Preparation of anti-hCG single domain antibody by antibody grafting technique using an antigen-binding peptide / 生物工程学报

We used the antibody grafting technology to prepare anti-hCG single-domain antibodies on the basis of antigen-binding peptide to simplify the single-domain antibody preparation process and improving the biochemical stability of peptide. By using a universal single-domain antibody backbone (cAbBCII10), CDR1 or CDR3 was replaced by the hCG-binding peptide, and the grafted antibody gene sequences were synthesized and cloned into the prokaryotic expression vector pET30a(+) in fusion with a C-terminal sfGFP gene, i.e. pET30a-(His6)-cAbBCII10-CDR1/hCGBP1-sfGFP and pET30a-(His6)-cAbBCII10-CDR3/hCGBP3-sfGFP. The recombinant plasmids were transformed into E. coli BL21(DE3), and the fusion proteins were induced by IPTG. Highly soluble recombinant fusion proteins were obtained and purified by Ni-NTA affinity column. SDS-PAGE confirmed the purified protein as the target protein. The antigen-antibody binding assay showed that both the CDR1 and CDR3 grafted antibodies have hCG-binding activities. While the titers of the two grafted antibodies were similar, the binding affinity of CDR3 grafted antibody was higher than that of CDR1 grafted protein (about 2-3 times). The grafted antibodies retained the relatively high biochemical stability of the single-domain antibody backbone and were relatively thermostable and alkaline tolerant. The obtained antibodies also had a relatively high antigen-binding specificity to hCG. This study provided a reliable experimental basis for further optimization of anti-hCG single domain antibody by antibody grafting technology using antigen-binding peptide.

Characteristics of IgH-CDR3 repertoire of peripheral B cells in a patient with primary biliary cholangitis: a preliminary study using high-throughput sequencing / 中华肝脏病杂志

Objective@#To analyze the characteristics of immunoglobulin heavy chain complementarity-determining region (IgH-CDR3) repertoire of peripheral B cells in a patient with primary biliary cholangitis (PBC) and to investigate the diversity of the immune system.@*Methods@#Arm-PCR was used to amplify the IgH-CDR3 region of circulating B cells isolated from a PBC patient, and high-throughput sequencing was used to analyze the amplified product. The characteristics of immune repertoire were analyzed by bioinformatics.@*Results@#In total, 329219 sequence reads were generated from the sample, with 325540 total CDR3 sequences and 72774 distinct CDR3 sequences, and the D50 of IGH-CDR3 was 7.7. The dominant CDR3 length of the sample was 45 nt (9.6%); the N addition with the highest frequency ranged from 13 to 14 nt (5.25%); the J trimming with the highest frequency was 0 nt (12.7%); the three most frequent V alleles were V4-59 (9.5%), V3-23 (8.1%), and V1-69 (6.4%).@*Conclusion@#The diversity of IgH-CDR3 repertoire is relatively low in this patient with PBC, with several B-cell clonal expansions. The specificity needs to be further verified after increasing the sample size.

Bioinformatic analysis of antibody repertoire development in response to influenza vaccination / 中华微生物学和免疫学杂志

Objective To analyze the immunogenomic characteristics of antibody repertoire in re-sponse to influenza vaccine in order to provide a theoretical basis for further development of antibody. Meth-ods Based on a time-series immunoglobulin heavy chain ( IGH) repertoire sequencing dataset, we analyzed the immunogenomic characteristics of antibody repertoire in response to trivalent influenza vaccine ( TIV ) from three aspects which included the features in complementarity-determining region 3 ( CDR3 ) , antibody mutation and VDJ usage. Results The frequency of antibody mutation increased significantly upon vaccina-tion. Analysis of the CDR3 region indicated that polar and aromatic amino acids had a higher preference. The length of CDR3 region in naive B cells followed a normal distribution, while specific CDR3 sequences with 15 to 18 amino acids in length occupied a dominant position after vaccination. In addition, the VDJ us-age altered obviously and IGHV3-7-derived antibody had a significant response to the vaccine. Response in-tensity reached the peak on day 7 and gradually weakened over time. Conclusion Antibody repertoire evolves dynamically to express specific antibody upon vaccination and the characteristics of immune responses at sequence level could be used to evaluate their effectiveness.

