rabbit serum used in the study were tested against a number of Vibrio strains, including 4 isolates from intestinal tracts of healthy fish and 98 isolates from sediments. V. salmonicida was detected in sediment samples from diseased farms several months after an outbreak of the disease. The bacterium was also detected in a sediment sample from a disease-free fish farm. No V. salmonicida could be detected in sediments not influenced by fish farming. The number of positive samples was generally higher with application of rabbit serum as opposed to use of monoclonal antibodies, indicating that the rabbit serum may cross-react with other bacteria.     

Natural antibodies as contaminants of hybridoma products

This report cites an example of natural antibodies in mouse serum and ascites fluid which may contaminate hybridoma products and cause difficulties in interpreting their reactions. These natural antibodies react with determinants expressed on human foetal glycoproteins (extracted from meconium) and on other blood group precursor-like substances which express a number of tumour associated- and differentiation antigens. Variable amounts of these antibodies may be present in the ascites fluid of mice obtained by intraperitoneal injection of cloned hydridomas. Although in most cases the hybridoma antibodies will be used at dilutions beyond the endpoint of these contaminating antibodies, it is important to be aware of possible reactions due to natural and acquired antibodies with diverse specificities in evaluating the reactions of hybridoma products harvested from any type of serum containing medium.     

Patterns of antibody specificity during the BALB/c immune response to hen eggwhite lysozyme.

We tested 49 BALB/c antilysozyme mAb from seven intervals during the immune response to lysozyme for patterns of specificity and avidity. We found that the antibody epitopes in composite covered at least 80% of the lysozyme surface, and their patterns of overlap suggest a continuum of potential antibody epitopes. Previously observed regional specificities, which emerged at different times in the immune response, were more discretely defined in late response antibodies, when the majority of mAb could be assigned to one of three functionally nonoverlapping complementation groups. The area covered by each antigenic region may be greater than an individual epitope, and may include multiple epitopes that overlap structurally and functionally to varying degrees. Connectivity between antigenic regions was seen in interactions among early and late stage antibodies, and among secondary stage mAb, but not among tertiary stage mAb from hyperimmunized mice. Patterns of overlap of early and late response antibodies suggest that the organization of antibody specificities change during the progression from primary to secondary to tertiary response. Over the same period in the response, the average relative avidity of IgG1 kappa mAb did not increase, suggesting that "affinity maturation" of serum antibodies reflects an increase in the number and diversity of antibodies, rather than an overall increase in the avidity of individual antibodies.     

Three distinct epitopes within the loop region of hen egg lysozyme defined with monoclonal antibodies.

Five monoclonal antibodies specific for the loop region of hen egg lysozyme were prepared by immunisation with a synthetic conjugate of a proteolytic fragment of lysozyme coupled to bovine serum albumin. Their fine specificities were investigated using a panel of variant lysozymes and peptide fragments of lysozyme in a quantitative radio-immunoassay procedure. Knowledge of the structure of hen lysozyme to high resolution and the use of computer graphics enables the localisation of the epitopes recognised by the antibodies with some precision. The antibodies were shown to define three distinct, overlapping epitopes within what was previously considered to be a single antigenic site. These results are discussed in relation to current ideas of the antigenic nature of proteins and other recent studies in which anti-protein antibodies have been elicited by immunisation with small peptides.     

Characterization of a serum inhibitor of MLC reactions. III. Specificity: HL-A-related antibodies.

A mixed leukocyte culture (MLC)-inhibitory serum from a healthy multipara, JH, has been characterized with regard to the specificity of its inhibitory antibody. When added directly to MLC, JH serum will inhibit most combinations. However, when lymphocytes intended as responder or stimulator cells in MLC were preincubated with this serum, the specificity narrowed considerably. Four groups of lymphocyte donors were recognized, depending upon whether their lymphocytes were inhibited as responders, as stimulators, as both, or as neither. Absorptions of inhibitory activity, followed by assay of the absorbed sera in pretested MLC combinations, yielded reliable data for determining which donors' cells shared pertinent antigens. An association of MLC inhibition by JH serum with the HL-A types of the involved lymphocytes was observed and these relationships are summarized in Table 4. The three HL-A specificities identified, W19, W29, and 12, correspond with the HL-A typing of the husband of the serum donor. Various cell types absorbed relevant inhibitory activity (against responder and stimulator functions) in the following order of efficiency: LCL cells, B lymphocytes, T lymphocytes, fibroblasts, and erythrocytes. When the above three HL-A specificities were removed by absorption, the serum was no longer inhibitory in any combinations. Whether the inhibitory activity of JH serum is directly related to anti-HL-A antibodies or to antibodies against closely related MLR determinants will depend to a large extent upon the degree of linkage disequilibria found between W19, W29, and 12 antigens and the MLR locus.     

Preparation and characterization of antibodies against 6-O-alpha-D-xylopyranosyl-beta-D-glucopyranose (beta-isoprimeverose), the disaccharide unit of xyloglucan in plant cell-walls

The p-aminophenyl beta-glycoside of 6-O-alpha-D-xylopyranosyl-D-glucopyranose (isoprimeverose), the disaccharide unit of plant xyloglucan, was coupled to bovine serum albumin, and the resulting glycoconjugate was used as an immunogen for the immunization of a rabbit. The immunochemical specificities of the rabbit antiserum raised against the glycoconjugate were characterized by immunodiffusion, quantitative precipitation, and hapten inhibition. After removal of anti-bovine serum albumin antibodies, the antiserum exhibited a specificity for the introduced disaccharide unit of the artificial antigen. The antibody-combining site was also shown to recognize the aglycon portion of the introduced hapten. The antiserum interacted with some xyloglucans, such as those from tamarind seed and the cell wall of pea stem. beta-Isoprimeverose and alpha-D-xylopyranosides were good inhibitors of the xyloglucan-antibody precipitation system, indicating that the antibodies recognize the beta-isoprimeverose unit of the xyloglucan.     

