从大容量噬菌体抗体库中筛选抗DNA-PKcs单链抗体

目的：从单链大容量噬菌体抗体库中筛选特异性的抗DNA-PKcs的人源抗体,用于肿瘤治疗或诊断目的。方法：经抗原性分析及BLAST比对,选定人DNA-PKcs蛋白中抗原性高且与其他蛋白没有同源性的片段,进行原核表达及纯化后将其固定在抗原管上,通过4轮“吸附－洗脱－扩增”过程从大容量抗体库中筛选特异性抗体,转化HB2151菌,制备抗DNA-PKcs的可溶性单链抗体;ELISA检测抗原-抗体结合活性。结果：经生物信息学分析,确定抗原性高且与其他蛋白没有同源性的DNA-PKcs片段DPK3（250个AA）、DPK4（257个AA）。经过4轮筛选,获得26个特异性结合DPK3及31个特异结合DPK4的克隆,指纹分析分别有5种和21种不同的可变区片段;成功制备了可溶性抗体。并做了抗原结合活性鉴定。结论：利用单链大容量抗体库获得抗DNA-PKcs的噬菌体抗体基因并且成功制备成可溶性抗体,为今后的研究和应用奠定了基础。     

鼠源性人乳腺癌单链抗体库的构建与乳腺癌相关抗体的筛选

目的:获得乳腺癌的噬菌体呈现型单链抗体(scFv)库,筛选与乳腺癌细胞特异结合的抗体,为乳腺癌的诊断和治疗奠定基础。方法:用乳腺癌细胞系MCF-7、T47D、MDA-MB-435免疫BALB/c小鼠,取脾脏提取总RNA,用RT-PCR分别扩增抗体重、轻链可变区(VH和VL)基因,经Linker连接形成scFv基因片段。将scFv基因片段与噬菌粒载体pCANTAB5E的连接产物转化大肠杆菌TG1。用辅助噬菌体M13KO7进行超感染,获得重组噬菌体抗体。选用乳腺癌细胞系MCF-7和人正常肝细胞系HL02做正负差异的筛选细胞,通过5轮筛选,随机挑取克隆,经phage-ELISA筛选特异性结合MCF-7细胞的scFv。结果:构建了1个库容为1.3×106的单链抗体库。筛选到2株与MCF-7细胞有较高结合活性的噬菌体-单链抗体scFv-873和scFv-874。数据库搜索表明这2株单链抗体基因是与以往抗体序列不同的新基因。用Westernblot检测了这2株单链抗体在琥珀密码子非抑制型菌株TOP10中的表达情况。结论:筛选到2个与乳腺癌细胞结合特异性较好的单链抗体,为乳腺癌的诊断和治疗研究奠定了基础。     

Antibodies against non-immunizing antigens derived from a large immune scFv library

Target-specific antibodies can be rapidly enriched and identified from an antibody library using phage display. Large, naïve antibody libraries derived from synthetic or unimmunized sources can yield antibodies against virtually any antigen, whereas libraries from immunized sources tend to be smaller and are used exclusively against the antigen of immunization. In this study, 25 scFv libraries made from the spleens of immunized rabbits, each with a size ranging from 10⁸ to higher than 10⁹, were combined into a single large library with > 10¹⁰ individual clones. Panning of this combined library yielded target-specific rabbit scFv clones against many non-immunizing antigens, including proteins, peptides, and a small molecule. Notably, specific scFv clones against a rabbit self-antigen (rabbit serum albumin) and a phosphorylated protein (epidermal growth factor receptor pTyr1173) could be isolated from the library. These results suggest that the immune library contained a significant number of unimmunized clones and that a sufficiently large immune library can be utilized similarly to a naïe library, i.e., against various non-immunizing antigens to yield specific antibodies.     

