A rapid and economic in-house DNA purification method using glass syringe filters

Background

Purity, yield, speed and cost are important considerations in plasmid purification, but it is difficult to achieve all of these at the same time. Currently, there are many protocols and kits for DNA purification, however none maximize all four considerations.

Methodology/Principal Findings

We now describe a fast, efficient and economic in-house protocol for plasmid preparation using glass syringe filters. Plasmid yield and quality as determined by enzyme digestion and transfection efficiency were equivalent to the expensive commercial kits. Importantly, the time required for purification was much less than that required using a commercial kit.

Conclusions/Significance

This method provides DNA yield and quality similar to that obtained with commercial kits, but is more rapid and less costly.

Structure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine

A double mutant of human purine nucleoside phosphorylase (hDM) with the amino acid mutations Glu201Gln:Asn243Asp cleaves adenosine-based prodrugs to their corresponding cytotoxic drugs. When fused to an anti-tumor targeting component, hDM is targeted to tumor cells, where it effectively catalyzes phosphorolysis of the prodrug, 2-fluoro-2'-deoxyadenosine (F-dAdo) to the cytotoxic drug, 2-fluoroadenine (F-Ade). This cytotoxicity should be restricted only to the tumor microenvironment, because the endogenously expressed wild type enzyme cannot use adenosine-based prodrugs as substrates. To gain insight into the interaction of hDM with F-dAdo, we have determined the crystal structures of hDM with F-dAdo and F-Ade. The structures reveal that despite the two mutations, the overall fold of hDM is nearly identical to the wild type enzyme. Importantly, the residues Gln201 and Asp243 introduced by the mutation form hydrogen bond contacts with F-dAdo that result in its binding and catalysis. Comparison of substrate and product complexes suggest that the side chains of Gln201 and Asp243 as well as the purine base rotate during catalysis possibly facilitating cleavage of the glycosidic bond. The two structures suggest why hDM, unlike the wild-type enzyme, can utilize F-dAdo as substrate. More importantly, they provide a critical foundation for further optimization of cleavage of adenosine-based prodrugs, such as F-dAdo by mutants of human purine nucleoside phosphorylase.

Humanized ADEPT comprised of an engineered human purine nucleoside phosphorylase and a tumor targeting peptide for treatment of cancer

Immunogenicity caused by the use of nonhuman enzymes in antibody-directed enzyme prodrug therapy has limited its clinical application. To overcome this problem, we have developed a mutant human purine nucleoside phosphorylase, which, unlike the wild-type enzyme, accepts (deoxy)adenosine-based prodrugs as substrates. Among the different mutants of human purine nucleoside phosphorylase tested, a double mutant with amino acid substitutions E201Q:N243D (hDM) is the most efficient in cleaving (deoxy)adenosine-based prodrugs. Although hDM is capable of using multiple prodrugs as substrates, it is most effective at cleaving 2-fluoro-2'-deoxyadenosine to a cytotoxic drug. To target hDM to the tumor site, the enzyme was fused to an anti-HER-2/neu peptide mimetic (AHNP). Treatment of HER-2/neu-expressing tumor cells with hDM-AHNP results in cellular localization of enzyme activity. As a consequence, harmless prodrug is converted to a cytotoxic drug in the vicinity of the tumor cells, resulting in tumor cell apoptosis. Unlike the nonhuman enzymes, the hDM should have minimal immunogenicity when used in antibody-directed enzyme prodrug therapy, thus providing a novel promising therapeutic agent for the treatment of tumors.

N-terminal domain-deleted mu transposase exhibits increased transposition activity with low target site preference in modified buffers

BACKGROUND

Transposition using MuA and the Mu-transposon is frequently used for insertional and deletional mutagenesis and to introduce primer sequences into DNA of unknown sequence. However, mutagenesis studies are often limited by the number of transposition events taking place within a small target sequence. Although the intrinsic target site preference of MuA is low, it nevertheless may limit the recovery of desired events.

METHODS

In the current study, we have compared the transposition activity of wild-type, C-terminally deleted, N-terminally deleted and both C- and N-terminally deleted MuA.

RESULTS

We found that N-terminally deleted MuA was most active with an about sevenfold increase in transposition efficiency compared to wild-type. In addition, we identified a novel reaction condition in which the transposition activity of N-terminally deleted MuA was increased about 45-fold.