Analysis of BCR CDR3 repertoire of peripheral blood with HBsAb titer higher than 10 000 mU/ml / 中国免疫学杂志

Objective:To acquire potential HBsAb sequences,we have analyzed the BCR CDR3 repertoire of the peripheral blood with HBsAb titer higher than 10 000 mU/ml,which could provide a data basis for follow-up study.Methods:Genomic DNA of pe-ripheral blood mononuclear cells was extracted from samples with HBsAb titer higher than 10 000 mU/ml.We have adopted Illumina Solexa high-throughput sequencing technology of the Adaptive Biotechnologies ImmunoSEQ platform to acquire sequence data.IMGT/High V-QUEST was used to preliminary analyze our sequence data,including usage of IGHV,IGHJ and IGHD gene subgroups,IGHV-J matching,distribution of CDR3 amino acid (AA) length and usage of total CDR3 AA.And these sequences were compared with the HBsAb sequences from NCBI database.Results:Experimental samples have highly selected gene subgroups IGHV3,IGHV4,IGHJ4, IGHJ6,IGHD3,IGHD6,and IGHV3-J4 pairing,IGHV3-J6 pairing.The AA length distributions of CDR3 region were normal distribution with the length of 14/15 AA as the midline.In the regard to amino acid usage in CDR3 region, each sample prior used Alanine, Tyrosine,Glycine,Alanine,Aspartic acid and Serine.The amino acid usages of 107,108,109,113,114 positions were diversified but 105,106,115,116,117 positions taking conservative amino acids usages.We have found 48 unique sequences that have same IGHV, IGHJ and CDR3 AA length with the HBsAb sequences from NCBI database.Conclusion:There were almost the same characteristics of BCR CDR3 repertoire of the peripheral blood with HBsAb titer higher than 10 000 mU/ml.The 48 unique sequences provided a solid data basis for the follow-up study.

γδ T cells response to Mycobacterium tuberculosis in pulmonary tuberculosis patients using preponderant complementary determinant region 3 sequence.

Background & objectives: The unique immunological functions of γδ T lymphocytes to contribute immunity against Mycobacterium tuberculosis attracted interest of researchers. However, little is known about the specificity of γδ Τ cell in tuberculosis patients and the lack of exact tuberculosis antigen recognized by γδ T cells limited its application. The analysis of complementary determinant region (CDR)3 sequence characteristic in γδ T cells of tuberculosis patients would contribute to understand the distribution specificity of γδ T cell. In present study, we investigated the diversity of the γ9/δ2 T cell immunorepertoire and analysed the specificity of the expressed CDR3 in pulmonary tuberculosis patients. Methods: The total RNA in peripheral blood mononuclear cell of 50 pulmonary tuberculosis patients and 10 healthy controls was extracted. The polymerase chain reaction was used to specifically amplify the CDR3 region of γ9 and δ2 chain. The PCR products were ligated into the pGEM-T easy vector. The plasmid DNA was sequenced using the ABI3700 and the T7 primer. Results: Our findings showed that predominant CDR3 sequence of δ2 chain in pulmonary tuberculosis patients was CACDTLVSTDKLIFGKG. The sequence specifically exists in almost all pulmonary tuberculosis patients. The conserved hydrophobic acid residue in 97 positions is present in the γδ T cell reactive to M. tuberculosis. The length of δ2 CDR3 in pulmonary tuberculosis patients has no relation with the disease progress. Interpretation & conclusions: Our results suggest that γδ T cells appear to use CDR3 sequence to recognise M. tuberculosis antigen. γδ T cells reactive to M. tuberculosis were diverse and polyclonal.

Expression of Epstein-Barr Virus Gene and Clonality of Infiltrated T Lymphocytes in Epstein-Barr Virus-associated Gastric Carcinoma

BACKGROUND: Epstein-Barr virus associated gastric lymphoepithelioma-like carcinoma (LELC) is characterized by the intensive infiltration of lymphoid cells, the presence of EBV, and the better prognosis over typical adenocarcinoma. Thus, it was assumable that viral latent proteins may be responsible for the recruitment of a certain T cell repertoire to EBV-associated gastric carcinoma. METHODS: To examine above possibility, EBV gene expression in gastric carcinoma tissues and usage of TCR among the tumor infiltrating lymphocytes were analyzed. RESULTS: EBV specific DNA and EBERs RNA were detected in 4 out of 30 patients. RT-PCR analysis revealed that all 4 of EBV-positive tumor tissues expressed EBNA1 mRNA and BARTs and LMP2a was detected only one sample out of 4. However, the EBNA2 and LMP-1 transcripts were not detected in these tissues. CD8+ T cells were the predominant population of infiltrating lymphocytes in the EBV-positive gastric carcinoma. According to spectra type analysis of infiltrating T cells, 10 predominant bands were detected by TCR Vbeta CDR3 specific RT-PCR from 4 EBV-positive tumor tissues. Sequence analysis of these bands revealed oligoclonal expansion of T cells. CONCLUSION: These findings suggest that clonally expanded T cells in vivo might be a population of cytotoxic T cells reactive to EBV-associated gastric carcinoma.

Polymerase Chain Reaction and Sequencing of Immunoglobulin Heavy Chain Gene Rearrangement in Formalin Fixed, Paraffin-embedded Tissue of Patients with B Cell Lymphoma

BACKGROUND: Immunoglobulin heavy chain (IgH) gene rearrangement has been known to be a useful marker for determining the clonality as well as detecting minimal residual disease in B cell malignancies. This study was performed to establish single polymerase chain reaction (PCR) methods for the detection of IgH gene rearrangements in formalin-fixed, paraffin-embedded tissue of patients with B cell lymphoma and determine the type of JH segments used. METHODS: We obtained formalin-fixed, paraffin-embedded tissue sections of 44 patients diagnosed with B cell lymphoma at Ajou University Hospital from January 2005 to January 2007 and reviewed medical records retrospectively. After the extraction of DNA, PCR was performed using VH3 and JHPST primers to detect the third complementarity determining region (CDR3) gene of IgH. Sequence analysis of the PCR products was also done in 23 patients. RESULTS: The CDR3 gene rearrangements were detected in 26 (59%) out of 44 patients with B cell lymphoma. Sequence analysis of the amplified CDR3 gene was successful in 16 (70%) of 23 patients. JH3, JH4, JH5, and JH6 segments were used for CDR3 gene rearrangements in 3 (25%), 4 (33%), 1 (8%), and 4 (33%) patients with diffuse large B cell lymphoma, respectively. CONCLUSION: Although there are some limitations due to a low sensitivity less than 60%, single PCR using consensus primers could be an effective tool for the detection of CDR3 gene rearrangements in routine laboratory settings. Furthermore, sequence analysis of the CDR3 PCR products will provide basic information necessary for further studies.

N-Region Addition in Immunoglobulin Kappa Light Chains in B Cell Subsets in Rheumatoid Arthritis: Evidence for Over-expression of TDT in B Lineage

BACKGROUND: Unusually high amounts of N region addition and CDR3 length diversity were found in immunoglobulin (Ig) light chain Vk and Jk joins in patients with rheumatoid arthritis (RA). We sought to determine whether this finding is due to excessive activity of the enzyme responsible for N region addition (terminal deoxynucleotidyl transferase [TdT]) in B lineage cells in bone marrow or from positive antigenic selection of B cells with long CDR3 lengths. METHODS: We used FACS to isolate IgM+ /IgD+ B cells (predominantly naive) and IgM- IgD- B cells (predominantly class-switched) B cells from peripheral blood of a patient with RA known to have enrichment for long Vk CDR3s and from that of two normal controls. RT-PCR of VkIII transcripts was performed, followed by sequencing of individual cDNA clones. We analyzed the CDR3 lengths and N region additions in 97 clones. RESULTS: There was enrichment for long CDR3 lengths (11 or 12 amino acids) in both IgM+ /IgD+ and IgM- IgD- B cells in RA compared to B cell subsets in the normal controls. The IgM+/IgD+ B cell subset in RA was markedly enriched for N region addition and was similar to that seen in the IgM-/IgD- subset. CONCLUSION: These data suggest that enrichment for N region addition and long CDR3 lengths in RA may result from unusually high or prolonged activity of TdT in bone marrow.

