T7 Phage Display cDNA Library Research Articles

Detection of Cystic Fibrosis Serological Biomarkers Using a T7 Phage Display Library

Cystic fibrosis (CF) is an autosomal recessive disorder affecting the cystic fibrosis transmembrane conductance regulator (CFTR). CF is characterized by repeated lung infections leading to respiratory failure. Using a high-throughput method, we developed a T7 phage display cDNA library derived from mRNA isolated from bronchoalveolar lavage (BAL) cells and leukocytes of sarcoidosis patients. This library was biopanned to obtain 1070 potential antigens. A microarray platform was constructed and immunoscreened with sera from healthy (n = 49), lung cancer (LC) (n = 31) and CF (n = 31) subjects. We built 1,000 naïve Bayes models on the training sets. We selected the top 20 frequently significant clones ranked with student t-test discriminating CF antigens from healthy controls and LC at a False Discovery Rate (FDR) < 0.01. The performances of the models were validated on an independent validation set. The mean of the area under the receiver operating characteristic (ROC) curve for the classifiers was 0.973 with a sensitivity of 0.999 and specificity of 0.959. Finally, we identified CF specific clones that correlate highly with sweat chloride test, BMI, and FEV1% predicted values. For the first time, we show that CF specific serological biomarkers can be identified through immunocreenings of a T7 phage display library with high accuracy, which may have utility in development of molecular therapy.

Identification of UQCRB as an oxymatrine recognizing protein using a T7 phage display screen

Ethnopharmacological relevanceSophora flavescens Aiton (Radix Sophorae Flavescentis, Kushen) is used in traditional Chinese medicine to treat chronic hepatitis B (CHB), and has the ability to clear heat and dampness from the body. Oxymatrine is one of the major bioactive compounds extracted from Sophora flavescens Aiton and constitutes more than 90% of the oxymatrine injection commonly used for CHB treatment in clinics in China. Aim of the studyWe aim to analyze the protein binding target of oxymatrine in treating CHB by screening a T7 phage display cDNA library of human CHB and examine the biochemistry of protein-ligand binding between oxymatrine and its ligands. Materials and methodsA T7 phage cDNA library of human CHB was biopanned by affinity selection using oxymatrine as bait. The interaction of oxymatrine with its candidate binding protein was investigated by affinity assay, molecular docking, Isothermal Titration Calorimetry (ITC) and Surface Plasmon Resonance (SPR). ResultsA library of potential oxymatrine binding peptides was generated. Ubiquinol-cytochrome c reductase binding protein (UQCRB) was one of the candidate binding proteins of oxymatrine. UQCRB-displaying T7 phage binding numbers in the oxymatrine group were significantly higher than that in the control group, biotin group, and matrine group (p<0.05 or p<0.01). Three-dimensional structure modeling of the UQCRB with oxymatrine showed that their binding interfaces matched and oxymatrine inserted into a deeper pocket of UQCRB, which mainly involved amino acid residues Tyr21, Arg33, Tyr83, Glu84, Asp86, Pro88, and Glu91. The binding affinity constant (Kb) from SPR was 4.2mM. The Kb from ITC experiment was 3.9mM and stoichiometry was fixed as 1, which fit very well with the result of SPR. The binding of oxymatrine to UQCRB was driven by strong enthalpy forces such as hydrogen bonds and polar interactions as the heat released was about 157kcal/mol and ΔG was less than zero. ConclusionsIn this study, using the T7 phage display system, we have identified UQCRB as a direct binding protein of oxymatrine. Furthermore, the specificity and molecular interaction of oxymatrine with UQCRB were also determined. The binding of UQCRB to oxymatrine suggests that UQCRB is a potential target of oxymatrine in treating CHB. These results provide new understanding into the mechanism of oxymatrine and insights into the strategy on the treatment of CHB.

Characterization and functional analysis of Trichinella spiralis Nudix hydrolase

Trichinella spiralis Nudix hydrolase (TsNd) was identified by screening a T7 phage display cDNA library from T. spiralis intestinal infective larvae (IIL), and vaccination of mice with recombinant TsNd protein (rTsNd) or TsNd DNA vaccine produced a partial protective immunity. The aim of this study was to identify the characteristics and biological functions of TsNd in the process of invasion and development of T. spiralis larvae. Transcription and expression of TsNd gene at all developmental stages of T. spiralis were observed by qPCR and immunofluorescent test (IFT). The rTsNd had the Nd enzymatic activity to dGTP, NAD, NADP and CoA. Its kinetic properties on the preferred substrate dGTP were calculated, and the Vmax, Km, and kcat/Km values at pH 8.0 were 3.19 μM min−1 μg−1, 370 μM, and 144 s−1 M−1, respectively, in reaction matrix containing 5 mM Zn2+ and 2 mM DTT. The rTsNd was active from 25 °C to 50 °C, with optimal activity at 37 °C. rTsNd was able to bind specifically to mouse intestinal epithelial cells (IECs) and promoted the larval invasion of IECs, whereas anti-rTsNd antibodies inhibited the larval invasion of IECs in a dose-dependent manner. Anti-rTsNd antibodies could kill T. spiralis infective larvae by an ADCC-mediated mechanism. Our results showed that the rTsNd protein was able to interact with host IECs, had the Nudix hydrolasing activity and the enzymatic activity appeared to be essential indispensable for the T. spiralis larval invasion, development and survival in host.

Development of a T7 Phage Display Library to Detect Sarcoidosis and Tuberculosis by a Panel of Novel Antigens

Sarcoidosis is a granulomatous inflammatory disease, diagnosed through tissue biopsy of involved organs in the absence of other causes such as tuberculosis (TB). No specific serologic test is available to diagnose and differentiate sarcoidosis from TB. Using a high throughput method, we developed a T7 phage display cDNA library derived from mRNA isolated from bronchoalveolar lavage (BAL) cells and leukocytes of sarcoidosis patients. This complex cDNA library was biopanned to obtain 1152 potential sarcoidosis antigens and a microarray was constructed to immunoscreen two different sets of sera from healthy controls and sarcoidosis. Meta-analysis identified 259 discriminating sarcoidosis antigens, and multivariate analysis identified 32 antigens with a sensitivity of 89% and a specificity of 83% to classify sarcoidosis from healthy controls. Additionally, interrogating the same microarray platform with sera from subjects with TB, we identified 50 clones that distinguish between TB, sarcoidosis and healthy controls. The top 10 sarcoidosis and TB specific clones were sequenced and homologies were searched in the public database revealing unique epitopes and mimotopes in each group. Here, we show for the first time that immunoscreenings of a library derived from sarcoidosis tissue differentiates between sarcoidosis and tuberculosis antigens. These novel biomarkers can improve diagnosis of sarcoidosis and TB, and may aid to develop or evaluate a TB vaccine.

Combination of phage display and SEREX for screening early lung cancer associated antigens

To screen out effective lung cancer associated antigens for early diagnosis in order to improve the level of early diagnosis. A T7 phage display cDNA library of human early lung cancer was developed. And then differential phage clones were picked out to be sequenced and bioinformatically analyzed. With the 8 screened differential phage clones a lung cancer associated antigen microarray was established to evaluate the single or combined roles of all the selected antigens in the diagnosis of lung cancer by the reaction of the antigens plus serum from normal subjects and patients with lung cancer, respectively. The titer of the constructed cDNA library was 3.71×10 (6); pfu/ml and the number of phage was 1.11×10 (6); pfu, with a recombination rate of cDNA library over 90%. Nine differential phage clones were initially screened out, but the genes of two antigens (A42 and A83) were found the same. Bioinformatics analyses showed that the genes of the 8 antigens were known before and they were all proven to be related with tumor except A64. The positive reaction rates of the 8 antigens with serum from lung cancer patients were significantly higher than that with serum from normal subjects (Ps<0.05). When keeping specificity no less than 60%, the sensitivity of each antigen in predicting lung cancer alone was under 70% and the areas under curve (AUC) of the antigens were all under 0.8. However, when all the antigens were combined to detect lung cancer, the sensitivity and specificity was 90.8% and 94.1%, respectively, and AUC reached up to 0.969. A T7 phage display cDNA library with a good quality of capacity, recombination rate and representativeness of human early lung cancer was successfully developed, and 8 lung cancer associated antigens were screened out. A combination of the 8 antigens can greatly improve their value to diagnose lung cancer with a higher sensitivity and specificity (both above 90%)．

