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Results for “Complementarity Determining Regions”

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PubMed2004

A human synthetic combinatorial library of arrayable single-chain antibodies based on shuffling in vivo formed CDRs into general framework regions.

We describe a novel approach for high-throughput screening of recombinant antibodies, based on their immobilization on solid cellulose-based supports. We constructed a large human synthetic single-chain Fv antibody library where in vivo formed complementarity determining regions were shuffled combinatorially onto germline-derived human variable-region frameworks. The arraying of library-derived scFvs was facilitated by our unique display/expression system, where scFvs are expressed as fusion proteins with a cellulose-binding domain (CBD). Escherichia coli cells expressing library-derived scFv-CBDs are grown on a porous master filter on top of a second cellulose-based filter that captures the antibodies secreted by the bacteria. The cellulose filter is probed with labeled antigen allowing the identification of specific binders and the recovery of the original bacterial clones from the master filter. These filters may be simultaneously probed with a number of antigens allowing the isolation of a number of binding specificities and the validation of specificity of binders. We screened the library against a number of cancer-related peptides, proteins, and peptide-protein complexes and yielded antibody fragments exhibiting dissociation constants in the low nanomolar range. We expect our new antibody phage library to become a valuable source of antibodies to many different targets, and to play a vital role in facilitating high-throughput target discovery and validation in the area of functional cancer genomics.

Antibodies↗

PubMed2001

Crystal structure of an isolated V(alpha) domain of the 2C T-cell receptor.

The T-cell receptor (TCR) is a heterodimeric cell-surface protein consisting of two chains, alpha and beta, each of which is composed of a variable (V) and a constant (C) domain. Crystals of the isolated V(alpha) domain of the murine TCR 2C were grown by serendipity from a solution containing the extracellular domains of the intact TCR 2C and CD3 gamma epsilon-chains. The V(alpha) crystal structure shows how crystal packing can substitute for another V(alpha) domain in a different fashion from that observed in V(alpha)/V(alpha) homodimer and V(alpha)/V(beta) heterodimer structures. Significant conformational changes occur in the CDR3 and beta(3)beta(4) loops that normally form part of the dimer interface. The monomeric V(alpha) domain provides the unique opportunity to study the effect of dimerization on the conformation of the unliganded complementarity-determining regions (CDR) of a TCR. This structure of an individual V(alpha) module has implications for stability and bioengineering of isolated antibody and immunoglobulin domains.

Animals↗

PubMed2006

Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity.

The mammalian alpha/beta T cell receptor (TCR) repertoire plays a pivotal role in adaptive immunity by recognizing short, processed, peptide antigens bound in the context of a highly diverse family of cell-surface major histocompatibility complexes (pMHCs). Despite the extensive TCR-MHC interaction surface, peptide-independent cross-reactivity of native TCRs is generally avoided through cell-mediated selection of molecules with low inherent affinity for MHC. Here we show that, contrary to expectations, the germ line-encoded complementarity determining regions (CDRs) of human TCRs, namely the CDR2s, which appear to contact only the MHC surface and not the bound peptide, can be engineered to yield soluble low nanomolar affinity ligands that retain a surprisingly high degree of specificity for the cognate pMHC target. Structural investigation of one such CDR2 mutant implicates shape complementarity of the mutant CDR2 contact interfaces as being a key determinant of the increased affinity. Our results suggest that manipulation of germ line CDR2 loops may provide a useful route to the production of high-affinity TCRs with therapeutic and diagnostic potential.

Antigens↗

PubMed2006

Functional class switch recombination may occur 'in vivo' in Waldenström macroglobulinaemia.

Waldenström macroglobulinaemia (WM) malignant cells have been considered incapable of undergoing class switch recombination (CSR). However, we report a WM patient who developed an IgG M-component 4 years after diagnosis. When the second monoclonal component appeared, reverse transcription-polymerase chain reaction showed the presence of pre (Cmu) and postswitch (Cgamma) clonotypic isotypes; sequencing of these isotypes demonstrated that both corresponded to the single clone amplified at diagnosis, including the same complementarity-determining region 3 and somatic mutation pattern. This proves that WM cells can undergo a functional in vivo CSR.