Construction and biological identification of the transfectant cells expressing ??TCR with specific CDR3 sequence / 中国免疫学杂志

Objective:To construct of transfectant cells expressing ??TCR with specific CDR3 sequence.Methods:Specific CDR3 region sequence of DBS4.3,a known ??T cell clone,was inserted into ?9 and ?2 chain to substitute original CDR3 sequence using overlapping PCR method.After the full-length ?9 and ?2 chains were ligated with expression vector pREP7and pREP9 respectively,they were co-trasfected into a cell line of human Jurkat cells with TCR ? chain gene-defective mutant J.RT3-T3.5.When the transfectant cells expressing specific ??TCR were stimulated by antigen,production of IL-2 was detected by ELISA and Realtime PCR.Results:By ELISA and Realtime PCR,it was exhibited that the transfectant cells expressing DBS4.3 specific ??TCR secreted IL-2 under stimulation of iso-butylamine and anti ??TCR antibody.Conclusion:The transfectant Jurkat cells expressing ??TCR with specific CDR3 sequence are successfully constructed.It provides a platform for the research of recognition mechanism of ??TCR.

Generation and maintenance of type II collagen-specific T-cell line expressing conserved TCR-CDR3 motifs among patients with rheumatoid arthritis Author

BACKGROUND: To determine the molecular structure of type II collagen-specific T-cell receptors associated with rheumatoid arthritis (RA). METHODS: We generated CII-specific T-cell lines of 8 RA patient s by prolonged in vitro culture with bovine CII (bCII) and the immunogenic peptide (256-270) of human CII. The proliferation response towards CII stimulation was measured from the uptake of 3 H-thymidine. Changes in the secretion of Th 1 and Th2 cytokines in the culture supernatent were measured by ELISA. The TCR clonotypes of these T-cells were examined by RT-PCR/ SSCP analyses of all 22 V beta chains. RESULTS: T-cells from patients' tissue exhibited strong proliferation index upon CII stimulation, which was maintained up to 6 months in the culture. The secretion of INF-gamma from these T-cells increased along with the duration of culture time, while the amount of IL-4 production did not show significant changes. The SSCP band patterns of patients' T-cells appear as discrete bands unlike the smeary streak produced from normal samples. Some SSCP bands, each representing selected expansion of a TCR containing certain subtype of V beta peptides, appeared to be identical in more than one patients. Among these, the expansion of SSCP band representing the V beta 14 CDR3 region persisted after switching the antigen to the immunogenic human peptide (256-270). CONCLUSION: CII-reactive T-cells expressing distinct CDR3 motifs are selectively expanded in the peripheral blood and synovial fluid of RA patients, and their persistent proliferation upon CII stimulation, as well as the production Th 1-type cytokines, may play pivotal roles in RA pathogenesis.

Clonality of Lymphocytic Interstitial Pneumonia in Common Variable Immunodeficiency / 대한소아혈액종양학회지

Common variable immunodeficiency (CVID) is a heterogenous syndrome characterized by hypogammaglobulinemia, various immunologic abnormalities and recurrent bacterial infections. Associated immunologic abnormalities consists of various kinds of autoimmune diseases and lymphoproliferative disorders. The lymphoproliferative disorder take several forms, such as malignant lymphoma, atypical lymphoid hyperplasia, and beniegn lymphoid hyperplasia. Lymphocytic interstitial pneumonia (LIP), which is a kind of atypical lymphoid hyperplasia, develop in young age groups and has controversy on its clonality. We experienced a 14-year-old female patient with LIP and CVID. We analysed the third complementarity-determining region (CDR3) of the immunoglobulin heavy chain gene for clonality analysis. Clonality analysis of lung biopsy specimen revealed that 6 of 13 colony and 4 of 13 colony have identical sequences respectively. We speculate that one of these 2 lymphoid cell clone may develop into malignant lymphoma in the future.