Translationally Controlled Tumor Protein, a Dual Functional Protein Involved in the Immune Response of the Silkworm, Bombyx mori

Insect gut immunity is the first line of defense against oral infection. Although a few immune-related molecules in insect intestine has been identified by genomics or proteomics approach with comparison to well-studied tissues, such as hemolymph or fat body, our knowledge about the molecular mechanism underlying the gut immunity which would involve a variety of unidentified molecules is still limited. To uncover additional molecules that might take part in pathogen recognition, signal transduction or immune regulation in insect intestine, a T7 phage display cDNA library of the silkworm midgut is constructed. By use of different ligands for biopanning, Translationally Controlled Tumor Protein (TCTP) has been selected. BmTCTP is produced in intestinal epithelial cells and released into the gut lumen. The protein level of BmTCTP increases at the early time points during oral microbial infection and declines afterwards. In vitro binding assay confirms its activity as a multi-ligand binding molecule and it can further function as an opsonin that promotes the phagocytosis of microorganisms. Moreover, it can induce the production of anti-microbial peptide via a signaling pathway in which ERK is required and a dynamic tyrosine phosphorylation of certain cytoplasmic membrane protein. Taken together, our results characterize BmTCTP as a dual-functional protein involved in both the cellular and the humoral immune response of the silkworm, Bombyx mori.

Subtractive phage display technology identifies zebrafish marcksb that is required for gastrulation

In the present study, we used a phage display technique to screen differentially expressed proteins from zebrafish post-gastrula embryos. With a subtractive screening approach, 6 types of single-chain Fv fragments (scFvs) were screened out from an scFv antibody phage display library by biopanning against zebrafish embryonic homogenate. Four scFv fragments (scFv1, scFv3, scFv4 and scFv6) showed significantly stronger binding to the tailbud embryos than to the 30%-epiboly embryos. A T7 phage display cDNA library was constructed from zebrafish tailbud embryos and used to identify the antigens potentially recognized by scFv1, which showed the highest frequency and strongest binding against the tailbud embryos. We acquired 4 candidate epitopes using scFv1 and the corresponding genes showed significantly higher expression levels at tailbud stage than at 30%-epiboly. The most potent epitope of scFv1 was the clone scFv1-2, which showed strong homology to zebrafish myristoylated alanine-rich C-kinase substrate b (Marcksb). Western blot analysis confirmed the high expression of marcksb in the post-gastrula embryos, and the endogenous expression of Marcksb was interfered by injection of scFv1. Zebrafish marcksb showed dynamic expression patterns during embryonic development. Knockdown of marcksb strongly affected gastrulation movements. Moreover, we revealed that zebrafish marcksb is required for cell membrane protrusion and F-actin alignment. Thus, our study uncovered 4 types of scFvs binding to zebrafish post-gastrula embryos, and the epitope of scFv1 was found to be required for normal gastrulation of zebrafish. To our knowledge, this was the first attempt to combine phage display technique with the embryonic and developmental study of vertebrates, and we were able to identify zebrafish marcksb that was required for gastrulation.

Construction and use of a Trichinella spiralis phage display library to identify the interactions between parasite and host enterocytes

Although it has been known for many years that Trichinella spiralis initiates infection by penetrating the columnar epithelium of the small intestine, the mechanisms by which T. spiralis infective larvae recognize and invade the intestinal epithelial cells (IECs) are unknown. It is speculated that the molecular interactions between the parasite and host enterocytes may mediate the recognition and invasion of IECs by T. spiralis. However, no Trichinella proteins that interact with the enterocytes have been identified previously. The aim of this study was to identify Trichinella proteins that bind to IECs by screening a T7 phage display cDNA library constructed using messenger RNA from T. spiralis intestinal infective larvae. Following five rounds of biopanning, sequencing, and bioinformatics analysis, ten T. spiralis proteins (Tsp1-Tsp10) with significant binding to normal mouse IECs were identified. The results of the protein classification showed that six proteins (Tsp1, calcium-transporting ATPase 2 protein; Tsp4, ovochymase-1; Tsp6, T-complex protein 1 subunit eta; Tsp7, glycosyl hydrolase family 47; Tsp8, DNA replication licensing factor MCM3; and Tsp10, nudix hydrolase) of these T. spiralis proteins were annotated with putative molecular functions. Out of the six proteins, five have catalytic activity, four have binding activity, and one has transporter activity. Anti-Tsp10 antibodies prevented the in vitro partial invasion of IECs by infective larvae and the mice immunized with the recombinant phage T7-Tsp10 showed a 62.8% reduction in adult worms following challenge with T. spiralis muscle larvae. Although their biological functions are not yet fully known, these proteins might be related to the larval invasion of host enterocytes. Future experiments will be necessary to ascertain whether these proteins play important roles in the recognition and invasion of host enterocytes. The construction and biopanning of Trichinella phage display libraries provide a novel approach for searching for candidate genes that are related to invasion and for identifying protein interactions between parasite and host.

吸烟者肺癌组织T7噬菌体cDNA文库构建

目的：为筛选吸烟人群中早期肺癌肿瘤标志物，构建吸烟者肺癌组织T7噬菌体展示cDNA文库。方法：用RNeasy Mini Kit提取吸烟者肺癌组织总RNA，分离纯化mRNA，逆转录合成双链cDNA，经末端修饰、定向EcoRI/HindIII接头连接、接头消化，使其两端分别带有EcoRI和HindIII粘性末端。用Mini Column分离cDNA片段，收集300 bp以上的双链cDNA，与T7Select 10-3b载体连接，体外包装后，以BLT5615为受体菌得到吸烟者肺癌组织T7噬菌体展示cDNA文库。结果：经测定，库容为1.35 × 106 pfu，扩增后文库滴度为4.4 × 1010 pfu/ml。PCR鉴定从原始文库中随机挑取的100个噬菌斑，重组率为97%，重组体中91%的插入片段长度>300 bp。结论：成功构建了吸烟者肺癌组织T7噬菌体cDNA文库，为下一步筛选吸烟人群中早期肺癌肿瘤标志物奠定基础。 Objective: To screen tumor markers of smokers, the T7 phage display cDNA library from the lung cancer of smokers was constructed. Methods: The mRNA was isolated from total RNA extracted from the lung cancer of smokers by RNeasy Mini Kit, and was used to synthesize double strain (ds) cDNA by the reverse transcription. Then the directional EcoRI/HindIII linkers were liquated into the ends of ds cDNA and the ds cDNA was further digested with EcoRI and HindIII, which resulted in ds cDNA with EcoRI and HindIII ends. The digested ds cDNA fragments longer than 300 bp in length were fractionated by Mini Column, and then liquated into the T7 Select 10-3b vertor with EcoRI and HindIII ends. After packaging in vitro, the T7 Select 10-3b vertor was tansformed into BLT5615 to construct the T7 phage display cDNA library. Results: Analysis showed that the library contained 1.35 × 106 clones and the titer of the applied library was 4.4 × 1010 pfu/ml. The PCR identification results of 100 clones picked at random showed that 97% clones were recombinant and 91% of recombinant clones contained cDNA fragments longer than 300 bp in length. Conclusion: A T7 phage display cDNA library from the lung cancer of smokers is successfully constructed.