Isolation of endothelial cell-specific human antibodies from a novel fully synthetic scFv library

We have isolated single-chain Fv fragments directed against human endothelial cells from a novel fully synthetic human scFv library (scFv 479). This library was constructed using the variable germline segments DP47 and DPkappa9 as scaffolds. Complementarity determining regions 3 (CDR) of the variable heavy and light chain were introduced with a length of 9 amino acid residues. In total, 16 amino acid positions of all six CDRs exposed in the antigen-binding site were randomized and the library was produced from synthetic oligonucleotides encoding the entire scFv fragment. From this library endothelial-specific scFv fragments were either selected using the recombinant extracellular domain of human endoglin (CD105) or by cell selections with human dermal microvascular endothelial cells (HDMEC). These scFv fragments might be useful for the generation of vascular or tumor targeting agents in cancer therapy.     

Construction and characterization of a pseudo-immune human antibody library using yeast surface display

Lymphocytes from eight individuals out of 60 healthy donors, whose plasmas showed relatively higher antibody titer for a target antigen of death receptor 5 (DR5), were selected for the source of antibody genes to construct so called an anti-DR5 pseudo-immune human single-chain fragment variable (scFv) library on the yeast cell surface (approximately 2x10(6) diversity). Compared with a large nonimmune human scFv library (approximately 1x10(9) diversity), the repertoire of the pseudo-immune scFv library was significantly biased toward the target antigen, which facilitated rapid enrichments of the target-specific high affinity scFvs during selections by fluorescence activated cell sortings. Isolated scFvs, HW5 and HW6, from the pseudo-immune library showed much higher specificity and affinity for the targeted antigen than those from the nonimmune library. Our results suggest that a pseudo-immune antibody library is very efficient to isolate target-specific high affinity antibody from a relatively small sized library.     

Construction of human Fab library and isolation of monoclonal Fabs with rabies virus-neutralizing ability

A combinatorial human Fab library was constructed using RNAs from peripheral blood lymphocytes of 6 rabies vaccine-boosted volunteers using pComb3X phagemid vector. The size of the constructed library was approximately 7.0 x 10(7) Escherichia coli transformants. The library was selected against purified rabies virus (RV) virion or purified RV glycoprotein for isolation of phages displaying RVneutralizing human Fab antibody. Among 132 selected clones, two Fab preparations revealed neutralizing activities against RV strain CVS when assayed in the rapid fluorescent focus inhibition test (RFFIT). The Fab preparation EP5G3 exhibited neutralizing activity with an infected cell count reduction of 76% at a dilution of 1: 2, and of 20% at a dilution of 1: 4. The Fab preparation GD2D12 also exhibited neutralizing activity with a 57% reduction at 1: 2 and 41% reduction at 1: 4. In the co-immunoprecipitation using strain CVS, the RV glycoprotein was precipitated in reactions with both Fab preparations. The RV neutralizing ability of the Fab preparations described in the study were not directly correlated with their binding specificity for RV antigens detected by ELISA.     

Selection and characterization of high affinity VEGFR1 antibodies from a novel human binary code scFv phage library

VEGFR1 is a receptor tyrosine kinase that has been implicated in cancer pathogenesis. It is upregulated in angiogenic endothelial cells and expressed on human tumor cells as well. VEGFR1 positive hematopoietic progenitor cells home to sites of distant metastases prior to the arrival of the tumor cells thus establishing a pre-metastatic niche. To discover high affinity human antibodies selective for VEGFR1 molecular imaging or for molecularly targeted therapy, a novel phage display scFv library was assembled and characterized. The library was constructed from the humanized 4D5 framework that was mostly comprised tyrosine and serine residues in four complimentarity determining regions (CDRs). The library produced diverse and functional antibodies against a panel of proteins, some of which are of biomedical interest including, CD44, VEGFA, and VEGFR1. After panning, these antibodies had affinity strong enough for molecular imaging or targeted drug delivery without the need for affinity maturation. One of the anti-VEGFR1 scFvs recognized its cognate receptor and was selective for the VEGFR1.     

