Differential screening of phage-ab libraries by oligonucleotide microarray technology

A novel and efficient tagArray technology was developed that allows rapid identification of antibodies which bind to receptors with a specific expression profile, in the absence of biological information. This method is based on the cloning of a specific, short nucleotide sequence (tag) in the phagemid coding for each phage-displayed antibody fragment (phage-Ab) present in a library. In order to set up and validate the method we identified about 10,000 different phage-Abs binding to receptors expressed in their native form on the cell surface (10 k Membranome collection) and tagged each individual phage-Ab. The frequency of each phage-Ab in a given population can at this point be inferred by measuring the frequency of its associated tag sequence through standard DNA hybridization methods. Using tiny amounts of biological samples we identified phage-Abs binding to receptors preferentially expressed on primary tumor cells rather than on cells obtained from matched normal tissues. These antibodies inhibited cell proliferation in vitro and tumor development in vivo, thus representing therapeutic lead candidates.     

Preparation of HMW DNA from Plant Nuclei and Chromosomes Isolated from Root Tips

Simple, fast and cost-effective method for preparation of DNA with high molecular weight (HMW DNA) from plant nuclei and mitotic chromosomes has been developed. The technique involves mechanical homogenization of formaldehyde-fixed root tips, purification of nuclei and/or chromosomes on sucrose gradient, embedding in low-melting-point agarose, and DNA isolation in agarose plugs. Alternatively, nuclei and chromosomes may be purified using flow cytometry. Majority of DNA obtained is megabase-sized and well digestible by restriction endonucleases. The method is highly efficient as microgram amounts of DNA can be obtained from only several milligrams of plant tissue. Handling negligible amounts of plant material reduces the consumption of chemicals. Furthermore, the use of root tips makes it possible to obtain high-quality DNA even from plant species with leaves that are rigid or rich in secondary metabolites such as polyphenols. It is expected that preparation of HMW DNA from root tip nuclei will facilitate long-range mapping and construction of large-insert DNA libraries also in these species. Successful isolation of HMW DNA from flow-sorted chromosomes opens a way for construction of chromosome-specific large-insert libraries in plants. This revised version was published online in July 2006 with corrections to the Cover Date.     

A library of monoclonal antibodies to nuclear proteins from Drosophila melanogaster embryos. Characterization by a cultured cell assay

To study the structure and function of the cell nucleus, a library of 170 monoclonal antibodies was produced to nuclear antigens from 3-6 h old Drosophila embryos. In preparation for immunization, nuclei were separated, at neutral pH and in the presence of polyamines, into two fractions containing either urea-soluble non-histone nuclear proteins or histones plus small quantities of non-histone proteins complexed to DNA. The antibodies were characterized in a rapid, indirect immunofluorescent assay employing cultured Drosophila cells (Schneider's line 2). Low backgrounds and high specific fluorescence were achieved in this assay by purifying the rhodamine-labelled second antibody on a polystyrene resin and washing the cells with optimal concentrations of detergents. The assay categorized antigens according to their cellular locations: in nuclei, in nuclei plus cytoplasm, or primarily in cytoplasm. A subset of nuclear antigens reacted specifically with the nuclear envelope. In addition, some antibodies were characterized by their reactions with polytene chromosomes. The cultured cell assay provides a new, efficient method for expanding this antibody library. The monoclonal antibodies in the library now provide highly specific tools for investigating structural nuclear proteins and proteins that may be regulatory during embryonic development.     

基于单个B细胞抗体基因扩增技术筛选马IgG1单克隆抗体*

在马的免疫学研究领域中,由于目前市场上缺乏商业化的马IgG单克隆抗体,使得对马的B细胞研究受到很大阻碍,IgG是B细胞受体(BCR)的重要构成成分,与B细胞分化成熟相关。为了获得马IgG特异性单克隆抗体,利用单个B细胞扩增技术进行抗体筛选。首先,将马IgG蛋白(EqIgG1-C)密码子优化后合成到真核表达载体pcDNA3.4上,纯化出抗原蛋白。随后,使用蛋白质免疫小鼠,分离脾细胞后利用流式细胞术分离特异性单个B细胞,扩增出抗体重链和轻链的可变区基因,用overlapping PCR方法扩增出线性化的完整抗体,并进行鉴定。结果从80个B细胞中获得了27株特异性重组单克隆抗体,并挑选出3株线性结合活性最强的抗体基因构建到表达载体上,共转染Expi293F^TM细胞后表达纯化,经过ELISA和Western blot验证,显示获得的抗体可以和EqIgG1-C蛋白有良好的结合作用。使用该方法可以省时高效的获得特异性抗体,为马的免疫学研究提供了重要研究工具,为鼠单克隆抗体筛选提供了技术拓展。     

Highly sensitive immunodetection of DNA on sections with exogenous terminal deoxynucleotidyl transferase and non-isotopic nucleotide analogues.