Establishment of the technique for the real-time fluorescence quantitative reverse transcription polymerase chain reaction by DNA melting curve analysis for detecting the CDR3 skewing of TCR alpha gene repertoire in the human peripheral blood / 中国免疫学杂志

Objective:To establish the technique for real-time fluorescence quantitative reverse transcription polymerase chain reaction(FQ-PCR)by DNA melting curve analysis for detecting the CDR3 shewing of TCR alpha gene repertoire in human peripheral blood.Methods:Total RNA of peripheral blood mononuclear cell(PBMC)from 4 healthy donors and 2 patients with lymphomatous leukemia were transcripted reversely into cDNA.The cDNA of 32 TRAV gene family CDR3 was amplified by FQ-PCR.Analysis of the monoclonal/oligoclonal/polyclonal CDR3 spectratyping with DNA melting curve.Results:The FQ-PCR products of 32 TRAV family CDR3 were showedas a blur land at the predicted of products size in healthy donors and parts of TRAV family CDR3 products disappeared in patients on 1.5% agarose gel by Gold-View staining.The 32 TRAV family CDR3 were showed with different frequencies by relative fluorescence quantitative in healthy donors and the patients.The CDR3 spetratyping for 32 TRAV families was showed as polyclonal peak(Gaussian distribution)in healthy donors but showed as different monoclonal/oligoclonal/polyclonal peak in the patients with lymphomatous leukemia with DNA melting curve analysis(we called "melting curve spectratyping of CDR3")Conclusion:The study suggests that the technique of "FQ-PCR with DNA melting curve analysis be convenience and celerity for detecting the CDR3 skewing of TCR alpha gene repertoire in human peripheral blood.

Analyses for the ?/? T Cell Receptor Gene Rearrangement and CDR3 Repertoire in Active Pulmonary Tuberculosis Patients / 中国免疫学杂志

Objective:To establish a method of multi-PCR to amplify the complete DNA sequence (CDS) of TCR ? and ? chain of the antigen-specific T lymphocytes in local pathologic specimen of active pulmonary tuberculosis patients, and to analyze ?/? T cell receptor gene rearrangement and CDR3 repertoire.Methods:The lymphocytes in bronchoalveolar lavage (BAL) of active pulmonary tuberculosis patients were separated. Following total RNA extraction, cDNA synthesis, Multi-PCR, recombinant clones construction, and sequencing, the CDS of TCR ? and ? chains from these lymphocytes were analyzed by using software of DNAstar and internet TCR resources.Results:24 of ? chain CDS and 13 of ? chain CDS from 3 samples of BAL were obtained. As for TCR ? chain, AV1S2 (54%), AV12S3 (41%), and AV12S2(5%) appeared frequently. BV2(38%), BV29S1(46%), BV14(3%), and BV4S2(3%) in TCR ? chain appeared more often. There were CDR3 diversities between samples and even in the same sample by amino acid sequence analysis, but there were a few identical or similar amino acid sequences. There was the same amino acid sequence of SVGTGTLHQETQY in CDR3 region of ? chain of BAL sample No.1 and No.2; The sequence of AVRDWAGNMLT appeared in two ? chains of BAL sample No.2 and No.3; Moreover, the sequence of AV…DNN…RLM appeared in ? chains of BAL sample No.2 and No.3.Conclusion:A method of Multi-PCR is used to amplify TCR ? and ? chain CDS of tuberculosis patients. There are characteristic T cell clones to proliferate,with TCR ? and ? chain repertiore skewing in local infective focus. The sequences of CDR3 in different TCR clones are mostly different but there are a few identical or similar sequences in the same patient or even between different patients. The identical amino acid sequences of CDR3 are possibly specific for recognizing MTB polypeptide.

Length diversity in CDR3 Domain of Immunoglobulin Kappa Chain during the Human Deelopment / 대한면역학회지

The third complementarity determining region (CDR3) of the immunoglobulin (Ig) kappa () chain is known to be located at the center of antigen binding groove and critical for antibody specificity. Ig chain has been characterized by limited junctional diversity due to the absence of N-region addition resulting in relative conservation of CDR3 lengths with 9 or 10 amino acids. CDR3 region of 11 amino acids is only possible with N-region addition. Recently, x transcripts with 11 amino acids CDR3 was found to be expressed in normal individuals, and in autoimrnune disease such as rheumatoid arthritis, the fraction of 11 amino acids CDR3 of humkv325-derived chains was overexpressed compared to conventional adult peripheral B cells. However, the significance of this bias is difficult to interpret without a clear understanding of normal repertoire of CDR3 length during development. The purpose of this study is to determine whether developmental regulation of CDR3 amino acids codon lengths exists in chains expressed in the fetal liver, cord blood, and adult peripheral blood lymphocytes (PBL). Lymphocytes were seperated from fetal liver, cord blood and adult PBL and cDNA was generated from extracted mRNA. PCR-based CDR3 finger- printing assay was performed with VI-IV family specific primers. CDR3 length diversity of Ig x chain increases as the development proceeds. The length diversity most frequently occured in Vlll family derived transcripts including 11 amino acids CDR3. transcripts with 11 amino acids CDR3 were consitently expressed in both fetal and adult Ig repertoire. These results support the hypothesis that v chain CDR3 length is developmentally regulated and implicates the diversity of antigen-antibody specificity generation.