CONCLUSION

The use of the N-terminally deleted MuA with the newly established condition enhanced the relative transposition activity about 280-fold compared to that of wild-type MuA with the conventional buffer. In addition, the optimized buffer decreased the target site preference of N-terminally deleted MuA resulting in a more even distribution of integration events throughout the target gene.

Transformation of E. coli by electroporation

Using electroporation to transform Escherichia coli results in transformation efficiencies greater than can be obtained using the best chemical methods. It is easy to obtain transformation efficiencies 10(8) per milligram DNA and efficiencies of 10(10) have been reported. This appendix describes a procedure for electroporation that can be used to transform many different types of bacteria.

Cloning, expression, and modification of antibody V regions

Cloned variable (V) regions of antibodies can be expressed joined to any constant (C) region, from either the same or a different species. The resulting antibodies will have the desired associated effector functions. Chimeric antibodies obtained by joining murine V regions to human C regions should have decreased immunogenicity in humans. The process of complementarity determining region (CDR) grafting, in which the CDRs from an antibody of one species are transferred to the framework regions of another species, constitutes a further modification of this approach. The protocols presented in this unit are designed to permit PCR-based cloning of heavy and light chain V regions. This is an advanced molecular biology protocol and should be employed only by investigators who are sufficiently skilled and experienced.

Proteases from Schistosoma mansoni cercariae cleave IgE at solvent exposed interdomain regions

Parasitic infections, including schistosomiasis, are associated with high titres of specific and non-specific IgE antibody, and many reports show an in vitro role for IgE in parasite killing. Despite an active immune response, schistosomes survive for long periods in the human bloodstream, implying that the parasite is able to overcome or evade the IgE response mounted against it. One such mechanism is through cleavage of IgE into non-functional fragments by potent parasite derived enzymes. Using domain swap antibodies, recombinant Fcepsilon, and C-terminally tagged Cepsilon4 domains, we have narrowed down the principal cleavage sites to the Cepsilon2/Cepsilon3 and Cepsilon3/Cepsilon4 interdomain region of the IgE-Fc. Two serine proteases, one chymotrypsin-like and the second trypsin-like, have been proposed to be involved. Inhibition assays using selective inhibitors confirmed that both proteases contribute to Fc cleavage, although the chymotrypsin-like enzyme makes the greater contribution. Protein sequencing of IgE fragments cleaved by highly pure preparations of the chymotrypsin-like enzyme revealed that cleavage also occurred post Lys residues within kappa light chain dimers (LELK/GA). Related sequences are found in myosin, thrombospondin, collagen and actin-related proteins; macromolecules present in the skin and through which cercariae must penetrate to initiate an infection. Chemical knockout experiments using specific inhibitors and chromogenic substrates allowed us to show that the trypsin-like enzyme was responsible for light chain cleavage. The finding that pathogenic proteases can cleave the Fc of IgE may provide a useful biochemical tool for the further analysis of IgE structure. Indeed, the finding may raise new possibilities for treatment of IgE-mediated allergic reactions mediated through Fcepsilon-receptors.

Targeting IFN-alpha to B cell lymphoma by a tumor-specific antibody elicits potent antitumor activities

IFN-alpha, a cytokine crucial for the innate immune response, also demonstrates antitumor activity. However, use of IFN-alpha as an anticancer drug is hampered by its short half-life and toxicity. One approach to improving IFN-alpha's therapeutic index is to increase its half-life and tumor localization by fusing it to a tumor-specific Ab. In the present study, we constructed a fusion protein consisting of anti-HER2/neu-IgG3 and IFN-alpha (anti-HER2/neu-IgG3-IFN-alpha) and investigated its effect on a murine B cell lymphoma, 38C13, expressing human HER2/neu. Anti-HER2/neu-IgG3-IFN-alpha exhibited potent inhibition of 38C13/HER2 tumor growth in vivo. Administration of three daily 1-microg doses of anti-HER2/neu-IgG3-IFN-alpha beginning 1 day after tumor challenge resulted in 88% of the mice remaining tumor free. Remarkably, anti-HER2/neu-IgG3-IFN-alpha demonstrated potent activity against established 38C13/HER2 tumors, with complete tumor remission observed in 38% of the mice treated with three daily doses of 5 microg of the fusion protein (p = 0.0001). Ab-mediated targeting of IFN-alpha induced growth arrest and apoptosis of lymphoma cells contributing to the antitumor effect. The fusion protein also had a longer in vivo half-life than rIFN-alpha. These results suggest that IFN-alpha Ab fusion proteins may be effective in the treatment of B cell lymphoma.