A new method is described for locating DNA on ultra-thin sections. Sections of aldehyde-fixed, plastic-embedded cells were incubated in a medium containing terminal deoxynucleotidyl transferase (TdT) and various non-isotopic nucleotide analogues. The labeled nucleotides bound to the surface of ultra-thin sections were then visualized by an indirect immunogold labeling technique. The resulting labeling pattern was strongly dependent on the divalent cation used in the TdT medium. The method revealed with great precision the specific DNA-containing structures within Ehrlich tumor cells, even where DNA was present in very low amounts. The method is compatible with all usual fixation and embedding procedures and can be combined with cytochemical methods. The in situ TdT method provides a very useful tool for pinpointing the precise location of DNA within biological material at the ultrastructural level.     

Immunomodulatory therapy of cancer with T cell-engaging BiTE antibody blinatumomab

Severe side effects and few long-term remissions frequently limit the treatment of advanced malignant diseases. Bispecific antibodies are currently emerging as a new option for the treatment of malignant diseases, which can potentially engage all cytotoxic T cells of a patient for tumor cell lysis. Blinatumomab, a bispecific single-chain BiTE antibody construct with dual specificity for CD19 and CD3, is a front runner of this antibody class. We here summarize the current state of development of blinatumomab for the treatment of patients with B-cell non-Hodgkin's lymphoma (NHL) and B-precursor acute lymphocytic leukemia (ALL). High response rates and durable remissions are observed in first clinical trials, indicating that T cells can be potently redirected for efficient and lasting elimination of malignant cells.     

Selection of antibodies against a single rare cell present in a heterogeneous population using phage display

Here we describe a new method applying phage-displayed antibody libraries to the selection of antibodies against a single identified cell on a glass slide. This is the only described method that has successfully achieved selection of antibodies against a single rare cell in a heterogeneous population of cells. The phage library is incubated with the slide containing the identified rare cell of interest; incubation is followed by UV irradiation while protecting the target cell with a minute disc. The UV light inactivates all phages outside the shielded area by cross-linking the DNA constituting their genomes. The expected yield is between one and ten phage particles from a single cell selection. The encoded antibodies are subsequently produced monoclonally and tested for specificity. This method can be applied within a week to carry out ten or more individual cell selections. Including subsequent testing of antibody specificity, a specific antibody can be identified within 2 months.     

Immunocytochemical localization of chick DNA polymerases alpha and beta +

An immunofluorescent method using specific antibodies was employed to detect DNA polymerases alpha and beta in chick cells. With monoclonal antibodies produced by four independent hybridoma clones, most of the DNA polymerase alpha was shown to be present in nuclei of cultured chick embryonic cells. With a polyclonal, but highly specific, antibody against DNA polymerase beta, this enzyme was also shown to be present in nuclei. DNA polymerase alpha was detected in proliferating cells before cell contact and in lesser amount in resting cells after cell contact, indicating that its content is closely correlated with cell proliferation. On the other hand, similar amounts of DNA polymerase beta were detected in proliferating and resting cells. Furthermore, DNA polymerase beta was detected in nuclei of most cells, while DNA polymerase alpha was detected only in large round nuclei in seminiferous tubules of chick testis. DNA polymerase alpha is presumably present in cells that are capable of DNA replication, and during the cell cycle it seems to remain in the nuclei during the G1, S, and G2 phases, but to leave from condensed chromatin for the cytoplasm during the mitotic phase.     

Intracellular delivery of antibodies using TAT fusion protein A

Internalization of antibodies into mammalian cells is a useful method for analyzing and regulating cellular function. In this study, we developed a novel method for the delivery of antibodies into cells using the TAT-fused protein. This fusion protein consists of two functional domains, the protein transduction domain of HIV-1 TAT and the B domain of staphylococcal protein A (SpA), which has an ability to bind to the IgG. The TAT-SpA fusion protein was mixed with fluorescence-labeled rabbit IgG and added to cells. The internalization of antibody was analyzed using confocal microscopy and flow cytometry in living cells. As a result, fluorescence-labeled IgG with the TAT-SpA fusion protein was observed intracellularly. Flow cytometry results demonstrated time course and dose dependence relationships of antibody internalization. These results suggest that the TAT-SpA fusion protein can be a useful reagent for the delivery of antibody into cells.     