Complementarity Determining Regions↗

PubMed2002

Changes in T-cell receptor VB repertoire in aplastic anemia: effects of different immunosuppressive regimens.

We studied the degree and the pattern of skewing of the variable region of beta-chain (VB) T-cell receptor (TCR) repertoire in aplastic anemia (AA) at initial presentation and after immunosuppression using a high-resolution analysis of the TCR VB complementarity-determining region 3 (CDR3). Age-matched healthy individuals and multitransfused patients with non-immune-mediated hematologic diseases were used as controls. In newly diagnosed AA, the average frequency of CDR3 size distribution deviation indicative of oligoclonal T-cell proliferation was increased (44% +/- 33% vs 9% +/- 9%; P =.0001); AA patients with human leukocyte antigen (HLA)-DR2 and those with expanded paroxysmal nocturnal hemoglobinuria clones showed more skewed VB repertoires. Nonrandom oligoclonal patterns were found for VB6, VB14-16, VB21, VB23, and VB24 subfamilies in more than 50%, and for VB15, VB21, and VB24 in more than 70% of AA patients with HLA-DR2. Patients received immunosuppression with antithymocyte globulin (ATG)/cyclosporine (CsA) or cyclophosphamide (CTX) with CsA in combination, and their VB repertoire was reanalyzed after treatment. Whereas no significant change in the degree of VB skewing in patients who had received ATG was seen, patients treated with CTX showed a much higher extent of oligoclonality within all VB families, consistent with a profound and long-lasting contraction of the T-cell repertoire. VB analysis did not correlate with the lymphocyte count prior to lymphocytotoxic therapy; however, after therapy the degree of VB skewing was highly reflective of the decrease in lymphocyte numbers, suggesting iatrogenic gaps in the VB repertoire rather than the emergence of clonal dominance. Our data indicate that multiple specific clones mediate the immune process in AA.

Adolescent↗

PubMed2004

The critical role of arginine residues in the binding of human monoclonal antibodies to cardiolipin.

Previously we reported that the variable heavy chain region (VH) of a human beta2 glycoprotein I-dependent monoclonal antiphospholipid antibody (IS4) was dominant in conferring the ability to bind cardiolipin (CL). In contrast, the identity of the paired variable light chain region (VL) determined the strength of CL binding. In the present study, we examine the importance of specific arginine residues in IS4VH and paired VL in CL binding. The distribution of arginine residues in complementarity determining regions (CDRs) of VH and VL sequences was altered by site-directed mutagenesis or by CDR exchange. Ten different 2a2 germline gene-derived VL sequences were expressed with IS4VH and the VH of an anti-dsDNA antibody, B3. Six variants of IS4VH, containing different patterns of arginine residues in CDR3, were paired with B3VL and IS4VL. The ability of the 32 expressed heavy chain/light chain combinations to bind CL was determined by ELISA. Of four arginine residues in IS4VH CDR3 substituted to serines, two residues at positions 100 and 100 g had a major influence on the strength of CL binding while the two residues at positions 96 and 97 had no effect. In CDR exchange studies, VL containing B3VL CDR1 were associated with elevated CL binding, which was reduced significantly by substitution of a CDR1 arginine residue at position 27a with serine. In contrast, arginine residues in VL CDR2 or VL CDR3 did not enhance CL binding, and in one case may have contributed to inhibition of this binding. Subsets of arginine residues at specific locations in the CDRs of heavy chains and light chains of pathogenic antiphospholipid antibodies are important in determining their ability to bind CL.

Amino Acid Sequence↗

PubMed2001

Prevalence of an ulcerative colitis-associated CD8+ T cell receptor beta-chain CDR3-region motif and its association with disease activity.