Demonstration of carbohydrate- and protein determined Ia antigens by monoclonal antibodies

Ten monoclonal alloantibodies were examined by submitting each antibody to five independent tests in order to determine whether they reacted primarily with the glycoprotein or glycolipid class of Ia antigens. The tests employed were as follows: (1) the ability to participate an Ia-like protein from the cell surface as detected by SDS-PAGE; (2) inhibition by protein-Ia extracts free of CHO-Ia; (3) inhibition by CHO-Ia extracts free of protein-Ia; (4) neuraminidase sensitivity of the antigen and (5) inhibition by simple sugars. Using these tests, three of the ten monoclonal antibodies were shown to recognize a CHO-Ia antigen while seven recognized the protein class of Ia antigens. The three CHO-Ia-specific monoclonal antibodies recognized Ia specificities 2, 9 and 17. Monoclonal antibodies recognizing protein-defined Ia.2 and 17 specificities were also characterized. These results imply that some Ia specificities, as defined by genetic testing, can occur both as carbohydrate-defined and protein-defined determinants.--Sugar inhibition studies showed that CHO-Ia.2 has D-glucosamine as its immunodominant sugar while CHO-Ia.17 shows preference for a beta-linked galactose. Furthermore, studies with neuraminidase demonstrated that sialic acid plays a role in the antigenic determinants of CHO-Ia.9 and CHO-Ia.17. Finally, it is noteworthy that CHO-Ia.2, the private specificity of the k haplotype, appears to be expressed only on cells and not in serum. These studies clearly demonstrate the existence of the two Ia antigen classes and emphasize the complexity of the murine I region.     

Stimulation of phospholipase A2 activity by high osmotic pressure on cholesterol-containing phospholipid vesicles

Bovine serum albumin conjugates of guanosine prepared by the periodate method was used as immunogen to elicit guanosine antibodies in rabbits. The specificities of the antibodies were studied by the inhibition of their binding to [3H]Gox-red, [32P]DNA and [3H]RNA by related non-radioactive compounds. A population of antibodies is specific to Gox-red with an average association constant of around 10(7) M-1 at 4 degrees C. There are a population of antibodies which bind to [32P]ssDNA and [3H]RNA specifically at guanosine residues. RNA binding antibodies were separated into two populations by affinity chromatography.     

Inhibition of secondary mouse mixed lymphocyte reaction by anti-Ia sera

Secondary mixed lymphocyte reaction (MLR-II) was studied in A.TH anti A.TL and A.TL anti-A.TH combinations in which stimulation was mainly due toH-2I-region differences. In both cases the MLR-II was specifically inhibited by the responder anti-stimulator Ia serum. The level of inhibition was dependent on the ratio of the amount of immune serum to the number of stimulating cells. The inhibitory activity and Ia antibodies were specifically absorbed and eluted together. The results confirm that the lymphocyte-activating determinants of the MLR-II (1) are carried by the Ia molecules and (2) are identical to the serologically defined Ia determinants. —Anti-Ia sera directed against private and public specificities of the stimulating cell induced a higher level of inhibition than anti-Ia sera directed only against public specificities, indicating that both private and public Ia specificities are involved in restimulation during MLR-II. — These results, in connection with others, suggest that the receptor of the proliferating T cell recognizes the same Ia determinant as the combining site of the Ia-recognizing antibody.Abbreviations used in this paper Lad lymphocyte-activating determinant - MLR mixed lymphocyte reaction - MLR-I, MLR-II primary, secondary MLR - PRC primed responder cells - LCT dye exclusion lymphocytotoxicity microtechnique - RR relative response     

Antibodies specific to two deoxyribotrinucleotide sequences.

Antibodies to the deoxyribotrinucleotides dpApTpA and dpApApT were prepared by injecting the bovine serum albumin conjugates of the respective haptens in rabbits. The specificities of the antibodies were determined by estimating the inhibition of the binding of the tritiated haptens to the immunoglobulins by various nonradioactive mono- and oligonucleotides, using nitrocellulose membrane binding assay. Anti-dpApTpA and anti-dpApApT antisera were found to contain antibodies which were highly specific to the respective hapten sequence.     

Characterization of monoclonal antibodies to bromodeoxyuridine

The characteristics of three mouse monoclonal antibodies to halogenated uridine derivatives are presented. Two, IU-1 and IU-2, are produced by hybridomas derived in our laboratory, and the third is the B-44 hybridoma described by Gratzner (7) and obtained commercially from Becton-Dickinson Monoclonal Center. Hybridomas IU-1 and IU-2 were derived from the fusion of spleen cells from a Biozzi High Responder mouse immunized with iododeoxyuridine (IdUrd) conjugated to bovine serum albumin and SP2/0 mouse myeloma cells. This paper presents methods and results for enzyme-linked immunosorbent assays (ELISA) against whole cells labeled with bromodeoxyuridine (BrdUrd), ELISA against BrdUrd-labeled DNA, and a competition ELISA for free BrdUrd. All three antibodies show similar binding affinities and specificities. The IU antibodies react with BrdUrd and IdUrd when the nucleosides are either free in solution or incorporated into single-stranded DNA (ss-DNA). The antibodies do not recognize either halogenated base in double-stranded DNA (ds-DNA), nor do they react with uracil or bromocytidine. Weak binding to thymidine, 5-fluorodeoxyuridine, and unsubstituted ss-DNA occurs.