Identification of the CDR3 Gene Sequence on the beta Chain of the T Cell Receptor in T Cell Leukemia Cell Line / 대한면역학회지

In order to develop a method for the detection of minimal residual leukemic disease (MRD) in T cell acute lymphocytic leukemia (T cell ALL), T cell leukemia cell line was used to detect clonal TCR p chain mRNA and to synthesize CDR3 specific oligonucleotide probe. For the Jurkat cell line clonal TCR p chain cDNA was amplified by using RT-PCR with oligonucleotide primer, Vp universal primer. As the result of RT-PCR an approximate 300 bp fragment of the TCR chain was obtained, and the partial identification of the TCR p chain gene and the amino acid sequence of the fragment were done by gene cloning and sequencing. The gene sequence of TCR p obtained was identified as Vp8-Jp1.2-Cp2. Diversity gene segment could not be found. Within the p chain, the CDR3 region was identified as 12 amino acids (SFSTCSANYGYT). It is kown that TCR is expressed in about 40% of the all T cell ALL. However it is not kown what percentage of the TCR p chain mRNA expression translates into the actual TCR molecule. It is not certain how many patients with MRD can be detected by this method used in this study, but this technique might be useful to detect MRD in at least 40% of the patients with T-cell ALL.

Discrepancy in T cell clonal expansions in synovial fluid and peripheral blood from rheumatoid arthritis patients

Rheumatoid arthritis (RA) is an autoimmune disease involving the synovial membrane of peripheral joints. T cells specific for self antigens may play a critical role. Identification of T cell receptors (TCR) of such specific T cell clones is very important for treatment, prevention and identification of relevant autoantigens. To identify specific T cells, TCR V beta family repertoire and the clonal expansion of T cells were analyzed in this study. The percentage of V beta 5+ or V beta 8+ cells in the synovial fluid mononuclear cells (SFMCs) was similar to that in the peripheral blood mononuclear cells (PBMCs). However, the percentage of DR+ T cells in the SFMCs was higher (p< 0.01). Analyzing the clonality of T cells in 8 V beta families (V beta 1, V beta 5, V beta 8, V beta 14, V beta 16, V beta 17, V beta 18, V beta 20), clonal expansions in CD8+ T cells from the SFMCs were found more frequently than in the PBMCs. The patterns of clonal expansions were discrepant between the SFMCs and the PBMCs even in the same patient, which suggests several inflamed tissue specific T cell clonal expansions in the SFMCs. These T cell clones might be activated by autoantigens which are not identified yet and responsible for the RA pathogenesis.

Immunoglobulin Gene Repertoire In Rheumatoid Synovium As A Model For Autoimmune Disease / 대한류마티스학회지

OBJECTIVE: To gain insights into structural characteristics of immunoglobulin kappa chain repertoire expressed in the inflammed synovium of rheumatoid arthritis (RA), we analyzed V kappa transcirpts expressed in the synovium of a patient with longstanding RA and compared to those expressed in the PBLs of RA and normal controls. METHODS: RT-PCR was done to amplify kappa chain transcripts from RA synovial lymphocytes and the cDNA sequences were compared to those from PBL of RA patient or normal control. RESULTS: Kappa chain repertoire from RA patient's synovial lymphocytes or PBL revealed increased somatic mutation and unusually long complementarity determining region (CDR) 3 compared to normal control. CONCLUSIONS: These changes in kappa chain repertoire in RA patient are suggesting that the antibody repertoire expressed in the synovium or PBL is unique and may be related with systemic dysregulation of B cell development