One-step preparation of antibody and oligonucleotide dual-labeled gold nanoparticle bio-probes and their properties

A novel method of one-step preparation of dual-labeled gold nanoparticle bio-probes was established by the electrostatic adsorption and the covalent bonding of gold nanoparticles with antibodies and thiol-modified oligonucleotides, respectively. Characterization of probes, the coverage and activity of antibodies and oligonucleotides on probe surfaces were detected. The results indicated that the gold nanoparticles labeled with antibodies and oligonucleotides possess good bioactivity and the coverage of oligonucleotide and antibody on a dual-labeled gold nanoparticle bio-probe was (92 ± 20) and (8 ± 3), respectively. The preparative method is simple and stable. The dual-labeled gold nanoparticle bio-probes have an application value in detection of ultramicro protein.     

Determination of genomic 5-hydroxymethyl-2’-deoxycytidine in human DNA by capillary electrophoresis with laser induced fluorescence

Recent studies reported the presence of 5-hydroxymethylcytosine (5 hmC) as an additional modification in mammalian genomic DNA. To date, 5 hmC has been detected only in mouse DNA isolated from embryonic stem cells, some adult tissues and in DNA from human bone marrow. Understanding its biological function will require the development of sensitive analytical methods that allow the detection and quantification of 5-hydroxymethylcytosine along with 5-methylcytosine and cytosine.

Here we report the validation of a fast and sensitive method for the quantification of global 5-hydroxymethyl-2'-deoxycytidine (5 hmdC) in DNA. The method is based on a procedure consisting of fluorescence labeling of deoxyribonucleotides and analysis by capillary electrophoresis with laser-induced fluorescence detection (CE-LIF). A double stranded DNA fragment containing a defined number of 5 hmdC residues was used for peak assignment, to establish separation conditions and to determine the limit of detection (LOD). The method yielded a LOD for 5 hmdC of 0.45 amol, which is equivalent to approximately to one 5 hmdC per 4,000 normal nucleotides (0.025%) using 1 μg of DNA as the matrix.

By applying the calibrated assay to the analysis of various DNAs we show that 5 hmdC is present in human tissue and human cancer cell lines. We demonstrate that by using CE-LIF DNA can be analyzed in one run for both methylation and hydroxymethylation of cytosine with high sensitivity and accuracy.     

鼠疫菌PsaA抗原的表达及抗体制备和应用

目的：制备鼠疫菌PsaA抗原及抗体,建立针对PsaA抗体的快速检测方法,并检测鼠疫感染猴血清标本中的PsaA抗体的阳性率。方法：利用PCR方法扩增出PsaA蛋白基因片段,在大肠杆菌原核表达系统中表达出重组PsaA抗原,以镍柱亲和层析纯化包涵体形式的表达蛋白,以尿素梯度透析复性成可溶蛋白。再以表达蛋白为免疫原,常规免疫家兔,收集兔血清制备多抗,并以正辛酸-硫酸铵法提纯获得PsaA抗体IgG。利用得到的PsaA抗原和抗体为材料,建立两种检测PsaA抗体的快速检测方法,即间接ELISA法和上转换发光（Up-converting Phospher Technology,UPT）免疫层析试纸条法。最后利用这两种方法检测18份猴血清标本中的PsaA抗体。结果：鼠疫菌感染猴血清标本中PsaA抗体的阳性率为62%（8/13）。结论：成功建立了针对鼠疫菌PsaA抗体的快速检测方法,并检测到13份鼠疫感染猴血清标本中的PsaA抗体的阳性率为62%。     

鼻咽癌患者血清中抗Epstein-Barr病毒早期和晚期膜抗原抗体的检测

对Epstein-Barr(EB)病毒抗原的研究,发现有淋巴细胞确定的膜抗原(Lydma)、早期抗原(EA)、壳抗原(VCA)、核抗原(EBNA)、早期膜抗原(EMA)和晚期膜抗原(LMA)。除了Lydma抗原外,鼻咽癌患者对上述抗原均产生相应的IgG和IgA抗体。因而研究这些抗体,对阐明EB病毒与鼻咽癌的关系及鼻咽癌的早期诊断都十分有价值。     

A Rapid and Simple PCR-based Method for Analysis of Transgenic Fish using a Restricted Amount of Fin Tissue

The protocol described in this paper offers a simple and rapid method for PCR analysis of transgenes using a restricted amount of fin tissue from small-sized transgenic fish. A simple preparation of fin lysate using a buffer containing a low concentration of an ionic detergent, SDS (0.01%), followed by neutralization with a second buffer containing higher concentrations of non-ionic detergents NP40 (2%) and Tween 20 (2%) consistently provides a reliable quantity of high-quality DNA template for PCR amplification of transgenes. Based on this protocol, transgenic fish can be clearly distinguished from non-transgenic fish using PCR in a rapid and reproducible manner. Tedious DNA purifications are avoided while fidelity of amplification and efficient identification of transgenic fish are maintained.     

