半合成抗体库的构建及抗Tie2 Fab抗体的筛选

构建一个半合成抗体库 ,不经免疫制备人源抗Tie2Fab抗体。通过RT PCR方法 ,从人脐带血淋巴细胞总RNA扩增轻链基因及重链VH段基因 ,将轻链基因插入pCOMb3载体中 ,得人轻链质粒库 ;从HBsAb的Fd段基因制备含有不同长度随机化CDR3的FR3 CDR3 J CH1片段 ,然后将VH段基因与随机化的CDR3融合 ,得到Fd基因片段 ,再将其插入轻链质粒库中 ,得半合成人Fab质粒库。通过多次建库 ,获得总容量为 2× 1 0 7的半合成抗体库。其Fd段和轻链基因的重组率为 5 0 %。经 3轮淘洗 ,从噬菌体抗体库中筛选到与Tie2抗原特异结合的噬菌体克隆。测序确定抗体基因序列     

半合成抗体库的构建及抗Tie2 Fab抗体的筛选*

构建一个半合成抗体库 ,不经免疫制备人源抗Tie2Fab抗体。通过RT PCR方法 ,从人脐带血淋巴细胞总RNA扩增轻链基因及重链VH段基因 ,将轻链基因插入pCOMb3载体中 ,得人轻链质粒库 ;从HBsAb的Fd段基因制备含有不同长度随机化CDR3的FR3 CDR3 J CH1片段 ,然后将VH段基因与随机化的CDR3融合 ,得到Fd基因片段 ,再将其插入轻链质粒库中 ,得半合成人Fab质粒库。通过多次建库 ,获得总容量为 2×10⁷的半合成抗体库。其Fd段和轻链基因的重组率为     

重组炭疽疫苗免疫人体产生抗体基因的生物信息学分析

目的:采用多种生物信息学手段,提取并分析前期获得的重组炭疽疫苗免疫人体产生的抗体基因序列的特征信息,探究与抗体进化规律和功能预测相关的线索。方法:利用R、Perl等语言编写了一系列数据处理和接口程序,整合集成Change-O等相关程序集和R语言包构建抗体基因序列分析平台,对抗体重链基因的VDJ基因使用频率、聚类分布、CDR3区理化特性及体细胞高频突变模式进行信息提取,并通过在线服务器得到部分数据可视化结果。结果:前期获得的抗体基因序列中IGHV3、IGHD3和IGHJ4的使用频率最高,而IGHV3和IGHD5、IGHD6和IGHJ4、IGHV3和IGHJ4的组合是序列中出现频率最高的组合方式;23.3%的保护性抗原(PA)结合抗体都出现在同一个抗体聚类(239号克隆组)中;中和抗体HCDR3区较其他抗体对于碱性和酸性氨基酸使用频率较低,偏向于使用疏水性氨基酸;抗体的体细胞高频突变多发生在AAAAC、GTTAA、AGCTC、AAGTA等热点motif。结论:相关生物信息学手段能够有效处理和分析大量的抗体基因序列,研究结果和方法可为重组疫苗评价以及抗体鉴定和改造提供信息和方法学帮助。     

1、3、5月龄BALB/c小鼠的外周血与脾脏BCR H-CDR3组库的构成

B细胞是机体适应性免疫的主要成分,是介导特异性体液免疫应答的主要细胞群,主要依靠B细胞受体(B cell receptor,BCR)与抗原发生应答反应。BCR的可变区为互补决定区(complementarity determining region,CDR)包括CDR1、CDR2、CDR3,其中CDR3具有最丰富的多样性。该文通过高通量测序并分析1、3、5月龄小鼠BCR重链(heavy chain,H)-CDR3组库的多样性、CDR3区的基因/氨基酸的组成特性和各亚家族的偏向取用等,结果发现,小鼠在发育过程中,其外周免疫器官(脾脏)和外周血BCR H-CDR3组库存在相应的动态变化。该研究探索了机体在发育过程中,BCR H-CDR3组库的构成变化,为病理条件下BCR H-CDR3组库的研究提供基础数据。     

抗HFRSV人单抗可变区基因克隆及其序列测定

从杂交瘤细胞株87—2提取细胞总RNA．反转录合成cDNA链,进行PCR反应。其中扩增重链可变区一对引物分别与人免疫球蛋白重链v区基因5＇端和J区基因3＇端互补;扩增人λ轻链可变区引物与人免疫球蛋白λ轻链v区基因5＇端和J区基因3＇端互补。将重、轻链可变区基因的PCR扩增产物分别插入M13噬菌体．经转化筛选分别获得重组克隆。双脱氧法测定其序列,所得核苷酸序列经计算机分析,轻、重链可变区基因长度分别为309bp和405pb,编码103个氨基酸和135个氨基酸,有明显抗体可变区特征,具有骨架区和抗原互补区。     

5例前列腺癌T细胞受体β链CDR3的多样性分析

T淋巴细胞受体(TCRs)在抗原识别免疫应答中作用重要,其多样性与宿主免疫反应及肿瘤预后判断密切相关。目的:采用高通量测序技术研究前列腺癌组织和癌旁组织中T细胞受体(TCR)克隆多样性及其克隆序列。方法:收集5例PC患者的癌组织和癌旁组织,提取DNA后经多重PCR技术对TCRβ链CDR3区进行扩增。用Illumina MiSeq进行测序,经过数据处理和比对分析,比较前列腺癌组织TCR CDR3组库的组成特征。结果:前列腺癌组织具有更高程度的克隆百分比和较高的高度扩增克隆比HEC(HEC:频率样本总读数的0. 5%的TCR克隆),并获得了24对在癌组织样本中差异表达的V-J基因组合、16对在癌旁组织样本中差异表达的V-J基因组合。结论:前列腺癌组织与癌旁组织均存在差异性的V-J基因组合以及高克隆表达的HEC,其中癌组织样品具有更高的HEC。PC发生发展对免疫学研究提供了新的数据,对PC免疫监视、T细胞受体变异标志等研究提供了参考,对以后继续研究打下了基础。     

人源抗肿瘤坏死因子—α噬菌体抗体的基因结构分析

从混合的噬菌体抗体库中筛选到了抗人ＴＮＦα的人源单克隆抗体,并对筛选到的抗体基因进行了序列测定和分析。结果表明,筛选到的４个特异性抗ＴＮＦα噬菌体抗体克隆的重链的重链基因序列相同,该重链基因长６８１ｂｐ,编码２２７个氨基酸残基,属于人免疫球蛋白第Ⅲ家族,其中１－１１９位氨基酸残基为重链可变区（ＶＨ）,１２０－２２７位为重链恒定区１（ＣＨ１）。４个噬菌体抗体克隆的轻链均缺失,因此实际上筛选到的是单重     

人源中和性抗甲型肝炎病毒抗体Fab段基因的序列分析及可溶性表达

在用噬菌体表面呈现系统获得人源抗甲型肝炎（甲肝）病毒中和发生基因工程Fab抗体的基础上,对所获得的4株中和性Fab抗体轻重链可变区进行了序列分析、可溶性表达及生物学特性鉴定。4株Fab抗体重链可变区拥有99％同源的核苷酸序列和相同的CDR区氨基酸序列,属于VHⅢ基因家族,而轻链可变区核苷酸序列同源性为95％和相似的CDR区氨基酸序列,属于VL5基因家族。这些重组抗体都能与人甲肝恢复期血清及具有中和活性的鼠抗甲肝克隆抗体产生竞争抑制反应,表明其针对甲肝癌病毒结构蛋白上的主要抗的决定簇。     

入源中和性抗甲型肝炎病毒抗体Fab段基因的序列分析及可溶性表达

在用噬菌体表面呈现系统获得人源抗甲型肝炎(甲肝)病毒中和性基因工程Fab抗体的基础上,对所获得的4株中和性Fab抗体轻重链可变区基因进行了序列分析、可溶性表达及生物学特性鉴定.4株Fab抗体重链可变区拥有99%同源的核苷酸序列和相同的CDR区氨基酸序列,属于VHⅢ基因家族.而轻链可变区核苷酸序列同源性为95%和相似的CDR区氨基酸序列,属于VL5基因家族.这些重组抗体都能与人甲肝恢复期血清及具有中和活性的鼠抗甲肝单克隆抗体产生竞争抑制反应,表明其针对甲肝病毒结构蛋白上的主要抗原决定簇.     

A型肉毒毒素表位多肽免疫和人源噬茵体单链抗体文库的构建

采用表位合成多肽免疫获得编码人源抗体的基因材料,抗体轻重链可变区基因通过剪接重叠延伸(SOE)技术进行组装后,亚克隆入噬菌体粒中构建免疫库。以重组制备的A型肉毒毒素保护性抗原为配体筛选结合子,ELISA鉴定,获得具有较高抗原结合力的噬菌体克隆,进行基因测序和家族定位分析。结果显示,表位合成多肽免疫,成功构建了库容大于10^8的重组抗体库。体外3轮免疫淘筛,筛选到人源A型肉毒抗毒素克隆,基因结构分析表明,其中ScFvB17全长750bp,可编码250个氨基酸残基：VH属于VH4家族,369bp,编码123个氨基酸残基;Vκ属于κ链Ⅱ家族,336bp,编码112个氨基酸残基。基因的同源分析表明,这是一株特异的单链抗体新基因。     

Partial versus productive immunoglobulin heavy locus rearrangements in chronic lymphocytic leukemia: implications for B-cell receptor stereotypy

The frequent occurrence of stereotyped heavy complementarity-determining region 3 (VH CDR3) sequences among unrelated cases with chronic lymphocytic leukemia (CLL) is widely taken as evidence for antigen selection. Stereotyped VH CDR3 sequences are often defined by the selective association of certain immunoglobulin heavy diversity (IGHD) genes in specific reading frames with certain immunoglobulin heavy joining (IGHJ ) genes. To gain insight into the mechanisms underlying VH CDR3 restrictions and also determine the developmental stage when restrictions in VH CDR3 are imposed, we analyzed partial IGHD-IGHJ rearrangements (D-J) in 829 CLL cases and compared the productively rearranged D-J joints (that is, in-frame junctions without junctional stop codons) to (a) the productive immunoglobulin heavy variable (IGHV )-IGHD-IGHJ rearrangements (V-D-J) from the same cases and (b) 174 D-J rearrangements from 160 precursor B-cell acute lymphoblastic leukemia cases (pre-B acute lymphoblastic leukemia [ALL]). Partial D-J rearrangements were detected in 272/829 CLL cases (32.8%). Sequence analysis was feasible in 238 of 272 D-J rearrangements; 198 of 238 (83.2%) were productively rearranged. The D-J joints in CLL did not differ significantly from those in pre-B ALL, except for higher frequency of the IGHD7-27 and IGHJ6 genes in the latter. Among CLL carrying productively rearranged D-J, comparison of the IGHD gene repertoire in productive V-D-J versus D-J revealed the following: (a) overuse of IGHD reading frames encoding hydrophilic peptides among V-D-J and (b) selection of the IGHD3-3 and IGHD6-19 genes in V-D-J junctions. These results document that the IGHD and IGHJ gene biases in the CLL expressed VH CDR3 repertoire are not stochastic but are directed by selection operating at the immunoglobulin protein level.     

The functional repertoire of rabbit antibodies and antibody discovery via next-generation sequencing

To gain insight into the functional antibody repertoire of rabbits, the VH and VL repertoires of bone marrow (BM) and spleen (SP) of a naïve New Zealand White rabbit (NZW; Oryctolagus cuniculus) and that of lymphocytes collected from a NZW rabbit immunized (IM) with a 16-mer peptide were deep-sequenced. Two closely related genes, IGHV1S40 (VH1a3) and IGHV1S45 (VH4), were found to dominate (~90%) the VH repertoire of BM and SP, whereas, IGHV1S69 (VH1a1) contributed significantly (~40%) to IM. BM and SP antibodies recombined predominantly with IGHJ4. A significant proportion (~30%) of IM sequences recombined with IGHJ2. The VK repertoire was encoded by nine IGKV genes recombined with one IGKJ gene, IGKJ1. No significant bias in the VK repertoire of the BM, SP and IM samples was observed. The complementarity-determining region (CDR)-H3 and -L3 length distributions were similar in the three samples following a Gaussian curve with average length of 12.2 ± 2.4 and 11.1 ± 1.1 amino acids, respectively. The amino acid composition of the predominant CDR-H3 and -L3 loop lengths was similar to that of humans and mice, rich in Tyr, Gly, Ser and, in some specific positions, Asp. The average number of mutations along the IGHV/KV genes was similar in BM, SP and IM; close to 12 and 15 mutations for VH and VL, respectively. A monoclonal antibody specific for the peptide used as immunogen was obtained from the IM rabbit. The CDR-H3 sequence was found in 1,559 of 61,728 (2.5%) sequences, at position 10, in the rank order of the CDR-H3 frequencies. The CDR-L3 was found in 24 of 11,215 (0.2%) sequences, ranking 102. No match was found in the BM and SP samples, indicating positive selection for the hybridoma sequence. Altogether, these findings lay foundations for engineering of rabbit V regions to enhance their potential as therapeutics, i.e., design of strategies for selection of specific rabbit V regions from NGS data mining, humanization and design of libraries for affinity maturation campaigns.     

The functional repertoire of rabbit antibodies and antibody discovery via next-generation sequencing

To gain insight into the functional antibody repertoire of rabbits, the VH and VL repertoires of bone marrow (BM) and spleen (SP) of a naïve New Zealand White rabbit (NZW; Oryctolagus cuniculus) and that of lymphocytes collected from a NZW rabbit immunized (IM) with a 16-mer peptide were deep-sequenced. Two closely related genes, IGHV1S40 (VH1a3) and IGHV1S45 (VH4), were found to dominate (~90%) the VH repertoire of BM and SP, whereas, IGHV1S69 (VH1a1) contributed significantly (~40%) to IM. BM and SP antibodies recombined predominantly with IGHJ4. A significant proportion (~30%) of IM sequences recombined with IGHJ2. The VK repertoire was encoded by nine IGKV genes recombined with one IGKJ gene, IGKJ1. No significant bias in the VK repertoire of the BM, SP and IM samples was observed. The complementarity-determining region (CDR)-H3 and -L3 length distributions were similar in the three samples following a Gaussian curve with average length of 12.2 ± 2.4 and 11.1 ± 1.1 amino acids, respectively. The amino acid composition of the predominant CDR-H3 and -L3 loop lengths was similar to that of humans and mice, rich in Tyr, Gly, Ser and, in some specific positions, Asp. The average number of mutations along the IGHV/KV genes was similar in BM, SP and IM; close to 12 and 15 mutations for VH and VL, respectively. A monoclonal antibody specific for the peptide used as immunogen was obtained from the IM rabbit. The CDR-H3 sequence was found in 1,559 of 61,728 (2.5%) sequences, at position 10, in the rank order of the CDR-H3 frequencies. The CDR-L3 was found in 24 of 11,215 (0.2%) sequences, ranking 102. No match was found in the BM and SP samples, indicating positive selection for the hybridoma sequence. Altogether, these findings lay foundations for engineering of rabbit V regions to enhance their potential as therapeutics, i.e., design of strategies for selection of specific rabbit V regions from NGS data mining, humanization and design of libraries for affinity maturation campaigns.     

绵羊肌肉生长抑制素MSTN原核表达及其纳米抗体文库的构建与鉴定

克隆绵羊肌肉生长抑制素（myostatin,MSTN）基因并在大肠杆菌中诱导表达,纯化重组蛋白免疫健康的双峰驼（Bactrian camel）,分离其外周血淋巴细胞提取总RNA,利用RT-PCR扩增骆驼重链抗体IgG2、IgG3的可变区（VHH）基因片段,将VHH片段与pCANTAB5E连接后电转入大肠杆菌TG1构建纳米抗体文库。结果显示,纳米抗体文库容量为9.5×10⁵,挑取部分克隆进行测序分析,所获得的纳米抗体文库具有良好的多态性,为进一步筛选绵羊MSTN的高特异性纳米抗体片段奠定了基础。     

Identification of two new alleles, IGHV3-23*04 and IGHJ6*04, and the complete sequence of the IGHV3-h pseudogene in the human immunoglobulin locus and their prevalences in Danish Caucasians

More than 100 variable (V), 27 diversity (D), and six joining (J) genes are encoded in the human heavy chain locus, and many of these genes exists in different allelic forms. The number of genes and the allelic differences help to create diversity in the immunoglobulin receptors, a key feature of the adaptive immune system. We here report the identification of two novel and seemingly functional alleles of human heavy chain genes. The variable IGHV3-23*04 allele is found with an allele frequency of 0.21 amongst Danish Caucasians, whereas the novel joining IGHJ6*04 allele is rare (allele frequency 0.02). We also report the full sequence of IGHV3-h. The gene exists in two allelic forms but is only found in 58% of the Danish Caucasians studied. The methionine translation initiation codon is mutated, ATG→AAG, and we therefore propose that the gene is a pseudogene incapable of being translated.     

Antigen binding and solubility effects upon the veneering of a camel VHH in framework-2 to mimic a VH

Heavy chain only antibodies of camelids bind their antigens with a single domain, the VHH, which acquired adaptations relative to classical VHs to function in the absence of a VL partner. Additional CDR loop conformations, outside the canonical loop structures of VHs, broaden the repertoire of the antigen-binding site. The combined effects of part of the CDR3 that folds over the "former" VL binding site and framework-2 mutations to more hydrophilic amino acids, enhance the solubility of VHH domains and prevent VL pairing. cAbAn33, a VHH domain specific for the carbohydrate moiety of the variant surface glycoprotein of trypanosomes, has a short CDR3 loop that does not cover the former VL binding site as well as a VH-specific Trp47 instead of the VHH-specific Gly47. Resurfacing its framework-2 region (mutations Tyr37Val, Glu44Gly and Arg45Leu) to mimic that of a human VH restores the VL binding capacity. In solution, the humanised VHH behaves as a soluble, monomeric entity, albeit with reduced thermodynamic stability and affinity for its antigen. Comparison of the crystal structures of cAbAn33 and its humanised derivative reveals steric hindrance exerted by VHH-specific residues Tyr37 and Arg45 that prevent the VL domain pairing, whereas Glu44 and Arg45 are key elements to avoid insolubility of the domain.     

<Emphasis Type="Italic">IGHV1</Emphasis>,<Emphasis Type="Italic"> IGHV5</Emphasis> and<Emphasis Type="Italic"> IGHV7</Emphasis> subgroup genes in the Rhesus macaque

The diversity of the antibody response is achieved, in part, by rearrangement of different immunoglobulin (Ig) genes. The Ig heavy chain is made up of a variable region (IGHV), a diversity region (IGHD) and a joining region (IGHJ). Human germline IGHV genes have been grouped into seven multigene subgroups. Size and usage of these subgroups is not equal, the IGHV3 subgroup is the most commonly used (36%), followed by IGHV1/7 (26%), then IGHV4, IGHV5, IGHV2, IGHV6 (15%, 12%, 4%, 3% respectively). The rhesus macaque (Macaca mulatta) is a useful non-human primate model for studies of infection and the database of germline Ig genes for the macaque is gradually growing to become a useful tool in the study of B-cell responses. The proportions of IGHV subgroup usage in the macaque are similar to those in man. Representatives from IGHV3 and IGHV4 subgroups for the macaque have been published, as have germline sequences of the IGHD and IGHJ genes. However, to date there have been no sequences published from the second largest IGHV subgroup, IGHV1. We report the isolation and sequencing of a genomic fragment containing an IGHV1 gene from the macaque. Polymerase chain reaction (PCR) primers designed from this sequence enabled us to amplify and sequence 25 new IGHV1 germline genes. We also isolated two IGHV7 genes, using the same primers, and two IGHV5 genes, using human IGHV5 primers.     

The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements

The existence of many highly similar genes in the lymphocyte receptor gene loci makes them difficult to investigate, and the determination of phased "haplotypes" has been particularly problematic. However, V(D)J gene rearrangements provide an opportunity to infer the association of Ig genes along the chromosomes. The chromosomal distribution of H chain genes in an Ig genotype can be inferred through analysis of VDJ rearrangements in individuals who are heterozygous at points within the IGH locus. We analyzed VDJ rearrangements from 44 individuals for whom sufficient unique rearrangements were available to allow comprehensive genotyping. Nine individuals were identified who were heterozygous at the IGHJ6 locus and for whom sufficient suitable VDJ rearrangements were available to allow comprehensive haplotyping. Each of the 18 resulting IGHV│IGHD│IGHJ haplotypes was unique. Apparent deletion polymorphisms were seen that involved as many as four contiguous, functional IGHV genes. Two deletion polymorphisms involving multiple contiguous IGHD genes were also inferred. Three previously unidentified gene duplications were detected, where two sequences recognized as allelic variants of a single gene were both inferred to be on a single chromosome. Phased genomic data brings clarity to the study of the contribution of each gene to the available repertoire of rearranged VDJ genes. Analysis of rearrangement frequencies suggests that particular genes may have substantially different yet predictable propensities for rearrangement within different haplotypes. Together with data highlighting the extent of haplotypic variation within the population, this suggests that there may be substantial variability in the available Ab repertoires of different individuals.     

Analysis of the expressed heavy chain variable-region genes of Macaca fascicularis and isolation of monoclonal antibodies specific for the Ebola virus' soluble glycoprotein

The cynomolgus macaque, Macaca fascicularis, is frequently used in immunological and other biomedical research as a model for man; understanding it's antibody repertoire is, therefore, of fundamental interest. The expressed variable-region gene repertoire of a single M. fascicularis, which was immune to the Ebola virus, was studied. Using 5′ rapid amplification of cDNA ends with immunoglobulin (Ig)G-specific primers, we obtained 30 clones encoding full-length variable, diversity, and joining domains. Similar to the human V_H repertoire, the M. fascicularis repertoire utilized numerous immunoglobulin heavy variable (IGHV) gene fragments, with the V_H3 (41%), V_H4 (39%), and V_H1 (14%) subgroups used more frequently than the V_H5 (3.9%) or V_H7 (1.7%) subgroups. Diverse immunoglobulin heavy joining (IGHJ) fragments also appeared to be utilized, including a putative homolog of JH5β gene segment identified in the related species Macaca mulatta, Rhesus macaque, but not in humans. Although the diverse V region genes in the IgG antibody repertoire of M. fascicularis had likely undergone somatic hypermutations (SHMs), they nevertheless showed high nucleotide identity with the corresponding human germline genes, 80–89% for IGHV and 72–92% for IGHJ. M. fascicularis and human V_H genes were also similar in other aspects: length of complementarity-determining regions and framework regions, and distribution of consensus sites for SHMs. Finally, we demonstrated that monoclonal antibodies (mAbs) specific for an Ebola protein could be obtained from M. fascicularis tissue samples by phage display technology. In summary, the study provides new insight into the M. fascicularis V region gene repertoire and further supports the idea that macaque-derived mAbs may be of therapeutic value to humans.