The normal human intestinal mucosa contains clonal T cell expansions. Clonal populations of T cells can be determined through evaluation of the idiotypic, hypervariable region of their T cell receptor (TCR). We have previously reported that there exists a highly conserved TCR pattern among intestinal CD8+ T cells in the majority of ulcerative colitis (UC) patients undergoing colectomy that was not present in normal control individuals. This TCR pattern, or motif, was characterized by particular beta-chain usage (TCRBV3 and TCRBJ1S6) and a defined length in the hypervariable third complementarity determining region (CDR3). The aim of this study was to assess the motif's relationship to disease activity. Subjects were 66 with UC, 19 with Crohn's disease, 14 inflammatory controls, and 6 normal controls. cDNA and gDNA were prepared from colonic biopsies and paraffin blocks, respectively, obtained from study subjects and used to assess TCRBV CDR3 region length and usage, as well as for cloning and sequencing of TCRs. The TCRBV CDR3 region was present in 25 of a series of 48 UC subjects but only 3 of 19 Crohn's disease patients and 3 of 14 inflammatory controls. The motif was more common in UC than either Crohn' s disease or inflammatory controls (chi2 = 7.5, P = 0.006, and chi2 = 4.1, P = 0.04, respectively). The motifs presence was not dependent upon histologic disease activity (either active or inactive UC). Clinical UC disease activity was also not significantly associated with an increased presence of the motif in 14 paired biopsies, which were taken during times of clinical activity or inactivity. There was a trend toward persistence of the motif, as it was present in 6 of 14 subjects over a 3- to 6-month time period. The previously described UC-associated TCRBV CDR3 region motif located in the intestinal CD8+ T-cell subset is found in a significant proportion of UC subjects. The TCR motif does not significantly discriminate active from inactive disease states. The persistent and diffuse nature of this TCR-associated motif in UC suggests that an ongoing T-cell response to a particular antigen(s) is occuring in this disorder.

Amino Acid Sequence↗

PubMedDate not supplied

Regulation of the antibody repertoire through control of HCDR3 diversity.

In man, as in mouse, diversification of the antibody repertoire appears to follow a strict developmental program whereby antigen specificities are serially acquired during ontogeny. When compared to the adult repertoire, the fetal antibody repertoire is highly enriched for polyreactive specificities of low affinity. Although the mechanisms governing the development of this fetal repertoire differ between human and mouse, the composition and structure of the fetal antibodies produced by both species are quite homologous. Specifically, both species use similar V gene segments and restrict the sequence and structure of the third complementarity determining region (HCDR3) of the antibody heavy chain. The precise role that this restriction of the HCDR3 might play in the development of immunocompetence in the human remains to be elucidated.

Animals↗

PubMed1989

Structural and idiotypic characterization of the L chains of human IgM autoantibodies with different specificities.

We have determined the V region amino acid sequence and/or serologic markers (kIIIb, PSL2, and PSL3) of 24 IgM monoclonal autoantibodies with specificities of anti-gamma-globulin (RF), anti-I (cold agglutinin), anti-low density lipoprotein and anti-intermediate filaments. The data emphasize the overwhelming selection of the HumKv325/VkIIIb L chain for this family of autoantibodies. The few amino acid substitutions found within the VL regions were mainly concentrated in the complementarity-determining region 1. JK and CK genes did not show the same pattern of restriction. There is a good correlation between the amino acid sequence and the presence of the kIIIb marker. The idiotypic marker PSL2 was present in 34 out of 35 kIIIb L chains analyzed (97%) and the PSL3 in 27 (80%). Moreover, the hydrophilicity and antigenic profiles of these L chains corroborate the presence of the epitopes detected by the anti-CRI. These results demonstrate a restricted selection of the Vk genes used by a family of self reacting proteins, and an unusual evolutionary conservation of the idiotypic structure that may be involved in the network regulation.

Agglutinins↗

PubMed2000

An unusual human IgM antibody with a protruding HCDR3 and high avidity for its peptide ligands.

