Administration of a phosphorothioate oligonucleotide antisense to murine endogenous retroviral MCF env causes immune effects in vivo in a sequence-specific manner

Development of Exon Skipping Therapies for Duchenne Muscular Dystrophy: A Critical Review and a Perspective on the Outstanding Issues

Duchenne muscular dystrophy (DMD) is a rare, severe, progressive muscle-wasting disease leading to disability and premature death. Patients lack the muscle membrane-stabilizing protein dystrophin. Antisense oligonucleotide (AON)-mediated exon skipping is a therapeutic approach that aims to induce production of partially functional dystrophins. Recently, an AON targeting exon 51 became the first of its class to be approved by the United States regulators [Food and Drug Administration (FDA)] for the treatment of DMD. A unique aspect of the exon-skipping approach for DMD is that, depending on the size and location of the mutation, different exons need to be skipped. This challenge raises a number of questions regarding the development and regulatory approval of those individual compounds. In this study, we present a perspective on those questions, following a European stakeholder meeting involving academics, regulators, and representatives from industry and patient organizations, and in the light of the most recent scientific and regulatory experience.

Early development of the Toll-like receptor 9 agonist, PF-3512676, for the treatment of patients with advanced cancers

BACKGROUND

Unmethylated oligodeoxynucleotides (ODNs) with cytosine-phosphate-guanine (CpG) motifs can potently activate the immune system through Toll-like receptor (TLR) 9. PF-3512676 is a synthetic CpG ODN that induces strong Th1-type immune responses through TLR9 and is now in clinical development.

OBJECTIVE

To review discovery and development of synthetic CpG ODNs and their effects on immune cells and to relate preclinical and early clinical development of PF-3512676.

METHODS

A literature search was performed on databases available through the National Library of Medicine (PubMed), the European Society of Medical Oncology and the American Society of Clinical Oncology.

RESULTS/CONCLUSIONS

Unmethylated CpG motifs were identified as the element of bacillus Calmette-Guérin responsible for immunostimulatory activity. Preclinical studies identified the mechanism of action (i.e., TLR9) and an optimal human sequence for antitumor activity. On the basis of preclinical studies, PF-3512676, a B-class CpG ODN, was selected for further clinical development. Phase I/II clinical trials have shown PF-3512676 to be well tolerated and to have antitumor activity as a single agent in patients with several types of advanced cancer, and to show promise as a vaccine adjuvant.

Novel oligonucleotides containing two 3'-ends complementary to target mRNA show optimal gene-silencing activity

Oligonucleotides are being employed for gene-silencing activity by a variety of mechanisms, including antisense, ribozyme, and siRNA. In the present studies, we designed novel oligonucleotides complementary to targeted mRNAs and studied the effect of 3'-end exposure and oligonucleotide length on gene-silencing activity. We synthesized both oligoribonucleotides (RNAs) and oligodeoxynucleotides (DNAs) with phosphorothioate backbones, consisting of two identical segments complementary to the targeted mRNA attached through their 5'-ends, thereby containing two accessible 3'-ends; these compounds are referred to as gene-silencing oligonucleotides (GSOs). RNA and/or DNA GSOs targeted to MyD88, VEGF, and TLR9 mRNAs had more potent gene-silencing activity than did antisense phosphorothioate oligonucleotides (PS-oligos) in cell-based assays and in vivo. Of the different lengths of GSOs evaluated, 19-mer long RNA and DNA GSOs had the best gene-silencing activity both in vitro and in vivo. These results suggest that GSOs are novel agents for gene silencing that can be delivered systemically with broader applicability.

Proteins involved in binding and cellular uptake of nucleic acids

The study of mechanisms of nucleic acid transport across the cell membrane is valuable both for understanding the biological function of extracellular nucleic acids and the practical use of nucleic acids in gene therapy. It has been clearly demonstrated that cell surface proteins are necessary for transport of nucleic acids into cells. A large amount of data has now been accumulated about the proteins that participate in nucleic acid transport. The methods for revealing and identification of these proteins, possible mechanisms of protein-mediated transport of nucleic acids, and cellular functions of these proteins are described.