Protein-tyrosine Phosphatase SHP2 Contributes to GDNF Neurotrophic Activity through Direct Binding to Phospho-Tyr687 in the RET Receptor Tyrosine Kinase

The signaling mechanisms by which neurotrophic receptors regulate neuronal survival and axonal growth are still incompletely understood. In the receptor tyrosine kinase RET, a receptor for GDNF (glial cell line-derived neurotrophic factor), the functions of the majority of tyrosine residues that become phosphorylated are still unknown. Here we have identified the protein-tyrosine phosphatase SHP2 as a novel direct interactor of RET and the first effector known to bind to phosphorylated Tyr(687) in the juxtamembrane region of the receptor. We show that SHP2 is recruited to RET upon ligand binding in a cooperative fashion, such that both interaction with Tyr(687) and association with components of the Tyr(1062) signaling complex are required for stable recruitment of SHP2 to the receptor. SHP2 recruitment contributes to the ability of RET to activate the PI3K/AKT pathway and promote survival and neurite outgrowth in primary neurons. Furthermore, we find that activation of protein kinase A (PKA) by forskolin reduces the recruitment of SHP2 to RET and negatively affects ligand-mediated neurite outgrowth. In agreement with this, mutation of Ser(696), a known PKA phosphorylation site in RET, enhances SHP2 binding to the receptor and eliminates the effect of forskolin on ligand-induced outgrowth. Together, these findings establish SHP2 as a novel positive regulator of the neurotrophic activities of RET and reveal Tyr(687) as a critical platform for integration of RET and PKA signals. We anticipate that several other phosphotyrosines of unknown function in neuronal receptor tyrosine kinases will also support similar regulatory functions.

Identification of NCAM that interacts with the PHE-CoV spike protein

BackgroundThe spike proteins of coronaviruses associate with cellular molecules to mediate infection of their target cells. The characterization of cellular proteins required for virus infection is essential for understanding viral life cycles and may provide cellular targets for antiviral therapies.ResultsWe identified Neural Cell Adhesion Molecule (NCAM) as a novel interacting partner of the PHE-CoV S protein. A T7 phage display cDNA library from N2a cells was constructed, and the library was screened with the soluble PHE-CoV S glycoproteins. We used a coimmunoprecipitation assay to show that only the NCAM was a binding partner of spike protein. We found that a soluble form of anti-NCAM antibody blocked association of the PHE-CoV with N2a cells. Furthermore, double-stranded siRNA targeted against NCAM inhibited PHE-CoV infection.ConclusionsA novel interaction was identified between NCAM and spike protein and this association is critical during PHE-CoV infection.

Construction and quality identification of T7 recombination expression cDNA library form human lung cancer

Objective Currently, only a limited numbers of tumor markers for non small lung cancer (NSCLC) diagnosis, new biomarker, such as serum autoantibodies may improve the early detection of lung cancer. Our objective is construction human lung squamous carcinoma and adenocarcinoma T7 phage display cDNA library from the tissues of NSCLC patients.

Construction of a t7 human lung cancer cDNA library.

Currently, only a limited numbers of tumor markers for non small lung cancer (NSCLC) diagnosis, new biomarker, such as serum autoantibody may improve the early detection of lung cancer. Our objective is construction human lung squamous carcinoma and adenocarcinoma T7 phage display cDNA library from the tissues of NSCLC patients. mRNA was isolated from a pool of total RNA extract from NSCLC tissues obtained from 5 adenocarcinomas and 5 squamous carcinomas, and then mRNA was reverse transcribed into double stranded cDNA. After digestion, the cDNA was inserted into T7Select 10-3 vector. The phage display cDNA library was constructed by package reaction in vitro and plate proliferation. Plaque assay and PCR were used to evaluate the library. Two T7 phage display cDNA library were established. Plaque assay show the titer of lung squamas carcinoma library was 1.8*10(6) pfu, and the adenocarcinoma library was 5*10(6) pfu. The phage titer of the amplified library were 3.2*10(10) pfu/mL and 2.5*10(10) pfu/mL. PCR amplification of random plaque show insert ratio were 100% (24/24) in adenocarcinoma library and 95.8% in human lung squamas carcinoma library (23/24). Insert range from 300 bp to 1 500 bp. Two phage display cDNA library from NSCLC were constructed.