The crystal structure of the Fv molecule from a human monoclonal IgM cryoglobulin (Mez) was determined at 2.6 A resolution. Amino acid sequences of framework regions (FR) of the Mez light (L) and heavy (H) chain variable domains (VL and VH) are highly similar to their counterparts in another human Fv (Pot) previously subjected to X-ray analysis in our laboratory. As expected, the three-dimensional (3-D) structures of FR are quite similar in the two proteins, as are four of the six complementarity-determining regions (CDRs): CDRs 1 and 2 for both L and H chains. Absence of Pro 95L from the LCDR3 loop in Mez VL (relative to Pot LCDR3) results in compression of this loop and creates more space in the VL-VH interface. In the two IgMs, HCDR3 conformations differ significantly from all previously defined conformations for these loops. Pot has a 12-residue HCDR3 that collapses to fill all available space in the VL-VH domain interface, resulting in the formation of a relatively flat platform for antigen binding. In Mez, the HCDR3 is two residues longer and is comprehensively different. A semi-rigid ascending segment dominated by a Pro-Pro-Tyr sequence protrudes out into solvent. The descending portion has the sequence Gly-Trp-Gly-Gly-Gly, which promotes high local flexibility. This segment folds across the VL-VH domain interface to interact with residues in LCDR3. These features partition the Mez active site into two compartments, a large cavity between VL and VH and a smaller cavity lined entirely by constituents of the three heavy chain CDRs. Such an unusual topographical feature indicates why the Mez IgM does not bind to the Fc portion of intact human IgG antibodies in immunoassays yet interacts with high avidity with many Fc-derived octapeptides. The cavities are expected to be the repositories for the Fc-derived peptides, while the semi-rigid protrusion of the Mez HCDR3 prevents the close approach of another macromolecule (e.g. intact IgG) to the active site.

Amino Acid Sequence↗

PubMed2002

Strong antigenic selection shaping the immunoglobulin heavy chain repertoire of B-1a lymphocytes in lambda 2(315) transgenic mice.

The B lymphocyte compartment of the recombinant mouse line L2 consists predominantly of CD5(+) B-1 cells that exclusively express the transgenic (Tg) lambda 2 L chain of the plasmacytoma MOPC315. Using such Tg mice as a simplified model to study positive selection processes, we show that restriction to a single L chain results in a strongly oligoclonal IgH chain repertoire in fetal and neonatal liver-derived B cells, as well as in peritoneal CD5(+) B-1 lymphocytes from adult mice. In contrast, in vitro differentiated fetal liver Pro/PreB-I cells from L2 embryos show a clear increase of complementarity determining region three (CDR3) diversity. These data suggest that the antibody repertoire of B-1a cells is strongly selected by antigen during fetal as well as adult peritoneal phase.

Amino Acid Sequence↗

PubMed2000

Most marginal zone B cells in rat express germline encoded Ig VH genes and are ligand selected.

The present study was performed to analyze whether marginal zone B (MZ-B) cells in nondeliberately immunized adult rats are selected on basis of the specificity of their B cell receptor, and to determine to what extent memory B cells contribute to the MZ-B cell subset. To this end, the Ig PC7183 V(H) gene repertoire was studied among V(H)DJ(H)-mu transcripts expressed in four sequential stages of B cell development, of two individual untreated adult rats. B cell subsets, i.e., pro/pre-B cells and newly formed B (NF-B) cells from bone marrow, and recirculating follicular B cells and MZ-B cells from spleen were sorted by flow cytometry. In addition, from one these rats, cells were microdissected from follicular and MZ areas of the spleen and productive PC7183 V(H) gene rearrangements were analyzed for the presence of somatic mutations. Sequence analysis reveals that most MZ-B cells in the adult rat, either defined by flow cytometry or by their anatomical location in the spleen, express germline encoded V(H) genes (naive MZ-B cells) and a minor fraction (about 20%) of the MZ-B cells carry somatic mutations (memory MZ-B cells). In addition, we show that naive MZ-B cells are a selected population of cells, both based on PC7183 V(H) gene repertoire and on the length of the Ig heavy (H) chain complementarity-determining region 3 (H-CDR3) region, i.e., PC7183 V(H)DJ(H)-mu transcripts of MZ-B cells carry significantly shorter H-CDR3 regions than other B cell subsets.

Amino Acid Sequence↗

PubMed2003

Simultaneous development of lymphoplasmacytic lymphoma and diffuse large B-cell lymphoma--analyses of the clonal relatedness by sequencing CDR3 in immunoglobulin heavy chain genes.