Generation and characterization of C305, a murine neutralizing scFv antibody that can inhibit BLyS binding to its receptor BCMA

B-lymphocyte stimulator (BLyS) is a member of the tumor necrosis factor (TNF) family and a key regulator of B cell response. Neutralizing single-chain fragment variable (scFv) antibody against BLyS binding to its receptor BCMA has the potential to play a prominent role in autoimmune disease therapy. A phage display scFv library constructed on pill protein of MI 3 filamentous phage was screened using BLyS.After five rounds of panning, their binding activity was characterized by phage-ELISA. Nucleotide sequencing revealed that at least two different scFv gene fragments (C305 and D416) were obtained. The two different scFv gene fragments were expressed to obtain the soluble scFv antibodies, then the soluble scFv antibodies were characterized by means of competitive ELISA and in vitro neutralization assay. The results indicated that C305 is the neutralizing scFv antibody that can inhibit BLyS binding to its receptor BCMA.     

Synthetic approach to the generation of antibody diversity

The in vitro antibody discovery technologies revolutionized the generation of target-specific antibodies that traditionally relied on the humoral response of immunized animals. An antibody library, a large collection of diverse, pre-constructed antibodies, can be rapidly screened using in vitro display technologies such as phage display. One of the keys to successful in vitro antibody discovery is the quality of the library diversity. Antibody diversity can be obtained either from natural B-cell sources or by the synthetic methods that combinatorially generate random nucleotide sequences. While the functionality of a natural antibody library depends largely upon the library size, various other factors can affect the quality of a synthetic antibody library, making the design and construction of synthetic antibody libraries complicated and challenging. In this review, we present various library designs and diversification methods for synthetic antibody library. From simple degenerate oligonucleotide synthesis to trinucleotide synthesis to physicochemically optimized library design, the synthetic approach is evolving beyond the simple emulation of natural antibodies, into a highly sophisticated method that is capable of producing high quality antibodies suitable for therapeutic, diagnostic, and other demanding applications. [BMB Reports 2015; 48(9): 489-494]     

Recombinant scFv antibodies against E protein and N protein of severe acute respiratory syndrome virus

Severe acute respiratory syndrome (SARS) brought aglobal outbreak in spring of 2003 [1–3], and more andmore attention has been paid on it when a new caseresurfaced in Singapore last September [4]. By the endof May in 2003, WHO reported a cumulative total of 8202infected cases with 725 deaths from 28 countries.Because of the high transmission and morality rate ofSARS, scientists in many countries have made theirefforts in studying SARS coronavirus (SARS-CoV)[5, 6]. Several genomes of…     

Construction of human Fab (gamma1/kappa) library and identification of human monoclonal Fab possessing neutralizing potency against Japanese encephalitis virus

A combinatorial human Fab library was constructed using RNAs from peripheral blood lymphocytes obtained from Japanese encephalitis virus hyper-immune volunteers on pComb3H phagemid vector. The size of the constructed Fab library was 3.3x10(8) Escherichia coli transformants. The library was panned 3 times on the purified Japanese encephalitis virus (JEV) virion, and phage clones displaying JEV antigen-specific Fab were enriched. The enriched phage pool was then screened for clones producing Fab molecule with JEV neutralizing activity by the focus reduction-neutralizing test. Among 188 randomly selected clones, 9 Fab preparations revealed neutralizing activities against JEV strain Nakayama. An E. coli transformed with TJE12B02 clone, which produced human monoclonal Fab with the highest neutralizing activity was cultured in a large scale, and the Fab molecule was purified using affinity chromatography. The purified FabTJE12B02 showed the 50% focus reduction endpoint at the concentration of 50.2 microg/ml (ca. 1,000 nM) when JEV strain Nakayama was used. The FabTJE12B02 recognized E protein of JEV strain Nakayama, and the dissociation equilibrium constant (Kd) of the FabTJE12B02 against purified JEV antigen was calculated as 1.21x10(-8) M. Sequence analysis demonstrated that TJE12B02 used a VH sequence homologous to the VH3 family showing 88.8% homology to germline VH3-23, and used a Vkappa sequence homologous to the VkappaII subgroup showing 92.8% homology to germline A17.     