人乳头瘤病毒(HPV)58型DNA疫苗免疫原性的初步分析

为了检测HPV 58型不同L1基因的DNA疫苗的免疫原性,以pcDNA3.1为载体分别构建含HFV 58型不同L1基因的DNA疫苗,命名为L1h、L1h△c、L1S、L1SM和L1wt.用免疫印迹法检测各DNA疫苗的体外表达情况;各重组质粒与pcDNA3.1-h58L2和pcDNA3.1-GFP共转染293FT细胞,检测其形成假病毒的能力;并将各DNA疫苗肌肉注射免疫小鼠,利用假病毒中和实验检测中和抗体水平,用ELISPOT检测细胞免疫情况.结果显示,本实验成功构建了五种DNA疫苗,L1h△c的体外表达量最高,L1S和L1SM的表达量次之,L1wt没有表达;重组质粒L1S能够形成假病毒,而其他四种重组质粒均不能形成假病毒.L1S和L1h均可在小鼠体内诱导中和抗体,但L1S诱导的中和抗体的平均滴度为1:6 400,明显高于L1h诱导的中和抗体水平(平均滴度为1:48),而其他疫苗在小鼠体内未产生中和抗体.对五种疫苗均未检测出特异性的细胞免疫反应.结果提示,体外能够组装成假病毒的DNA疫苗在免疫动物后可诱导高滴度的中和抗体,为今后DNA疫苗的筛选提供参考.     

从噬菌体抗体库中淘选血纤维蛋白特异的单链抗体

为构建小鼠噬菌体抗体库 ,以获得对人血纤维蛋白特异的抗体 ,由小鼠脾脏提取 m RNA,经反转录 PCR扩增出抗体重链、轻链可变区基因片段 ,将二者和一段编码十五肽 (Gly4 Ser) 3的 DNA接头借助重组 PCR组装成为单链抗体 (single- chain antibody,Sc Ab)基因 .将单链抗体基因插入噬菌体展示载体 p CANTAB- 5E,通过电击法转化大肠杆菌 TG1细胞 ,用辅助噬菌体 M1 3K0 7超感染 ,构建了库容量在 1 0 8以上的噬菌体单链抗体库 .利用亲和选择方法 (淘选 ) ,从噬菌体抗体库中选得血纤维蛋白特异的单链抗体 .模拟抗体成熟过程 ,用 DNA改组 (DNA shuffling)技术使抗体基因重新组合 ,构建新的改组抗体库 ,并从中选择到提高了亲和力的噬菌体单链抗体 .抗体基因在大肠杆菌中表达 ,表达蛋白经 Sephadex G- 75柱层析分离 ,得到初步纯化的单链抗体蛋白 .     

Methylated DNA Immunoprecipitation

The identification of DNA methylation patterns is a common procedure in the study of epigenetics, as methylation is known to have significant effects on gene expression, and is involved with normal development as well as disease ^1-4. Thus, the ability to discriminate between methylated DNA and non-methylated DNA is essential for generating methylation profiles for such studies. Methylated DNA immunoprecipitation (MeDIP) is an efficient technique for the extraction of methylated DNA from a sample of interest ^5-7. A sample of as little as 200 ng of DNA is sufficient for the antibody, or immunoprecipitation (IP), reaction. DNA is sonicated into fragments ranging in size from 300-1000 bp, and is divided into immunoprecipitated (IP) and input (IN) portions. IP DNA is subsequently heat denatured and then incubated with anti-5''mC, allowing the monoclonal antibody to bind methylated DNA. After this, magnetic beads containing a secondary antibody with affinity for the primary antibody are added, and incubated. These bead-linked antibodies will bind the monoclonal antibody used in the first step. DNA bound to the antibody complex (methylated DNA) is separated from the rest of the DNA by using a magnet to pull the complexes out of solution. Several washes using IP buffer are then performed to remove the unbound, non-methylated DNA. The methylated DNA/antibody complexes are then digested with Proteinase K to digest the antibodies leaving only the methylated DNA intact. The enriched DNA is purified by phenol:chloroform extraction to remove the protein matter and then precipitated and resuspended in water for later use. PCR techniques can be used to validate the efficiency of the MeDIP procedure by analyzing the amplification products of IP and IN DNA for regions known to lack and known to contain methylated sequences. The purified methylated DNA can then be used for locus-specific (PCR) or genome-wide (microarray and sequencing) methylation studies, and is particularly useful when applied in conjunction with other research tools such as gene expression profiling and array comparative genome hybridization (CGH) ⁸. Further investigation into DNA methylation will lead to the discovery of new epigenetic targets, which in turn, may be useful in developing new therapeutic or prognostic research tools for diseases such as cancer that are characterized by aberrantly methylated DNA ^{2, 4, 9-11}.     