A 75-yr-old male simultaneously having lymphoplasmacytic lymphoma (LPL) and diffuse large B-cell lymphoma (DLBCL) is presented. He had manifested with lumbago, high-grade fever, and confusion. Physical examination on admission showed disorientation and severe back pain. There were neither lymphadenopathy nor hepatosplenomegaly. Routine laboratory tests showed moderate pancytopenia, hypercalcemia (serum calcium, 15.9 mg/dL), IgM lambda-type monoclonal gammopathy (IgG, 405 mg/dL; IgA, 42 mg/dL; and IgM, 2023 mg/dL), and lambda-type Bence-Jones protein in the urine (0.8 g/d). Bone marrow biopsy showed the clusters of surface lambda-positive small-sized mature-appearing lymphoplasmacytoid cells. Bone survey and computed tomographic scan showed multiple osteolytic lesions and a tumor involving the third lumbar spine (L3). An open biopsy of the L3 tumor showed diffuse proliferation of CD20- and lambda-positive large cells. We thus diagnosed the patient as simultaneously having LPL and DLBCL. Although the combination chemotherapy was at least partially effective, he died of bacteremia and organ failure after three courses of chemotherapy. To clarify the clonal relatedness between LPL and DLBCL, we analyzed the sequences of the complementarity-determining region 3 in immunoglobulin heavy-chain genes. The data showed that LPL and DLBCL in the present patient originated from two independent clones.

Aged↗

PubMed2003

Unusually long germline DH genes contribute to large sized CDR3H in bovine antibodies.

We demonstrated earlier the existence of an exceptionally long third complementarity-determining region of the heavy chain (CDR3H) (up to 61 amino acids (aa)), with multiple cysteine residues, in some functional IgM antibodies of cattle. To understand the origin of such a long CDR3H, we have now characterized the germline diversity gene (D(H)) of the cattle. A 2.3kb genomic DNA fragment hybridizing with a newly developed DNA probe to putative bovine D(H) gene sequences was isolated, cloned and its nucleotide sequence determined. Inspection of the nucleotide sequence led to identification of three bovine germline D(H) gene segments of varying size: 42bp (14 possible codons), 58bp (19 possible codons) and 148bp (49 possible codons). The characteristic repetitive GGT and TAT codons, remarkable in the CDR3H region of fetal VDJ rearrangements likely encoded by germline genes, are noted in two of the identified germline D(H) genes. These D(H) genes are preferentially expressed in the third reading frame to encode hydrophilic glycine and tyrosine residues in the CDR3H region. Phylogenetic analysis suggests that bovine D(H) genes are closest to rabbit and chicken D(H) genes. Thus, both short and long germline D(H) genes exist in cattle and these are capable of directly contributing to CDR3H size heterogeneity including the exceptionally long CDR3H region, apart from recombination associated mechanistic factors.

Amino Acid Sequence↗

PubMed2003

Modulations of anti-D affinity following promiscuous binding of the heavy chain with naïve light chains.

BACKGROUND: It is generally accepted that the antibody heavy (H) chain is more important than the light (L) chain for determining antigen specificity. In the case of anti-D, the predominant role of H chains in antigen binding is well recognized, but much less is known about the function of L chains. In this work, the contribution of L chains from non-D-immunized donors to the specificity and reactivity of anti-Ds was studied with L-chain shuffling. STUDY DESIGN AND METHODS: A kappa L chain library was recombined with the H chain of the 43F10 anti-D in a phagemid vector system (pComb3H, Scripps Institute). D-specific F(ab) phages were selected by panning on RBCs. Soluble F(ab)s were prepared, and their reactivity was assessed by RBC agglutination. The nucleotide and amino acid sequences of the variable region of the L chains were analyzed. RESULTS: The L chains of the six D-specific 43F10 F(ab) clones studied used five different germline genes from three Vkappa families and three different Jkappa segments. The L chains were all cationic with isoelectric points ranging from 8.1 to 10.2. CONCLUSION: The 43F10 anti-D H chain could bind promiscuously to a diversity of L chains from non-D-immunized donors without losing the D-antigen specificity. Relationships between the anti-D affinity and the cationic charge of the L chain as well as with the presence of an arginine residue in the L-chain complementarity-determining region 1 were observed.

Antibody Affinity↗

PubMed2003

Improving selection of alphaIIbbeta3-binding phage antibodies with increased reactivity derived from immunized donors.

Although many studies of the immune response in polytransfused Glanzmann thrombasthenia (GT) patients and in autoimmune thrombocytopenic purpura (AITP) have demonstrated the frequent development of Abs directed against the alphaIIbbeta3 integrin, little is known about the induced anti-alphaIIbbeta3 autoantibodies at the molecular level. Phage display is a powerful technology for selecting and engineering mAbs expressed on the surface of filamentous bacteriophage. Combinatorial libraries of single-chain IgG were constructed from splenocytes from two patients with AITP and one patient with GT. In a previous study, activated platelets or alphaIIbbeta3-expressing CHO cells selection was performed to isolate human IgG anti-alphaIIbbeta3 binding fragments using combinatorial libraries created from the B cells of a GT and an AITP patient. However, we have experienced practical problems such as enrichment of truncated antibodies during selection. We decided to test prolonged treatments with elution agents after screening on the purified form of the alphaIIbbeta3 integrin activated with the RGD peptide. We obtained a higher percentage of clones with full-size antibody fragments as well as an enrichment of more specific alphaIIbbeta3-binding phage-Abs. Some of them, recognizing the activated form of the integrin, would be interesting to further study as potential diagnostic or therapeutic agents in acute coronary syndromes. Sequencing of selected phage-Abs revealed that they used different VH and VL genes with, for the majority of them, a high level of extensive hypermutations in the complementarity determining regions, indicating the diversity of the antigen-driven immune response that occurred in GT and AITP patients.

Animals↗

PubMed2000

Follicular lymphoma with monocytoid B-cell proliferation: molecular assessment of the clonal relationship between the follicular and monocytoid B-cell components.

Although a number of studies have recognized that follicular lymphomas may be accompanied by a prominent proliferation of monocytoid B-cells, the clonal relationship between these components has not been adequately assessed. Using laser capture microdissection, we isolated the follicular and monocytoid B-cell components from four well-characterized cases of follicular lymphoma with prominent monocytoid B-cells. DNA from each component was analyzed using polymerase chain reaction (PCR)-based methods to assess for clonal rearrangements of the immunoglobulin heavy chain gene (IgH) and for the presence of the bcl-2 gene major breakpoint region/joining region (MBR/JH) DNA fusion products by conventional PCR and fluorescence melting curve analysis. Evidence of clonal identity was established in the follicular and monocytoid B-cell components of three cases by demonstration of IgH gene rearrangements of identical size using IgH PCR, by comparison of complementarity determining region III (CDRIII) DNA sequences, or by detection of bcl-2 MBR/JH fusion products of identical size and/or melting temperature. Molecular analysis of the fourth case revealed a monoclonal and MBR/JH-positive follicular component accompanied by a polyclonal and MBR/JH-negative monocytoid B-cell proliferation. We conclude that the follicular and monocytoid B-cell components of this variant of follicular lymphoma are clonally identical in the majority of cases. However, in a minority of these cases, the monocytoid B-cell component is reactive. Larger studies that assess the prognostic significance of follicular lymphoma with monocytoid B-cells will benefit from molecular studies that assess the clonal relationship of both components.

B-Lymphocytes↗

PubMed2004

Single-cell PCR analysis of the immunoglobulin heavy-chain CDR3 region for the diagnosis of leptomeningeal involvement of B-cell malignancies using standard cerebrospinal fluid cytospins.

The diagnosis of leptomeningeal B-cell malignancies is based on the identification of malignant B cells in the cerebrospinal fluid (CSF). We have established a polymerase chain reaction (PCR) approach to characterize the clonally diverse gene encoding the immunoglobulin heavy-chain (IgH) third complementarity determining region (CDR3) of single B cells. We demonstrate that single-cell PCR is readily applicable to individual cells derived from routine CSF cytospins and is a powerful method to discriminate monoclonal neoplastic from polyclonal reactive B-cell responses. Single-cell PCR analysis, as a new tool for the diagnosis and monitoring of neoplastic meningitis associated with B-cell malignancies, is particularly important if cytology, immunocytochemistry, flow cytometry and automated gene scanning of CSF samples are unable to detect malignant monoclonal proliferation.

B-Lymphocytes↗