Construction and diversity analysis of a murine IgE phage surface display library

INTR0DUCTI0NIn0urprevi0usstudy0fV5andVKfromfouranti-TCSIgEhybrid0masestab-lishedin0urlaboratory,wefoundVKfr0mallfourcl0nesusedfragmentsfromthesamegermlinegenefamilyVK21,andabiasintheuse0fJk1genefragmentwasalsoobserved.Ontheotherhand,thegeneusageofVHwaJsquitediverse.WespeculatedthatinIgEresponsest0TCS,thelightchainmayplayam0reimpor-tantroleinspecificbindingtoallergenicdeterminant0nTCS[1].However,duet0thelimitationofhybrid0matechnology,itisdifficulttoachievealargenumberofanti-TCSI…     

人源抗ICAM-1单链抗体的制备及其生物学活性鉴定

利用噬菌体展示技术筛选特异性人源抗ICAM-1单链抗体（Anti-human ICAM-1 scFv）并进行生物学活性鉴定。应用Tomlinson I+J噬菌体抗体库,以P1抗原肽为包被抗原,经过4轮“吸附-洗脱-扩增”进行亲和富集筛选。以PCR反应、ELISA抗原交叉反应和Dot blotting实验进行阳性克隆的鉴定。scFv经原核表达和分离纯化后,以Western blotting实验、竞争ELISA实验和细胞黏附抑制实验对其生物学活性进行初步鉴定。Tomlinson I+J噬菌体抗体库经4轮亲和富集筛选,利用ELISA方法成功筛出4株阳性克隆。通过PCR鉴定反应、ELISA抗原交叉反应和Dot blotting实验,最终获得了1株既能与P1抗原肽特异结合又能与人ICAM-1抗原特异结合的阳性克隆J-A1。对scFv进行原核表达和亲和层析后获得了高纯度的目的蛋白。竞争ELISA实验和细胞黏附抑制实验证实纯化的scFv具有良好的亲和活性和抗细胞黏附活性。文中成功利用噬菌体展示技术筛选到特异性人源抗ICAM-1 scFv,为进一步探索该抗体在炎症相关性疾病治疗中的应用奠定了基础。     

Comparing CDRH3 diversity captured from secondary lymphoid organs for the generation of recombinant human antibodies

The plasticity of natural immunoglobulin repertoires can be exploited for the generation of phage display libraries. Secondary lymphoid organs, such as the spleen and the lymph nodes, constitute interesting sources of diversity because they are rich in B cells, part of which can be affinity matured. These organs, however, differ in their anatomical structure, reflecting the different fluids they drain, which affects the B cell repertoires. The CDRH3 repertoires from these organs, extracted from naïve or immunized mice, were compared in the context of phage display libraries using human antibody framework families. Deep sequencing analysis revealed that all libraries displayed different CDRH3 repertoires, but the one derived from lymph nodes of naïve mice was the most diverse. Library performance was assessed by in vitro selection. For both organs, immunization increased substantially the frequency of molecules able to bind to the immunogen. The library derived from lymph nodes from naïve mice, however, was the most effective in generating diverse and high affinity candidates. These results illustrate that the use of a biased CDRH3 repertoire increases the performance of libraries, but reduces the clonal diversity, which may be detrimental for certain strategies.     

噬菌体抗体库的构建及抗乳腺癌细胞单链抗体的筛选

构建抗人乳腺癌细胞MCF 7的噬菌体单链抗体库 ,从中筛选MCF 7细胞特异性单链抗体。用MCF-7细胞免疫BALB C小鼠 ,取脾脏 ,提取总RNA ,用RT-PCR技术扩增小鼠抗体重链 (V_H)和轻链 (V_L)可变区基因 ,经重叠PCR(SOE-PCR) ,在体外将V_H和V_{L连接成单链抗体 (scFv)基因 ,并克隆到噬菌粒载体pCANTAB5E中 ,电转化至大肠杆菌TG1,经辅助噬菌体超感染 ,构建噬菌体单链抗体库。从该抗体库中筛选特异性识别MCF-7细胞的噬菌体单链抗体 ,将表面展示单链抗体的单克隆噬菌体转化大肠杆菌TOP10进行可溶性表达。成功地构建了库容为12×10⁶ 的抗MCF-7乳腺癌细胞的单链抗体库 ,初步筛选到了与MCF 7细胞特异性结合的scFv,Westernblot检测表明 ,在大肠杆菌TOP10中实现了单链抗体可溶性表达}     