In vivo selection of inflammation markers on leukocytes in ischemic hearts

Loss of function of endothelial cells promotes an inflammation reaction, which induces the expression of inflammation-specific surface proteins. Adhesion molecules and chemotactic factors mediate the entry of leukocytes into the artery wall. Here, we attempt to identify genes expressing cell surface markers involved in the reaction of endothelial cells to injury. For this purpose, we have generated a T7 phage display cDNA library from maturated bone marrow cells containing about 25% monocytes taken from healthy human donors. It has been shown previously that during myocardial ischemia-reperfusion injury the myocardium and endothelium undergo an inflammatory-like response. Thus, as a model we used Langendorff preparations of isolated mouse hearts that are subjected to ischemic stopped-flow conditions followed by reperfusion. After several rounds of binding of the phage display library to ischemic and healthy hearts we successfully enriched for phages, which bind specifically to ischemic hearts. The selected phages have been isolated and several clones of both known and novel genes have been identified. Conclusion Identifying novel leukocyte inflammation markers as well as their binding partners on endothelial cells should provide insight into the mechanisms of interaction between leukocytes and endothelial cells during inflammation reactions. This might lead to the development of drugs preventing ischemic reperfusion injury. Clinical Pharmacology & Therapeutics (2005) 77, P65–P65; doi: 10.1016/j.clpt.2004.12.139

Identification of immunogenic antigens using a phage-displayed cDNA library from an invasive ductal breast carcinoma tumour.

The identification of immunogenic antigens for serological testing and vaccine development is a major challenge facing cancer immunology research. To study the humoral immune response in patients with breast cancer, a T7 phage display cDNA library from an invasive ductal breast carcinoma was panned on patient serum IgG antibodies. By monitoring the selection with an immunoscreening technique, positive phage-displayed cDNA products reacting with breast cancer patient IgG antibodies were selected. Sequence analysis identified immunogenic antigens such as the cytochrome oxidase I, sp100 and Ran GTPase activating protein. Additionally, immunogenic uncharacterized gene products were also identified. Both the known and unknown immunoselected gene products should offer an additional source for cancer gene discovery for diagnostic testing and vaccine development.

Structural reliability assessment and large scale testing: Lucia, A. C. Comm. Eur. Communities Report No 12274 1989 pp437–453

Trichinella spiralis Nudix hydrolase (TsNd) was identified by screening a T7 phage display cDNA library from T. spiralis intestinal infective larvae (IIL), and vaccination of mice with recombinant TsNd protein (rTsNd) or TsNd DNA vaccine produced a partial protective immunity. The aim of this study was to identify the characteristics and biological functions of TsNd in the process of invasion and development of T. spiralis larvae. Transcription and expression of TsNd gene at all developmental stages of T. spiralis were observed by qPCR and immunofluorescent test (IFT). The rTsNd had the Nd enzymatic activity to dGTP, NAD, NADP and CoA. Its kinetic properties on the preferred substrate dGTP were calculated, and the Vmax, Km, and kcat/Km values at pH 8.0 were 3.19 μM min−1 μg−1, 370 μM, and 144 s−1 M−1, respectively, in reaction matrix containing 5 mM Zn2+ and 2 mM DTT. The rTsNd was active from 25 °C to 50 °C, with optimal activity at 37 °C. rTsNd was able to bind specifically to mouse intestinal epithelial cells (IECs) and promoted the larval invasion of IECs, whereas anti-rTsNd antibodies inhibited the larval invasion of IECs in a dose-dependent manner. Anti-rTsNd antibodies could kill T. spiralis infective larvae by an ADCC-mediated mechanism. Our results showed that the rTsNd protein was able to interact with host IECs, had the Nudix hydrolasing activity and the enzymatic activity appeared to be essential indispensable for the T. spiralis larval invasion, development and survival in host.