CpG motifs in bacterial DNA and their immune effects

Unmethylated CpG motifs are prevalent in bacterial but not vertebrate genomic DNAs. Oligodeoxynucleotides (ODN) containing CpG motifs activate host defense mechanisms leading to innate and acquired immune responses. The recognition of CpG motifs requires Toll-like receptor (TLR) 9, which triggers alterations in cellular redox balance and the induction of cell signaling pathways including the mitogen activated protein kinases (MAPKs) and NF kappa B. Cells that express TLR-9, which include plasmacytoid dendritic cells (PDCs) and B cells, produce Th1-like proinflammatory cytokines, interferons, and chemokines. Certain CpG motifs (CpG-A) are especially potent at activating NK cells and inducing IFN-alpha production by PDCs, while other motifs (CpG-B) are especially potent B cell activators. CpG-induced activation of innate immunity protects against lethal challenge with a wide variety of pathogens, and has therapeutic activity in murine models of cancer and allergy. CpG ODN also enhance the development of acquired immune responses for prophylactic and therapeutic vaccination.

The role of surface ig binding in the activation of human B cells by phosphorothioate oligodeoxynucleotides

Phosphorothioate oligodeoxynucleotides (sODNs) can induce T-cell-independent polyclonal activation of human B cells by a mechanism that depends on both sequence and back-bone structure. Because matrix-bound as well as soluble sODNs are mitogenic, this stimulation may result from the engagement of surface receptor(s). In order to investigate whether surface immunoglobin (Ig) could be a receptor for sODNs, the interaction of sODNs-fluorescein isothiocyanate (FITC) with Ig-coated beads was examined. sODNs specifically bound to human IgM and IgG. Moreover, binding of sODN to human B cells induced temperature-dependent capping of bound receptors and colocalization of FITC-sODN and IgM into aggregated caps on the surface of human B cells. A role of surface Ig was furthermore shown by observations that antibody-mediated capping of B-cell surface IgM or IgD inhibited subsequent binding of sODNs and that the capacity of sODN to stimulate human B cells was blocked by excess IgM or IgG, by nonstimulatory antibodies to sIgM, as well as by a variety of negatively charged molecules. Together, these results indicate that sODNs engage surface Ig by charge-charge interactions that lead to activation of human B cells.

The role of cell surface receptors in the activation of human B cells by phosphorothioate oligonucleotides

Phosphorothioate oligodeoxynucleotides (sODN) containing the CpG motif or TCG repeats induce T cell-independent polyclonal activation of human B cells. To elucidate the mechanism of this response, the role of cell surface receptors was investigated. Sepharose beads coated with stimulatory but not nonstimulatory sODNs induced B cell proliferation comparably with soluble sODNs. The B cell stimulatory activity of Sepharose-bound sODN did not result from free sODN released from the beads since media incubated with coated beads were inactive. Using FITC-labeled sODNs as probes, binding to human B cells could be detected by flow cytometry. Binding was rapid, saturable, initially temperature independent, but with a rapid off-rate. Competition studies indicated that both stimulatory sODNs and minimally stimulatory sODNs bound to the same receptor. By contrast, phosphodiester oligonucleotides with the same nucleotide sequence as sODNs and bacterial DNA inhibited the binding of sODNs to B cells minimally. Charge appeared to contribute to the binding of sODNs to B cells since binding of sODNs was competitively inhibited by negatively charged molecules, including fucoidan, poly I, and polyvinyl sulfate. These data indicate that human B cells bind sODNs by a receptor-mediated mechanism that is necessary but not sufficient for polyclonal activation.

Responses of human B cells to DNA and phosphorothioate oligodeoxynucleotides

Emerging information has documented that certain DNA and sODNs can be both immunogenic and immunostimulatory. sODNs, but not DNA, induce T-cell-independent polyclonal activation of human B cells by engaging cell-surface receptors. Manifestations of sODN-induced human B-cell activation include expression of activation markers, proliferation, Ig production and anti-DNA antibody production. IL-2 and intact T cells enhanced B-cell responses to sODNs but were not required. Monocytes also provided a modest enhancement of human B-cell responses induced by sODNs. The chemical nature of sODNs capable of stimulating human B cells and the specific cell-surface receptors involved have not been completely delineated. Further studies will be necessary to elucidate the potential role of stimulatory sODNs in disease pathogenesis and to develop a means to employ ODNs as therapeutic agents in humans.

CpG DNA as a Th1 trigger

Over the last few years, it has been recognized that along with structural components and products of bacteria, bacterial DNA is also capable of signaling infectious danger to cells of the innate immune system. Particular DNA sequences (CpG motifs), which are abundant in prokaryotic (bacterial) but not in mammalian DNA, cause the activation and stimulation of immune cells. Research has been catalyzed by the finding that certain synthetic oligodeoxynucleotides mimic the action of bacterial DNA. Immunostimulation induced by bacterial DNA or synthetic oligonucleotides not only contributes to our knowledge of the pathogen-host interrelationship during infection, but can also be used therapeutically to condition or modify ongoing immune responses of the adaptive immune system. Accordingly, CpG motifs have been used as vaccine adjuvants as well as instructing agents to selectively induce Th1-dominated immune responses. Hence, CpG motifs might be used in the future as adjuvants and/or immunomodulatory agents to treat or prevent undesired Th2-dominated immune responses, such as allergy.

Mechanisms and applications of immune stimulatory CpG oligodeoxynucleotides

Immune stimulation has been widely recognized as an undesirable side effect of certain antisense oligodeoxynucleotides (ODN) which can interfere with their therapeutic application. It is now clear that these dose-dependent immune stimulatory effects primarily result from the presence of an unmethylated CpG dinucleotide in particular base contexts ('CpG motif). The sequence-specific immune activation is not just an experimental artifact, but is actually a highly evolved immune defense mechanism whose actual 'goal' is the detection of microbial nucleic acids. In contrast to vertebrate DNA, in which CpG dinucleotides are 'suppressed' and are highly methylated, microbial genomes do not generally feature CpG suppression or methylation [1]. Immune effector cells such as B cells, macrophages, dendritic cells, and natural killer cells appear to have evolved pattern recognition receptors (PRR) that by binding the microbe-restricted structure of CpG motifs, trigger protective immune responses. Although the specific immune activation appears to have a variety of potential therapeutic applications, it is generally undesirable in antisense ODN. Immune stimulation may be avoided in antisense oligos by the selection of CpG-free target sequences, by the use of ODN backbones that do not support immune stimulation, or by selective modifications of the cytosine in any CpG dinucleotides.

Preclinical and clinical pharmacology of antisense oligonucleotides

Antisense oligonucleotides are short (typically 15-20 bases in length pieces of synthetically manufactured, chemically modified DNA or RNA. They are designed to interact by Watson-Crick base pairing with mRNA transcripts encoding proteins of interest, and by virtue of this interaction inhibit the expression of the protein encoded in the mRNA. Since their first proposed use in 1978, antisense oligonucleotides have become come widely used as tools to modulate gene expression in tissue culture. The great specificity that these compounds exhibited in vitro has also led them to be viewed as potentially therapeutically useful. This interest has resulted in the progression of (to date) a dozen compounds into human clinical trials for a variety of indications ranging from cancer to inflammatory diseases. Here, we will review some of the progress that has been made with antisense pharmacology, both in vitro and in vivo, as well as describe the current status of this class of compound in clinical trials.

Activation of spleen lymphocytes by plasmid DNA

It was shown that plasmid pUC19 DNA stimulates in vitro proliferation of CBA mouse splenocytes in a dose-dependent manner. Stimulation effect of the plasmid DNA is additive with COn A or LPS, synergistic with PMA and is inhibited by nonimmunogenic phosphodiester oligonucleotides and Fab fragments of antimouse Ig antibodies. These data and the data of affinity labelling of ODN-binding proteins indicate that immunoglobulin receptors are involved in DNA-induced lymphocyte activation.

Activation of spleen lymphocytes by plasmid DNA

Plasmid pUC19 DNA was shown to stimulate in vitro proliferation of CBA mouse splenocytes in a dose-dependent manner. Simultaneous treatment of the cells with the plasmid DNA and Con A or LPS produced an additive effect, while PMA acted synergistically with DNA. Monovalent Fab fragments of rabbit anti-mouse Ig (RAMIg) antibodies significantly inhibited plasmid DNA-induced polyclonal lymphocyte activation suggesting the involvement of Ig receptors in this process. Affinity modification of lymphocytes membrane-cytosole proteins with a 32P-labeled alkylating oligonucleotide derivative resulted in labeling of 67-82 and 23 kDa polypeptides corresponding to IgD and IgM heavy and light chains respectively. The immunoglobulin nature of the 82 and 23 kDa oligonucleotide-binding polypeptides was confirmed by immunoprecipitation with RAMIg antibodies.

Possible involvement of endogenous retroviruses in the development of autoimmune disorders, especially multiple sclerosis

Endogenous retroviruses are normal elements in vertebrate genomes. Many aspects concerning these genomic elements are still uncertain. In mice some endogenous retroviral sequences seem to be involved in the regulation of immune responses and there is even evidence that a retroviral element is responsible for the development of an autoimmune disease in a mouse strain. Whether endogenous retroviruses also contribute to the development of autoimmune diseases in humans is not known, but it is an interesting possibility. Below we briefly review endogenous retroviruses as potential etiological factors in autoimmunity and we discuss a possible association between MS and endogenous retroviruses on the basis of results from our laboratory.

Molecular therapy for renal diseases

The introduction of molecular therapy through the delivery of nucleic acids either as oligonucleotides or genetic constructs holds enormous promise for the treatment of renal disease. Significant barriers remain, however, before successful organ-specific molecular therapy can be applied to the kidney. These include the development of methods to target the kidney selectively, the definition of vectors that transduce renal tissue, the identification of appropriate molecular targets, the development of constructs that are regulated and expressed for long periods of time, the demonstration of efficacy in vivo, and the demonstration of safety in humans. As the genetic and pathophysiologic basis of renal disease is clarified, obvious targets for therapy will be defined, for example, polycystin in polycystic kidney disease, human immunodeficiency virus (HIV) type 1 in HIV-associated nephropathy, alpha-galactosidase A in Fabry's disease, insulin in diabetic nephropathy, and the "minor" collagen IV chains in Alport's syndrome. In addition, several potential mediators of progressive renal disease may be amenable to molecular therapeutic strategies, such as interleukin-6, basic fibroblast growth factor (bFGF), platelet-derived growth factor (PDGF), and transforming growth factor-beta(TGF-beta). To test the in vivo efficacy of molecular therapy, appropriate animal models for these disease states must be developed, an area that has received too little attention. For the successful delivery of genetic constructs to the kidney, both viral and nonviral vector systems will be required. The kidney has a major advantage over other solid organs since it is accessible by many routes, including intrarenal artery infusion, retrograde delivery through the uroexcretory pathways, and ex vivo during transplantation. To further restrict expression to the kidney, tropic vectors and tissue-specific promoters also must be developed. For the purpose of inhibition of endogenous or exogenous genes, current therapeutic modalities include the delivery of antisense oligodeoxynucleotides or ribozymes. For these approaches to succeed, we must gain a much better understanding of the nature of their transport into the kidney, requirements for specificity, and in vivo mechanisms of action. The danger of a rush to clinical application is that superficial approaches to these issues will likely fail and enthusiasm will be lost for an area that should be one of the most exciting developments in therapeutics in the next decade.

Amplification of antibody production by phosphorothioate oligodeoxynucleotides

A phosphorothioate oligodeoxynucleotide that is complementary (antisense) to the initiation region of the rev gene of HIV-1 causes hypergammaglobulinemia and splenomegaly in mice, and it induces B cell proliferation and differentiation in mouse spleen mononuclear cells (SMNCs) and human peripheral blood mononuclear cells in vitro. The current studies were performed to investigate the specificity of these immunomodulatory effects. Both the sense and antisense rev oligomers stimulated tritiated thymidine incorporation and secretion of immunoglobulin M (IgM) and immunoglobulin G (IgG) by mouse SMNCs in a concentration-dependent fashion, but the antisense oligomer produced greater immune effects. Studies comparing phosphorothioate oligomers (anti-rev, c-myc, and c-myb) either methylated or unmethylated at CpG dinucleotides showed that methylation effectively abrogated the proliferative effect and tended to reduce the immunoglobulin secretory activity, but the latter was not statistically significant except in the case of IgG in anti-rev oligomer-treated cultures. Mice were injected with the sense or antisense rev oligomers singly or in combination. The animals then were immunized with tetanus toxoid and received a booster 21 days later. Oligodeoxynucleotide-treated mice had significantly higher levels of IgM antibodies on days 28 and 35 and of IgG antibodies on days 14 and 35 as compared with mice that were immunized but received vehicle alone. There was no evidence for additive, synergistic, or antagonistic interactions of the sense and antisense rev oligomers. These results indicate that the unmethylated anti-rev oligomer is the most potent of the phosphorothioate oligomers tested at activating lymphocyte proliferation and differentiation and that a single intravenous injection of this oligodeoxynucleotide augments antibody production to a specific antigen as long as 35 days later.

Stimulation of human lymphocyte proliferation and CD40 antigen expression by phosphorothioate oligonucleotides complementary to hepatitis B virus genome

We have studied the proliferation and CD40 antigen expression of lymphocytes, and the cytotoxicity to monocytes, of antisense phosphorothioate oligodeoxynucleotides complementary to the SP II promoter of HBV mRNA (sequence I) and the X gene (sequence II) in patients with chronic hepatitis B. The oligo sequence I stimulated proliferation of both T and, to a lesser extent, B cells. The percentage of cells expressing CD40 in T and B cell co-cultures increased from 4.2% to 13.8% after oligo stimulation in patients, while it increased form 4.7% to 48.6% in healthy controls. The sense sequence (sequence III) of the X gene also enhanced the expression of CD40 antigen in patients with hepatitis B. The proportion of CD40 cells (26%) in a resting B-cell preparation from hepatitis B patients decreased to zero after a 5-day culture with sequence I, but IgG levels in the culture supernatant increased. The cytotoxic properties of monocytes were not influenced by the oligos. These findings indicate that antisense oligos against hepatitis B virus (HBV) have mitogenic effects on the proliferation of human lymphocytes in a non-specific manner and may activate T cells to express CD40 antigen.

Leukemia treatment in severe combined immunodeficiency mice by antisense oligodeoxynucleotides targeting cooperating oncogenes

Transformation of hematopoietic cells by the p210bcr/abl tyrosine kinase appears to require the expression of a functional MYC protein, suggesting that simultaneous targeting of BCR-ABL and c-myc might be a rational strategy for attempting treatment of Phil-adelphia leukemia. To test this hypothesis, severe combined immunodeficiency mice injected with Philadelphia leukemic cells were treated systemically with equal doses of bcr-abl or c-myc antisense oligodeoxynucleotides (ODNs) or with both ODNs in combination. Compared with the mice treated with individual agents, the disease process was much slower in the group treated with both ODNs, as revealed by flow cytometry, clonogenic assay, and reverse transcriptase-polymerase chain reaction analysis to detect leukemic cells in mouse tissue cell suspensions, and by enumeration of liver metastases. The retardation of the disease process was positively correlated with a markedly increased survival of leukemic mice treated with both ODNs. These data demonstrate the therapeutic potential of targeting multiple cooperating oncogenes.

Antisense oligonucleotide strategies in physiology

Antisense oligonucleotides can inhibit gene expression in living cells by binding to complementary sequences of DNA, RNA or mRNA. The mechanisms include inhibition of RNA synthesis, RNA splicing, mRNA export, binding of initiation factors, assembly of ribosome subunits and of sliding of the ribosome along the mRNA coding sequence. The most efficient antisense oligonucleotides also activate RNAse H, an ubiquitous enzyme that cleaves the mRNA at sites of mRNA/oligonucleotide duplex formation. A staggering number of oligonucleotide modifications have been proposed to retard degradation by nucleases, enhance cellular uptake, increase binding to the target sequence, and minimize non-specific binding to related nucleic acid sequences. Phosphorothioates are the most popular oligonucleotides used in cell culture and in vivo, although sequence non-specificity remains an underreported problem. Recently developed chimeras between methylphosphonates and phosphodiester oligonucleotides appear to combine the advantages of water solubility, nuclease resistance, enhanced cellular uptake, activation of RNAse H, and high sequence selectivity. Antigene oligonucleotides are also promising, because they can inhibit gene expression by triple helix formation with DNA or by binding to one of the DNA strands. They have so far been little used in physiological studies. Cost is still a prohibitive factor, especially for suppressing the expression of a hormone or hormone receptor gene in rats, for example. However, patch-clamp dialysis of single cells or nuclear microinjections in culture, exposure of cultures to extracellular oligonucleotides, and intra-cerebral microinjections of oligonucleotides are feasible and highly rewarding approaches in physiology.

Stimulation of murine lymphocyte proliferation by a phosphorothioate oligonucleotide with antisense activity for herpes simplex virus

To investigate further the immunological properties of nucleic acids, the mitogenicity of a phosphorothioate oligonucleotide (S-oligo 1082) with antisense activity for herpes simplex virus was tested. This compound stimulated proliferation and antibody production by murine lymphocytes in in vitro cultures. Proliferation was dose-dependent and unaffected by T cell depletion. Furthermore, inclusion of a non-mitogenic DNA in the medium did not block stimulation. Since 1082 does not have homology to a known gene involved in lymphocyte activation, these observations suggest that S-oligo antisense compounds may display non-specific activating effects, at least on murine B cells.

In vivo toxicological effects of rel A antisense phosphorothioates in CD-1 mice

To characterize the in vivo toxicity of phosphorothioate antisense oligonucleotides against rel A (p65 subunit of NF-kappa B transcription factor), forty-eight 6-week-old CD-1 mice were split into 4 groups (6/sex/group) receiving vehicle (phosphate-buffered saline) or doses of 50, 100, and 150 mg/kg of rel A antisense oligonucleotides intraperitoneally 3 times weekly for 2 weeks. Clinical signs of toxicity included weakness, and decreased motor activity and food consumption with body weight loss. Mortality occurred in 7 of 12 mice in the 150-mg/kg group and in 2 of 12 mice in the 100-mg/kg group, most of which died within the first 2 to 4 days of treatment. The remaining mice were necropsied on day 15. The major hematological finding was severe dose-dependent thrombocytopenia. The liver enzyme levels were mildly elevated in the serum of mid- and high-dose animals. At necropsy, increased spleen and liver weights were observed in treated mice, some of which also had mild pleural and/or peritoneal effusions. Histopathological examination revealed the likely cause of death to be acute renal failure due to renal cortical or tubular necrosis. Treatment-related changes were also found in the liver, spleen, bone marrow, and several other organs. In summary, the kidney, liver, and bone marrow (megakaryocytic lineage) were identified as the major target organs for toxicity with rel A antisense therapy.

A sense phosphorothioate oligonucleotide directed to the initiation codon of transcription factor NF-kappa B p65 causes sequence-specific immune stimulation

Antisense oligonucleotides have proved effective in achieving targeted inhibition of gene expression. In such experiments, sense oligonucleotides have frequently been used as a control for nonspecific effects, but the results have been variable, raising questions about the reliability of sense oligomers as a control. It is possible that some of the effects of sense oligonucleotides may be specific. We have shown that phosphorothioate antisense oligonucleotides to the p65 subunit of NF-kappa B, a transcription factor, cause a block in cell adhesion. In our efforts to test the efficacy of NF-kappa B p65 oligonucleotides in vivo, we unexpectedly observed that the control p65-sense, but not the p65-antisense, oligonucleotides caused massive splenomegaly in mice. In the current study we demonstrate a sequence-specific stimulation of splenic cell proliferation, both in vivo and in vitro, by treatment with p65-sense oligonucleotides. Cells expanded by this treatment are primarily B-220+, sIg+ B cells. The secretion of immunoglobulins by the p65-sense oligonucleotide-treated splenocytes is also enhanced. In addition, the p65-sense-treated splenocytes, but not several other cell lines, showed an upregulation of NF-kappa B-like activity in the nuclear extracts, an effect not dependent on new protein or RNA synthesis. These results demonstrate that phosphorothioate oligonucleotides can exert sequence-specific effects in vivo, irrespective of sense or antisense orientation.