Incomplete assembly of IgA2m(2) in Chinese hamster ovary cells

Myeloma and Chinese hamster ovary (CHO) cells are frequently used for the production of recombinant antibodies. With increasing interest in producing recombinant IgA for protection against infectious agents, it is essential to characterize the IgA produced in these cells. Here we show that while myeloma cells secrete IgA2m(2) predominantly as H(2)L(2), CHO cells secrete H(2)L and H(2) in addition to fully assembled H(2)L(2). When the CHO cells also synthesize J chain and secretory component (SC), polymeric IgA and secretory IgA in which SC is disulfide bonded to the polymeric IgA are produced. Blocking cysteines on purified IgA2m(2) protein by alkylating with iodoacetamide stabilizes the disulfide bonds between the H and L chains suggesting that the disulfide bonds between H and L chains are unstable. Taken together our results suggest that the covalent assembly of IgA2m(2) is different in myeloma and CHO cells.

Targeting, imaging, and therapy using a humanized antiprostate stem cell antigen (PSCA) antibody

The murine 1G8 (micro1G8) monoclonal antibody directed against prostate stem cell antigen (PSCA) prevents prostate tumor establishment, growth, and metastasis in murine models. To further delineate in vivo targeting properties, micro1G8 was radiolabeled with In-111 and evaluated in nude mice bearing PC3-PSCA xenografts. Tumor activity ranged from 11.8% to 17.1% injected dose per gram (ID/g) at 24 to 96 hours postinjection. To extend the clinical applicability of micro1G8, a chimeric 1G8 antibody was produced that exhibited specific binding to PSCA and significant antitumor effect over micro1G8 in established LAPC-9 prostate cancer xenografts (P=0.0014). However, low expression yields and instability prompted us to humanize 1G8 by grafting the complementary determining regions onto the stable, human Fv framework of anti-p185 4D5v8 (trastuzumab). Two humanized 1G8 (hu1G8) versions (A and B) that differed in the number of murine residues present in the C-terminal half of CDR-H2, were produced. Biacore binding studies demonstrated affinities of 1.47 nM for micro1G8 and 3.74 nM for hu2B3-B, representing a 2.5-fold reduction. Tumor targeting of version B radioiodinated with I was evaluated by serial microPET imaging. Specific tumor targeting of I-hu1G8-B to PC3-PSCA [12.7 (+/-1.6)% ID/g at 94 h] and LAPC-9 [6.6 (+/-0.9)% ID/g at 168 h) xenografts was observed. Inhibition of tumor growth by hu1G8-B was demonstrated in mice bearing low-expressing SW-780-PSCA bladder carcinoma xenografts. In this model, the micro1G8 was ineffective, whereas the hu1G8-B exhibited approximately 50% inhibitory effect. These data support further development of hu1G8 anti-PSCA antibody for targeted imaging and therapy for tumors of urogenital origin.

Human immunoglobulin G2 (IgG2) and IgG4, but not IgG1 or IgG3, protect mice against Cryptococcus neoformans infection

The encapsulated yeast Cryptococcus neoformans is a significant cause of meningitis and death in patients with AIDS. Some murine monoclonal antibodies (MAbs) against the glucuronoxylomannan (GXM) component of the C. neoformans capsular polysaccharide can prolong the lives of infected mice, while others have no effect or can even shorten survival. To date, no one has systematically compared the efficacies of antibodies with the same variable regions and different human constant regions with their unique combination of effector functions in providing protection against murine C. neoformans infection. In the present study, we examined the efficacies of anti-GXM MAbs of the four human immunoglobulin G (IgG) subclasses, which have identical variable regions but differ in their capacities to bind the three types of Fc receptors for IgG (FcgammaR), their abilities to activate complement, and their half-lives. IgG2 and IgG4 anti-GXM prolonged the lives of infected BALB/c mice, IgG3 anti-GXM did not affect animal survival, while mice treated with IgG1 anti-GXM died earlier than mice treated with phosphate-buffered saline or irrelevant isotype-matched MAbs. All MAbs decreased serum GXM in infected animals. Effector pathways traditionally believed to be important in defense against microbes, such as opsonophagocytosis and complement binding, negatively correlated with antibody efficacy. It is generally accepted that human IgG1 has the most favorable combination of effector functions for therapeutic use against infections. Therefore, our findings have significant implications for humanization of the mouse IgG1 currently in clinical trials for cryptococcal meningitis and for the design of antibody therapeutics to treat other infectious diseases as well.

Recombinant IgA Antibodies

The production of monoclonal antibodies and the development of recombinant antibody technology have made antibodies one of the largest classes of drugs in development for prophylactic, therapeutic and diagnostic purposes. Currently, all of the Food and Drug Administration (FDA)- approved antibodies are immunoglobulin Gs (IgGs). However, more than 95%of the infections are initiated at the mucosal surfaces, where IgA is the primary immune effector antibody.

The IgD CH1 region contains the binding site for the human respiratory pathogenMoraxella catarrhalis IgD-binding protein MID

The Moraxella catarrhalis IgD-binding protein (MID) has a unique specificity for human IgD, and the sequence with maximal IgD binding is located within the amino acids MID962-1200. In the present paper, we examined the MID binding site on IgD using a series of recombinant Ig. Full-length IgD, IgD F(ab')2, and an IgD F(ab') C290R mutant lacking the inter-heavy-chain cysteine 290 were manufactured. Furthermore, a series of IgD/IgG chimeras were constructed. ELISA, dot blot and flow cytometry were used to study the binding of purified Ig to native MID, recombinant MID962-1200 or to Moraxella with or without MID. MID962-1200 bound both the IgD F(ab')2 and F(ab') C290R, indicating that the binding occurred independently of antibody structure. When amino acids 157-224 of the IgD CH1 region were substituted with IgG sequences, binding by M. catarrhalis or recombinant MID962-1200 was abolished. Subsequent smaller substitutions of IgD CH1 157-224 with IgG sequences led us to conclude that IgD CH1 amino acids 198-206 were crucial for the interaction between MID and IgD.

Molecular events contributing to cell death in malignant human hematopoietic cells elicited by an IgG3-avidin fusion protein targeting the transferrin receptor

We have previously reported that an anti-human transferrin receptor IgG3-avidin fusion protein (anti-hTfR IgG3-Av) inhibits the proliferation of an erythroleukemia-cell line. We have now found that anti-hTfR IgG3-Av also inhibits the proliferation of additional human malignant B and plasma cells. Anti-hTfR IgG3-Av induces internalization and rapid degradation of the TfR. These events can be reproduced in cells treated with anti-hTfR IgG3 cross-linked with a secondary Ab, suggesting that they result from increased TfR cross-linking. Confocal microscopy of cells treated with anti-hTfR IgG3-Av shows that the TfR is directed to an intracellular compartment expressing the lysosomal marker LAMP-1. The degradation of TfR is partially blocked by cysteine protease inhibitors. Furthermore, cells treated with anti-hTfR IgG3-Av exhibit mitochondrial depolarization and activation of caspases 9, 8, and 3. The mitochondrial damage and cell death can be prevented by iron supplementation, but cannot be fully blocked by a pan-caspase inhibitor. These results suggest that anti-hTfR IgG3-Av induces lethal iron deprivation, but the resulting cell death does not solely depend on caspase activation. This report provides insights into the mechanism of cell death induced by anti-TfR Abs such as anti-hTfR IgG3-Av, a molecule that may be useful in the treatment of B-cell malignancies such as multiple myeloma.

Development of new models for the analysis of Fc–FcRn interactions

An important question remains as to which FcRn binding parameters, if any, correlate with the serum half-life of antibodies. In the present study, we used a BIACore surface plasmon resonance (SPR) device to study kinetic properties of antibody binding to FcRn at different pHs and under different binding reaction conditions. The ability of many different models to fit the data was tested. The previous models could not adequately explain all of the data collected. We now present models that have intuitive appeal and fit a broader range of data than previous models. Specifically, the model assumes that there are two forms of FcRn on the BIAcore chip and that, in addition to monomeric IgG, there is some aggregated IgG that can function as ligand. Although this model represents an improvement over previous models, it is still not globally valid for the entire range of data that was collected. Even with these limitations, the model provides a powerful new tool to analyze not only FcRn-IgG interactions but also other complex protein-protein interactions.

Anti-HER2/neu IgG3–(IL-2) and anti-HER2/neu IgG3–(GM-CSF) promote HER2/neu processing and presentation by dendritic cells: Implications in immunotherapy and vaccination strategies

HER2/neu, a transmembrane glycoprotein overexpressed in several types of human cancers, is a potential target for active immunotherapy. However, this protein and especially its extracellular domain (ECD(HER2)), is weakly immunogenic and is poorly processed by dendritic cells (DCs). Previously, we showed that anti-HER2/neu IgG3-(IL-2) and anti-HER2/neu IgG3-(GM-CSF) fusion proteins can enhance the immunogenicity of ECD(HER2) in mice, and that the non-covalent physical association between each antibody fusion proteins and ECD(HER2) was critical to elicit optimal protective immunity against HER2/neu expressing tumors. We now use the professional antigen-presenting DCs to investigate the effect of the antibody fusion protein binding to ECD(HER2) on its trafficking and presentation. We found that when the extracellular domain of HER2/neu fused to ovalbumin (OVA-ECD(HER2)) is bound by HER2/neu-specific antibody-(IL-2) or antibody-(GM-CSF) fusion proteins, the bound antigen is more efficiently processed by murine bone-marrow-derived dendritic cells (BMDCs) and presented to OVA-specific T-cells than the unbound OVA-ECD(HER2). We also found that ECD(HER2) bound by anti-HER2/neu IgG3-(IL-2) is very efficiently internalized and that the internalized ECD(HER2) is not retained in the early endosomal compartments but traffics to the antigen-processing compartments. These results are consistent with our earlier in vivo studies and suggest that both antibody-(IL-2) and antibody-(GM-CSF) fusion proteins can be used to enhance the immune response to poorly immunogenic antigens including tumor-associated antigens (TAAs).

A Trimeric Anti-HER2/neuScFv and Tumor Necrosis Factor-α Fusion Protein Induces HER2/neuSignaling and Facilitates Repair of Injured Epithelia

Tumor necrosis factor (TNF)-alpha genetically fused to the carboxyl terminus of a single-chain Fv (ScFv) antibody specific for the human HER2/neu (anti-HER2/neu ScFv-TNF-alpha) forms a homotrimeric structure that retains both TNF-alpha activity and the ability to bind HER2/neu. In contrast to anti-HER2/neu IgG3, anti-HER2/neu ScFv-TNF-alpha induces potent HER2/neu signaling, activating the downstream mitogen-activated protein kinase (MAPK) and Akt pathways in SKBR3 cells. Activation of MAPK and Akt by anti-HER2/neu ScFv-TNF-alpha inhibited the apoptosis of SKBR3 cells induced by actinomycin D. Remarkably, anti-HER2/neu ScFv-TNF-alpha facilitated the repair of injured epithelia. Accelerated wound healing required binding to HER2/neu but not TNF-alpha activity since anti-HER2/neu ScFv-TNF-alpha (S147Y), containing a mutant TNF-alpha with significantly decreased biological activity, demonstrated equivalent ability to facilitate wound healing and soluble HER2/neu inhibited the effect. These results suggest that trimeric anti-HER2/neu ScFv has the potential to facilitate wound healing. In addition, fusion with TNF-alpha provides a novel approach to producing polymeric antibodies.

Enhanced inhibition of murine tumor and human breast tumor xenografts using targeted delivery of an antibody-endostatin fusion protein

Endostatin can inhibit angiogenesis and tumor growth in mice. A potential limitation of endostatin as an antitumor agent in humans is the short serum half-life of the protein that may decrease effective concentration at the site of tumor and necessitate frequent dosing. In an effort to improve antitumor activity, endostatin was fused to an antibody specific for the tumor-selective HER2 antigen to create an antibody-endostatin fusion protein (anti-HER2 IgG3-endostatin). Normal endostatin rapidly cleared from serum in mice (T(1/2)(2), = 0.6-3.8 hours), whereas anti-HER2 IgG3-endostatin had a prolonged half-life (90% intact; T(1/2)(2), 40.2-44.0 hours). Antigen-specific targeting of anti-HER2 IgG3-endostatin was evaluated in BALB/c mice implanted with CT26 tumors or CT26 tumors engineered to express the HER2 antigen (CT26-HER2). Radio-iodinated anti-HER2 IgG3-endostatin preferentially localized to CT26-HER2 tumors relative to CT26 tumors. Administration of anti-HER2 IgG3-endostatin to mice showed preferential inhibition of CT26-HER2 tumor growth compared with CT26. Anti-HER2 IgG3-endostatin also markedly inhibited the growth of human breast cancer SK-BR-3 xenografts in severe combined immunodeficient mice. Anti-HER2 IgG3-endostatin inhibited tumor growth significantly more effectively than endostatin, anti-HER2 IgG3 antibody, or the combination of antibody and endostatin. CT26-HER2 tumors treated with the endostatin fusion protein had decreased blood vessel density and branching compared with untreated CT26-HER2 or CT26 treated with the fusion protein. The enhanced effectiveness of anti-HER2 IgG3-endostatin may be due to a longer half-life, improved serum stability, and selective targeting of endostatin to tumors, resulting in decreased angiogenesis. Linking of an antiangiogenic protein, such as endostatin, to a targeting antibody represents a promising and versatile approach to antitumor therapy.

Insights into the mechanism of anti-tumor immunity in mice vaccinated with the human HER2/neu extracellular domain plus anti-HER2/neu IgG3-(IL-2) or anti-HER2/neu IgG3-(GM-CSF) fusion protein

In the present study, we demonstrate that a physical association between the extracellular domain of human HER2/neu receptor (ECDHER2) plus anti-HER2/neu IgG3-(IL-2) or anti-HER2/neu IgG3-(GM-CSF) was required to elicit the most effective anti-tumor immune response against a syngeneic tumor expressing rat HER2/neu. Immune effectors including CD4+, CD8+, and NK cells contributed to protection against tumor growth. Vaccinated B-cell deficient mice did not elicit tumor protection, suggesting a critical role for B-cells in a protective immune response. These results provide insights into the mechanisms responsible for the protective tumor immunity elicited when antibody-(IL-2 or GM-CSF) are used as enhancers of vaccines targeting tumor antigens.

Analysis of a family of antibodies with different half-lives in mice fails to find a correlation between affinity for FcRn and serum half-life

In this study we analyzed mouse FcRn binding to different recombinant chimeric antibodies with human constant regions. This system has the advantage that in vivo half-life in animals expressing the receptor can be directly correlated with receptor binding kinetics. The goal was to determine which FcRn binding parameters, if any, correlate with the serum half-life of antibodies. We used a BIAcore surface plasmon resonance (SPR) device to study kinetic properties at different pHs and concentrations. The data were analyzed using a new model, the dual bivalent analyte model (DBVA), which postulates that there are two types of FcRn bound to the chip, one low affinity and one high affinity. In addition, it takes into consideration the possibility that the ligand, immunoglobulin G (IgG), can exist as both monomer and as higher molecular forms. While some antibodies bind to FcRn with different kinetics, including antibodies that differ only by containing the kappa or lambda light chain--a result which itself is unexpected--we cannot identify a single FcRn binding parameter that directly correlates with Ab half-life. Importantly, we demonstrate that some IgGs with higher affinity for FcRn do not have extended in vivo half-lives.

Production of human monoclonal antibody in eggs of chimeric chickens

The tubular gland of the chicken oviduct is an attractive system for protein expression as large quantities of proteins are deposited in the egg, the production of eggs is easily scalable and good manufacturing practices for therapeutics from eggs have been established. Here we examined the ability of upstream and downstream DNA sequences of ovalbumin, a protein produced exclusively in very high quantities in chicken egg white, to drive tissue-specific expression of human mAb in chicken eggs. To accommodate these large regulatory regions, we established and transfected lines of chicken embryonic stem (cES) cells and formed chimeras that express mAb from cES cell-derived tubular gland cells. Eggs from high-grade chimeras contained up to 3 mg of mAb that possesses enhanced antibody-dependent cellular cytotoxicity (ADCC), nonantigenic glycosylation, acceptable half-life, excellent antigen recognition and good rates of internalization.