Rapid selection of single cells with high antibody production rates by microwell array

Selection of single cells capable of producing target proteins at high rates is crucial for the development of protein manufacturing processes. Here, we present the rapid selection of single cells producing immunoglobulin antibodies at high specific rates by microwell array and microengraving. Chinese hamster ovary (CHO) cells secreting chimeric antibodies were deposited in a microwell array in a manner such that each microwell contained a single cell. Secreted antibodies in the microwells were transferred onto a glass slide by microengraving, followed by interrogation using fluorescence-based immunoassay. Single cells displaying high signal intensities were selected, retrieved, and clonally expanded to assess their specific antibody production rates. Three successive rounds of the process resulted in the selection of single cells showing significantly increased antibody production rates. The present approach can be applied to the selection of single cells for producing other therapeutic proteins in a high-throughput manner.     

Optimal construction of non-immune scFv phage display libraries from mouse bone marrow and spleen established to select specific scFvs efficiently binding to antigen

Monoclonal antibodies (MAbs) are widely applied in basic research, medicine, and the pharmaceutical industry. Recently, applications and generations of MAbs have been increasingly attracting attention in many research areas since MAbs could be produced in large quantities with the development of genetic technology and antibody engineering. On the other hand, in recent years, phage display system has been developed for high-throughput isolation and generation of novel MAbs that have high affinity with various antigens. This technology is capable of constructing "Library" containing billions of phage repertoires displaying various antibody fragments, and rapid selection of a specific MAb from this phage library. Additionally, this technology has a great advantage that MAbs can be generated without immunization to animals. However, there are still relatively few reports confirming that useful MAbs can be derived from non-immune antibody libraries. The latter, as undertaken by current methods, seem unable to achieve the high quality required to produce useful MAbs for any desired antigen because cloning of antibody gene from non-immune donors is inefficient. This problem is caused by the fact that their RT-PCR primer sets, PCR conditions, and efficiency of subcloning through construction of antibody gene library cannot encompass all the antibody diversity. In an attempt to overcome some of these earlier problems, here we describe an optimized method to establish a high quality, non-immune library from mouse bone-marrow and spleen, and assess its diversity in terms of content of multiple antibodies for a wide antigenic repertoire. As an example of the application of the methodology, we describe the selection of specific MAbs binding to Luciferase and identify at least 18 different clones. Using this non-immune mouse antibody library, we also obtained MAbs for VEGF, VEGF receptor 2, TNF-alpha, and Pseudomonas Exotoxin, confirming the high quality of the library and its suitability for this application.     

Amber suppression coupled with inducible surface display identifies cells with high recombinant protein productivity

Cell line development (CLD) for biotherapeutics is a time- and resource-intensive process requiring the isolation and screening of large numbers of clones to identify high producers. Novel methods aimed at enhancing cell line screening efficiency using markers predictive of productivity early in the CLD process are needed to reliably generate high-yielding cell lines. To enable efficient and selective isolation of antibody expressing Chinese hamster ovary cells by fluorescence-activated cell sorting, we developed a strategy for the expression of antibodies containing a switchable membrane-associated domain to anchor an antibody to the membrane of the expressing cell. The switchable nature of the membrane domain is governed by the function of an orthogonal aminoacyl transfer RNA synthetase/tRNApyl pair, which directs a nonnatural amino acid (nnAA) to an amber codon encoded between the antibody and the membrane anchor. The process is “switchable” in response to nnAA in the medium, enabling a rapid transition between the surface display and secretion. We demonstrate that the level of cell surface display correlates with productivity and provides a method for enriching phenotypically stable high-producer cells. The strategy provides a means for selecting high-producing cells with potential applications to multiple biotherapeutic protein formats.