抗乙型肝炎病毒表面抗原T7噬菌体抗体库的构建

构建T7噬菌体单链抗体(scFv)库筛选抗乙型肝炎病毒表面抗原抗体.从抗-HBs阳性患者外周血淋巴细胞中提取总RNA,反转录合成cDNA第1条链,PCR分别扩增抗体重链可变区基因(VH)和轻链可变区基因(VL),经重叠延伸拼接(SOE)PCR组成scFv基因,并将其与T7噬菌体载体的2个臂相连接.体外包装后,在宿主菌BLT5403中,扩增重组噬菌体抗体库.以乙型肝炎病毒表面抗原进行4轮“吸附-洗脱-扩增”的筛选,酶免疫实验检测抗体活性.所建抗体库库容为1.53×107,扩增后初级库滴度为2.42×1010pfu/mL.以乙型肝炎病毒表面抗原筛选后抗体出现特异性富集,经酶免疫实验鉴定,得到2株与HBsAg抗原特异结合的噬菌体抗体,成功构建了抗HBsAg蛋白T7噬菌体抗体库.     

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.     

The Production of Miniantibodies Against Human Granulocyte Colony-Stimulating Factor Using the Murine scFv Combinatory Library

To develop a phage display of single-chain antibodies (scFv), fractions of total cell DNA and RNA were obtained from splenocytes of naive mice. The DNA fragments encoding variable regions of light and heavy immunoglobulin chains were amplified and isolated using primers specific to the conservative regions of these genes. The construction of the library was based on the principle of stochastic combining the DNA fragments encoding the light and heavy antibody chains with the DNA linker, whose structure corresponded to the (Gly₄Ser)₃ sequence. The scFv library was constructed using the E. coli TG1 strain and the phagemid vector pHEN1. The repertoire of the library exceeded 5 × 10⁷ independent recombinant clones. The clones producing antibodies to human granulocyte colony-stimulating factor were isolated. The affinity constants of the resulting scFv were in the range of 2 × 10⁴ to 1.8 × 10⁷ M^–1.     

Multivalent scFv display of phagemid repertoires for the selection of carbohydrate-specific antibodies and its application to the Thomsen-Friedenreich antigen

The Thomsen-Friedenreich disaccharide (TF) is a promising target antigen for tumor immunotherapy, since it is almost exclusively expressed in carcinoma tissues. The TF-specific antibodies generated so far are IgMs of mouse origin with limited therapeutic potential. Phage-displayed scFv repertoires are an established source for recombinant antibodies; however, we were unable to identify scFvs binding to TF when applying libraries in the standard monovalent display format of phagemid systems. Here, we report on the successful selection of TF-specific antibody fragments using a multivalent scFv phagemid library format based on shortened linkers (one amino acid residue). The libraries were constructed from mice immunized with asialoglycophorin and selected using TF displayed on two different carrier molecules in combination with the proteolytically cleavable helper phage KM13. All isolated clones encoded the same framework genes and the same complementarity-determining regions. After affinity maturation only scFv with the founder sequence were selected from secondary repertoires. This indicates a very narrow sequence window for TF-specific antibodies. Investigating other linker-length formats revealed a clear inverse correlation between linker length and binding activity both as soluble proteins and displayed on phages. The highest affinity was obtained with the tetrameric format. The selected scFv was specific for TF on various carrier molecules and tumor cells and performed well in ELISA and immunohistochemistry. We postulate that scFv phagemid library formats with short linkers (i.e. multimeric scFvs) may, in general, be advantageous in selections for the generation of scFvs against carbohydrate epitopes or other epitopes associated with low intrinsic affinity per binding site), and expect that they will be superior in applications for diagnosis or therapy.     

A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties

This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds.