Generation of sequence-specific, high affinity anti-DNA antibodies

Complexes of DNA with fluorescent dyes are effective reagents for detection of autoimmune antibodies

To date, there are multiple assays developed that detect and quantify antibodies in biofluids. Nevertheless, there is still a lack of simple approaches that specifically detect autoimmune antibodies to double-stranded DNA. Herein we investigate the potential of novel nucleic acid complexes as targets for these antibodies. This is done in a simple, rapid and specific immunofluorescence assay. Specifically, employing 3D nanostructures (DNA origami), we present a new approach in the detection and study of human antibodies to DNA. We demonstrate the detection of anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We tested the most potent non-covalent pairs of DNA and fluorescent dyes. Several complexes showed specific recognition of autoimmune antibodies in human samples of lupus patients using a simple one-step immunofluorescence method. This makes the novel assay developed herein a promising tool for research and point-of-care monitoring of anti-DNA antibodies. Using this method, we for the first time experimentally confirm that the disease-specific autoimmune antibodies are sensitive to the 3D structure of nucleic acids and not only to the nucleotide sequence, as was previously thought.

An anti-DNA antibody prefers damaged dsDNA over native

DNA-protein interactions, including DNA-antibody complexes, have both fundamental and practical significance. In particular, antibodies against double-stranded DNA play an important role in the pathogenesis of autoimmune diseases. Elucidation of structural mechanisms of an antigen recognition and interaction of anti-DNA antibodies provides a basis for understanding the role of DNA-containing immune complexes in human pathologies and for new treatments. Here we used Molecular Dynamic simulations of bimolecular complexes of a segment of dsDNA with a monoclonal anti-DNA antibody's Fab-fragment to obtain detailed structural and physical characteristics of the dynamic intermolecular interactions. Using a computationally modified crystal structure of a Fab-DNA complex (PDB: 3VW3), we studied in silico equilibrium Molecular Dynamics of the Fab-fragment associated with two homologous dsDNA fragments, containing or not containing dimerized thymine, a product of DNA photodamage. The Fab-fragment interactions with the thymine dimer-containing DNA was thermodynamically more stable than with the native DNA. The amino acid residues constituting a paratope and the complementary nucleotide epitopes for both Fab-DNA constructs were identified. Stacking and electrostatic interactions were shown to play the main role in the antibody-dsDNA contacts, while hydrogen bonds were less significant. The aggregate of data show that the chemically modified dsDNA (containing a covalent thymine dimer) has a higher affinity toward the antibody and forms a stronger immune complex. These findings provide a mechanistic insight into formation and properties of the pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus, associated with skin photosensibilization and DNA photodamage.

In situ click chemistry: from small molecule discovery to synthetic antibodies

Advances in the fields of proteomics, molecular imaging, and therapeutics are closely linked to the availability of affinity reagents that selectively recognize their biological targets. Here we present a review of Iterative Peptide In Situ Click Chemistry (IPISC), a novel screening technology for designing peptide multiligands with high affinity and specificity. This technology builds upon in situ click chemistry, a kinetic target-guided synthesis approach where the protein target catalyzes the conjugation of two small molecules, typically through the azide-alkyne Huisgen cycloaddition. Integrating this methodology with solid phase peptide libraries enables the assembly of linear and branched peptide multiligands we refer to as Protein Catalyzed Capture Agents (PCC Agents). The resulting structures can be thought of as analogous to the antigen recognition site of antibodies and serve as antibody replacements in biochemical and cell-based applications. In this review, we discuss the recent progress in ligand design through IPISC and related approaches, focusing on the improvements in affinity and specificity as multiligands are assembled by target-catalyzed peptide conjugation. We compare the IPISC process to small molecule in situ click chemistry with particular emphasis on the advantages and technical challenges of constructing antibody-like PCC Agents.

Selective binding of anti-DNA antibodies to native dsDNA fragments of differing sequence

Systemic autoimmune diseases are characterized by the development of autoantibodies directed against a limited subset of nuclear antigens, including DNA. DNA-specific B cells take up mammalian DNA through their B cell receptor, and this DNA is subsequently transported to an endosomal compartment where it can potentially engage TLR9. We have previously shown that ssDNA-specific B cells preferentially bind to particular DNA sequences, and antibody specificity for short synthetic oligodeoxynucleotides (ODNs). Since CpG-rich DNA, the ligand for TLR9 is found in low abundance in mammalian DNA, we sought to determine whether antibodies derived from DNA-reactive B cells showed binding preference for CpG-rich native dsDNA, and thereby select immunostimulatory DNA for delivery to TLR9. We examined a panel of anti-DNA antibodies for binding to CpG-rich and CpG-poor DNA fragments. We show that a number of anti-DNA antibodies do show preference for binding to certain native dsDNA fragments of differing sequence, but this does not correlate directly with the presence of CpG dinucleotides. An antibody with preference for binding to a fragment containing optimal CpG motifs was able to promote B cell proliferation to this fragment at 10-fold lower antibody concentrations than an antibody that did not selectively bind to this fragment, indicating that antibody binding preference can influence autoreactive B cell responses.

Gene silencing by cell-penetrating, sequence-selective and nucleic-acid hydrolyzing antibodies

Targeting particular mRNAs for degradation is a fascinating approach to achieve gene silencing. Here we describe a new gene silencing tool exploiting a cell-penetrating, nucleic-acid hydrolyzing, single-domain antibody of the light-chain variable domain, 3D8 VL. We generated a synthetic library of 3D8 VL on the yeast surface by randomizing residues located in one of two β-sheets. Using 18-bp single-stranded nucleic acids as target substrates, including the human Her2/neu-targeting sequence, we selected 3D8 VL variants that had ∼100–1000-fold higher affinity and ∼2–5-fold greater selective hydrolyzing activity for target substrates than for off targets. 3D8 VL variants efficiently penetrated into living cells to be accumulated in the cytosol and selectively decreased the amount of target sequence-carrying mRNAs as well as the proteins encoded by these mRNAs with minimal effects on off-target genes. In particular, one 3D8 VL variant targeting the Her2 sequence showed more efficient downregulation of Her2 expression than a small-interfering RNA targeting the same Her2 sequence, resulting in apoptotic cell death of Her2-overexpressing breast cancer cells. Our results demonstrate that cell-penetrating 3D8 VL variants with sequence-selective, nucleic-acid-hydrolyzing activity can selectively degrade target mRNAs in the cytosol, providing a new gene silencing tool mediated by antibody.

Autoreactive B cells discriminate CpG-rich and CpG-poor DNA and this response is modulated by IFN-alpha

Autoreactive B cells are activated by DNA, chromatin, or chromatin-containing immune complexes (ICs) through a mechanism dependent on dual engagement of the BCR and TLR9. We examined the contribution of endogenous DNA sequence elements to this process. DNA sequence can determine both recognition by the BCR and by TLR9. DNA fragments containing CpG islands, a natural source of unmethylated CpG dinucleotides, promote the activation of DNA-reactive B cells derived from BCR transgenic mice as well as DNA-reactive B cells present in the normal repertoire. ICs containing these CpG island fragments are potent ligands for AM14 IgG2a-reactive B cells. In contrast, ICs containing total mammalian DNA, or DNA fragments lacking immunostimulatory motifs, fail to induce B cell proliferation, indicating that BCR crosslinking alone is insufficient to activate low-affinity autoreactive B cells. Importantly, priming B cells with IFN-alpha lowers the BCR activation threshold and relaxes the selectivity for CpG-containing DNA. Taken together, our findings underscore the importance of endogenous CpG-containing DNAs in the TLR9-dependent activation of autoreactive B cells and further identify an important mechanism through which IFN-alpha can contribute to the pathogenesis of systemic lupus erythematosus.

A quasi-spontaneous amyloid route in a DNA binding gene regulatory domain: The papillomavirus HPV16 E2 protein

The DNA binding domain of papillomavirus E2 proteins is at the center of the regulation of gene transcription and replication of the virus. Its unique fold consists of a beta-barrel domain that combines an eight-stranded dimeric beta-barrel core interface with two symmetrical DNA binding alpha-helices and other two helices, packed against the central barrel. Treatment with low amounts of trifluoroethanol readily leads to a mostly beta-sheet oligomeric species, with a loss of near-UV circular dichroism signal and increase in its ANS binding capacity, indicating that buried hydrophobic surfaces become accessible to the solvent. This species subsequently undergoes a slow transition into amyloid aggregates as determined by light scattering and Congo red and thioflavin T binding. Electron microscopy shows short amyloid fibers with a curly aspect as the end product. The amyloid route is completely prevented by addition of stoichiometrical amounts of specific DNA, strongly suggesting that unfolding of the DNA binding alpha-helix is required for the formation of the intermediate. The slow nature of this expanded beta-oligomeric species and the availability of several different conformational probes make it an excellent model for investigating amyloid mechanisms. The mild perturbation required for entering an amyloid route is indicative of a preexisting equilibrium. Oligomerization processes are required for the assembly of transcription initiation and DNA replication machineries, where proteins from different viruses must come together with host cell proteins. The E2 protein is a virus-encoded multifunctional master regulator that may exert one of its multiple functions through its ability to oligomerize.

Specific recognition of a DNA immunogen by its elicited antibody

DNA recognition by antibodies is a key feature of autoimmune diseases, yet model systems with structural information are very limited. The monoclonal antibody ED-10 recognizes one of the strands of the DNA duplex used in the immunogenic complex. Modifications of the 5' end decrease the binding affinity and short oligonucleotides retain high binding affinity. We determined crystal structures for the Fab bound to a 6-mer oligonucleotide containing the specific sequence that raised the antibody and compared it with the unliganded Fab. Only the first two bases from the 5' end (dTdC) display electron density and we observe four key hydrogen bonds at the interface. The thymine ring is stacked between TrpH50 and TrpH95, and the cytosine ring is packed against TyrL32. Upon DNA binding, TyrH97 and TrpH95 rearrange to allow subnanomolar binding affinity, five orders of magnitude higher than other reported complexes, possibly because of having gone through affinity maturation. This structure represents the first bona fide antibody DNA immunogen complex described in atomic detail.

Immunity and autoimmunity induced by polyomaviruses: clinical, experimental and theoretical aspects

In this chapter, polyomaviruses will be presented in an immunological context. Principal observations will be discussed to elucidate humoral and cellular immune responses to different species of the polyomaviruses and to individual viral structural and regulatory proteins. The role of immune responses towards the viruses or their proteins in context of protection against polyomavirus induced tumors will be described. One central aspect of this presentation is the ability of polyomaviruses, and particularly large T-antigen, to terminate immunological tolerance to nucleosomes, DNA and histones. Thus, in the present chapter we will focus on clinical, experimental and theoretical aspects of the immunity to polyomaviruses.

Heavy and Light Chain Variable Single Domains of an Anti-DNA Binding Antibody Hydrolyze Both Double- and Single-stranded DNAs without Sequence Specificity

Anti-DNA antibodies (Abs) are of biomedical interest because they are associated with autoimmune diseases in human and mice. Previously we isolated an anti-DNA monoclonal Ab 3D8 from an autoimmune-prone MRL-lpr/lpr mouse. Here we have characterized DNA binding kinetics and hydrolyzing activities of the recombinant single chain variable fragment (scFv) and the single variable domains of heavy chain (VH) and light chain (VL) using various single-stranded (ss) and double-stranded (ds) DNA substrates. All the Abs bound to both ds- and ssDNAs without significant preferential sequence specificity showing scFv higher affinities (KD = approximately 17-74 nm) than VH (KD = approximately 2.4-8.4 microm) and VL (KD = approximately 3.2-72 microm), and efficiently hydrolyzed both ds- and ssDNAs without sequence specificity in a Mg2+-dependent manner, except for the poor activity of 3D8 scFv for ss-(dT)40. Elucidated crystal structure-based His to Ala mutations on the complementarity determining regions of VH (His-H35 --> Ala) and/or VL (His-L94 --> Ala) of 3D8 scFv significantly inhibited the catalytic activities, indicating that the His residues are involved in the catalytic mechanism of 3D8 scFv. However, the DNA hydrolyzing activities of single domain VH and VL were not affected by the mutations, indicative of their different catalytic mechanisms from that of 3D8 scFv. Our results demonstrate single domain Abs with DNase activities for the first time, which might provide new insights into substrate recognition and catalytic mechanisms of anti-DNA Abs.

Llama Single Domain Antibodies as a Tool for Molecular Mimicry

In camelids, a subset of the immunoglobulins consists of heavy-chain homodimers devoid of light chains, and are thus called heavy-chain IgGs (hcIgGs). Their variable region (VHH) is the smallest antigen-binding fragment possible, and being just one polypeptide chain it is especially suitable for engineering. In particular, camelid single domain antibodies might be very useful for molecular mimicry and anti-idiotypic vaccination. In the present work, we show that llamas immunized with an anti-DNA mouse mAb develop an important anti-Id response. Selection of VHHs by phage display, with specific elution of bound phages with the external antigenic DNA, shows that selected private anti-Id VHHs compete for binding to the external antigen and bear a functional mimicry of the DNA. These results indicate that llama anti-Id single domain antibodies would be an excellent tool for molecular mimicry studies.

Origin and anti-tumor effects of anti-dsDNA autoantibodies in cancer patients and tumor-bearing mice

In the present investigation, we detected anti-dsDNA autoantibodies in cancer patients and modeled the production of anti-dsDNA autoantibodies by inoculating tumors in BALB/c mice. Moreover, induction of anti-dsDNA autoantibodies by immunization with inactivated tumor cells and their DNA indicated that DNA of tumor cells was probably the primary antigen, which was supported by the significantly increasing levels of sera free DNA in cancer patients and tumor-bearing mice. cELISA and indirect immunofluorescence assay showed that the anti-dsDNA autoantibodies could bind to the surface components of tumor cells. In vitro assay showed that immunosera at week 6 from immunized mice displayed significant cytotoxicity to tumor cells compared to that of negative control, but no cytotoxicity mediated by immunosera at week 22 was observed. In addition, by flow cytometry and electrophoresis of fragmented DNA, the cytotoxicity might probably be mediated by apoptosis. Our data also showed that the ability of the anti-dsDNA autoantibodies to induce apoptosis of SP2/0 and Wehi 164 cells was significantly correlated (r = 0.990, p < 0.01 and r = 0.901, p < 0.05) with their functional affinity. In vivo, the growth of solid tumors was significantly inhibited in the immunized mice inoculated directly with SP2/0 and Wehi 164 cells, or in the naïve mice which were inoculated with SP2/0 cells preincubated with immunosera containing anti-dsDNA autoantibodies. In conclusion, we demonstrated the origin of anti-dsDNA autoantibodies in cancer patients and tumor-bearing mice. And our data also showed that these autoantibodies revealed anti-tumor effect by inducing apoptosis.

Preparation and characterization of an anti-DNA monoclonal antibody showing size selectivity toward DNA fragments

Anti-DNA monoclonal antibodies were prepared using an in vitro immunization method. Balb/c mouse splenocytes were immunized with HeLa cell nuclear extract in the presence of N-acetylmuramyl-L-alanyl-D-isoglutamine and fused with P3U1 myeloma cells using PEG 4000. After HAT selection and ELISA using fragmented HeLa genomic DNA, an anti-DNA monoclonal antibody was obtained. The monoclonal antibody D-1-1, whose isotype was IgM, interacted with a variety of double-stranded DNA. The antibody reacted only with DNA fragments longer than 0.8 kbp, and its apparent dissociation constant for a 1.0-kbp DNA fragment was 34 nM. This antibody will be a helpful tool for the detection of DNA structures.

Specific recognition of a dsDNA sequence motif by an immunoglobulin VH homodimer

Anti-DNA antibodies have the potential to be applied in vast fields of fundamental as well as medical research. They are found in autoimmune diseases, such as systemic lupus erythemotosus. In most cases, anti-dsDNA antibodies do not present sequence specificity and are of low affinity. The dominant role of VH domains in DNA recognition induced us to search for binders based on VH dimers (VHD), previously reported to bind different protein antigens. We screened a phage displayed homo-VHD library against a 19-bp dsDNA sequence. A sequence-specific binder was selected, which recognizes the terminal located CTGC motif with a Kd of 250 nM. Association of the two identical VH domains of the molecule was shown to be essential for binding.

Interleukin-2, but not interleukin-15, is required to terminate experimentally induced clonal T-cell anergy

It has been demonstrated that T cells stimulated with nucleosome-polyomavirus T-antigen (self-nonself) complexes, but not nucleosomes, activate autoimmune nucleosome-specific T cells. As these cells may be naïve, such observations do not show that anergic T cells are reactivated. To understand the regulation of autoimmunity, this is important to assess, and this is the focus of this study. T-cell anergy was induced by antigen stimulation in the presence of antibodies to the costimulatory molecules CD80/CD86. Requirements for the reactivation of anergic T cells were analysed by the ability of antigen and interleukin-2 (IL-2) or IL-15 to increase T-cell proliferation and IL-2 transcription. Data demonstrate that stimulation of T cells with T-antigen and anti-CD80/86 antibodies promotes long-lasting clonal T-cell anergy. While T-antigen did not reactivate anergic T cells, proliferation and upregulation of IL-2 gene transcription was initiated by stimulation with antigen, costimulation and IL-2 added to the cultures. Proliferation per se was not sufficient to promote the reactivation of anergic T cells, as both IL-2 and IL-15 induced proliferation, while antigen and IL-2, but not IL-15, upregulated IL-2 mRNA levels. These data demonstrate that the innate immune system and IL-2 are central to the initiation and termination of T-cell anergy.

Specificity and immunochemical properties of anti-DNA antibodies induced in normal mice by immunization with mammalian DNA with a CpG oligonucleotide as adjuvant

To elucidate the role of DNA antigen drive in the anti-DNA response, the specificity and immunochemical properties of anti-DNA antibodies induced in normal mice by immunization with double stranded (ds) mammalian DNA with a CpG oligonucleotide (ODN) adjuvant were characterized. Like spontaneous anti-DNA from MRL/lpr mice, the induced anti-DNA bound cross-reactively to DNA from five different species by ELISA. The induced antibodies displayed a predominance of IgG2a and had much lower amount of IgG3 than spontaneous antibodies. Surface plasmon resonance indicated that the induced and spontaneous anti-DNA antibodies have a similar range of avidity and binding kinetics. While sera from the MRL/lpr mice had substantial binding to histones and nucleosomes, the immunized mice had antibody levels to these antigens similar to those of mice treated only with incomplete Freund's adjuvant. Together, these results indicate that normal mice can produce autoantibodies to dsDNA, with a CpG ODN allowing the generation of antibodies resembling those in spontaneous autoimmunity.

Specific antibody-DNA interaction: a novel strategy for tight DNA recognition

Anti-double-stranded DNA monoclonal antibodies against a viral transcriptional regulatory site are capable of discriminating single-base replacements with affinities of 1 x 10(-)(9) M, which were optimized for the length of the duplex used as the immunogen. Their affinity for DNA duplexes of increasing length is lower, but reaches a plateau at 2 x 10(-)(8) M, still a fairly high affinity compared to those of most known natural anti-DNA antibodies. The ability of the antibodies to bind to a 166 bp DNA fragment containing the specific sequence strongly suggests that these have the potential of binding the specific sequence within larger genomic DNA fragments. Electrostatic interactions do not play a significant role, the opposite of what is observed in natural DNA binding interfaces. In addition, the insensitivity of the antibody-DNA interaction to solute effects is indicative of a marginal participation of water molecules at the interface compared to the level of participation at the natural E2-DNA interface. Spectroscopic evidence of base unstacking strongly suggests substantial denaturation of antibody-bound DNA, in agreement with thermodynamic results that show an unusual positive heat capacity change, which could be explained at least in part by the exposure of DNA bases upon binding. Lower local DNA stability cooperates with sequence recognition in producing the highest binding affinity. A slow rate of antibody-DNA association indicates an energy barrier imposed by conformational rearrangements, as opposed to an electrostatically assisted diffusion-controlled collision in the E2 DNA binding domain. While the E2-DNA interaction takes place through a typical direct readout mechanism, the anti-double-stranded DNA monoclonal antibody-DNA interaction could be viewed as a distinctive case of indirect readout with a significant distortion in the DNA conformation. However, the precise mechanism with which the DNA bases are accommodated in the antibody combining site will require structural analysis at atomic resolution. These results constitute a first stage for unveiling the unusual molecular recognition mechanism of a specific DNA sequence by antibodies. This mechanism could represent the strategy with which the immune system tightly and specifically recognizes a DNA antigen.

Autoimmunity to nucleosomes related to viral infection: a focus on hapten-carrier complex formation

Systemic lupus erythematosus (SLE) is an autoimmune disorder with unknown aetiology. The major hallmark of this disease is the presence of antibodies against nuclear components, including double-stranded (ds)DNA and histones. The disease affects different organs, particularly the skin, kidneys and the nervous system. Although the exact molecular mechanisms underlying the pathophysiological processes in SLE remain unknown, several inherent and environmental factors seem to be involved in the ethiopathogenesis of this disorder. Viruses may be one of the factors that induce the production of autoreactive antibodies although the involved mechanisms are still incompletely understood. One proposed mechanism for virus-induced production of autoantibodies is molecular mimicry. Another mechanism derives from studies with the human polyomavirus BK. In these studies, in vivo binding of the polyomaviruses large T-antigen to chromatin of infected cells may render chromatin immunogenic. The large T-antigen-chromatin complex may thus function as a hapten-carrier model with subsequent production of anti-chromatin antibodies, including anti-dsDNA and anti-histones antibodies. This review focuses on the recent findings suggesting that this model may be applicable for other human viruses associated with SLE.

Antibody response to a viral transcriptional regulator

The E2 transcriptional activator of the human papillomavirus regulates the expression of most viral transcripts. Its binding to specific target DNA sequences involves large conformational changes in the interacting macromolecules. The high stability of the E2:DNA complex prompted us to analyze the role of macromolecular interactions and adjuvant emulsions in the appearance of conformation-specific antibodies. We demonstrate that immunization with free or DNA-complexed E2 emulsified in an oil-in-water adjuvant elicits a humoral response shifted to the recognition of discontinuous epitopes. Epitope mapping and functional analysis of the generated anti-E2 mAbs reveals that two separate antibodies populations can be obtained: those able to form a stable ternary complex with protein and DNA, and those which recognize the DNA-binding surface of the transcription factor, interfering with E2 binding to DNA.

Green fluorescent protein modified to bind DNA initiates production of anti-DNA antibodies when expressed in vivo

Studies have clearly demonstrated that DNA itself is not or scarcely immunogenic in experimental animals. We have previously demonstrated that linking human polyomavirus large T-antigen to DNA rendered DNA immunogenic irrespective of the source or the structure of DNA. As an alternative to this artificial system, in vivo expression of the DNA binding protein large T-antigen of human polyomaviruses also resulted in the production of anti-DNA antibodies. This observation demonstrates that the large T-antigen concept is operational in vivo and supports the idea that complex formation between a non-self DNA-binding protein and DNA renders DNA immunogenic in analogy to a hapten-carrier model. To further investigate this model, the DNA binding domain (DBD) of a self-protein (glucocorticoid receptor) was linked to a non-DNA binding non-self protein, the green fluorescent protein (GFP). Immunization of mice with an expression plasmid for this fusion protein resulted in the production of anti-DNA antibodies, while mice inoculated with either a plasmid encoding the GFP or a plasmid encoding the DBD of the glucocorticoid receptor failed to produce anti-DNA antibodies. These results demonstrate that DNA may become immunogenic through in vivo association with any non-self DNA binding protein. Considering these data in context of results obtained with the polyomavirus large T-antigen, one may conclude that viral DNA-binding proteins may affect the regulation of immune tolerance to DNA and nucleosomes in vivo.