Patent Application
20240207385
The instant application contains a Sequence Listing which has been submitted electronically via Patent Center in ASCII plain text format and is hereby incorporated by reference in its entirety. The name of the file containing the Sequence Listing is WIST-006-US-SEQ LIST_ST25. The size of the text file is 400,050 bytes and the text file was created on Dec. 23, 2023.
The disclosure generally relates to compositions comprising self-assembling vaccines and methods of using the same. The disclosure provides compositions comprising an expressible nucleic acid sequence comprising a first nucleic acid sequence encoding a self-assembling polypeptide or a pharmaceutically acceptable salt thereof and a second nucleic acid sequence encoding a viral antigen or a pharmaceutically acceptable salt thereof. The disclosure further provides compositions comprising an expressible nucleic acid sequence comprising a first nucleic acid sequence encoding a self-assembling polypeptide or a pharmaceutically acceptable salt thereof and a second nucleic acid sequence encoding a CD40 ligand polypeptide. Methods of using any of the disclosed compositions are also provided.
Vaccination is an extremely important public health measure that has demonstrated prophylactic and therapeutic utility against many infectious diseases [1-3], and impacted some forms of cancer [4]. In the past decade, advances in material engineering has allowed for the development and study of a new generation of nanoparticle vaccines [5-7]. Hepatitis B and human papillomavirus (HPV) vaccines are such examples of self-assembling virus-like particles which have impacted millions of people [8, 9]. Nanoparticles may come in several shapes and forms. Inorganic materials [10, 11], nontoxic phospholipids [12], virus-like particles (VLPs) or self-assembling protein nanoparticles (SAPN) [13-16] can all scaffold and present antigens in repetitive multimeric manners to robustly stimulate immunity in animal models [16-18].
However, some intrinsic production challenges have impeded broader translation of nano-vaccines into the clinical space [19, 20]. VLP vaccines are often produced at low yields in mammalian cell lines and are difficult to purify, requiring complex reassembly processes and additional post-hoc characterization [13, 21, 22]. Production of HPV VLPs, for example, requires three sequential purification steps of strong cation exchange chromatography, size-exclusion chromatography, and hydroxyapatite chromatography [23]. Large-scale production of liposome-based nano-vaccines is challenging, as slight variations in the methods of production result in heterogeneity of the liposomes produced [19]. Production of nano-vaccines for a global market could therefore require specialized pipelines which raise costs. In addition, regulatory approval of drugs for use in humans can be complex for development of multicomponent nano-medicines [24]. Technologies that would allow de novo nanoparticle assemblies in the hosts from materials that are inexpensive, simple and stable, which bypass these complex biochemical processes and downstream purifications, may be of interest.
In this regard, computational protein engineering is an extremely powerful tool and has facilitated the design of novel biologics as well as specific potent nano-vaccines [15, 26]. One such example is the eOD-GT8-60mer, which is a priming immunogen engineered to activate precursors of HIV-1 broadly neutralizing antibodies [27-29]. When scaffolded with the C-terminus of the lumazine synthase (LS) enzyme from Aquifex Aeolicus, eOD-GT8 can assemble into a 60-mer nanoparticle to induce stronger humoral immunity and higher frequencies of antigen-specific IgG+ memory B cells [27]. In terms of vaccine delivery, DNA vaccines have been studied for induction of humoral and cellular immunity [30-32]. Additionally, delivery of optimized DNA plasmids encoding monomeric immunogens via adaptively-controlled electroporation (EP) can result in 1000-fold enhancement of in vivo expression and longer-term in vivo production of the encoded antigens [34-36]. The newer DNA platform is also a robust method of eliciting adaptive immune responses in humans, having demonstrated immune potency in the clinic against such diseases as ZIKA, Ebola, HIV, MERS and clinical efficacy against HPV-driven cervical dysplasia [4, 37-40].
While simple multimerization domains, such as heptamer domain IMX313P, have been employed to improve DNA vaccine responses [41, 42], the disclosure relates to methods of inducing both therapeutically effective B- and T-cell responses by administration of nucleic acid vaccines computationally designed to include nucleic acid sequences encoding nanoparticle monomer peptides (such as 7, 24, 60, and 180-mers) that self-assemble with a fusion of antigens.
Nanotechnologies are considered to be of growing importance to the vaccine field. Through decoration of immunogens on multivalent nanoparticles, designed nano-vaccines can elicit improved humoral immunity. However, significant practical and monetary challenges in large-scale production of nano-vaccines have impeded their widespread clinical translation. Compositions comprising self-assembling vaccines and methods of using the same have been previously described in International Application No. PCT/US2019/068444 filed on Dec. 23, 2018, which is incorporated by reference in its entirety herewith. In the present disclosure, an alternative approach integrating computational protein modeling and adaptive electroporation mediated synthetic DNA delivery thus enabling direct in vivo production of nano-vaccines is provided. eOD-GT8-60mer is currently being clinically evaluated as a recombinant protein vaccine [43], and was examined as a prototype for DNA delivery. It is demonstrated that DNA-launched nanoparticles decorated with COD-GT8 (herein referred as DLnano_LS_GT8 for DNA-Launched nanoparticle Lumazine Synthase decorated with eOD-GT8) could spontaneously self-assembled in vivo into nanoparticles. DNA-launched nano-vaccines induced stronger humoral responses than their monomeric counterparts in both mice and guinea pigs, and uniquely elicited CD8+ effector T-cell immunity as compared to recombinant protein nano-vaccines. Improvements in vaccine responses were recapitulated when DNA-launched nano-vaccines with alternative scaffolds and decorated antigen were designed and evaluated. Finally, evaluation of functional immune responses induced by DLnano-vaccines demonstrated that, in comparison to control mice or mice immunized with DNA-encoded hemagglutinin monomer, mice immunized with a DNA-launched hemagglutinin nanoparticle vaccine fully survived a lethal influenza challenge, and had substantially lower viral load, weight loss and influenza-induced lung pathology. Synthetic DNA/EP technology can, therefore, be used to direct in vivo assembly of computationally designed nano-vaccines, which elicit more potent functional immunological responses. This combination can be important for rapid development of vaccines and immunotherapies thus offering advantages for immunization against multiple disease targets.
Accordingly, the disclosure relates to a composition comprising an expressible nucleic acid sequence comprising: a) a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide; and b) a second nucleic acid sequence encoding a viral antigen, and optionally, wherein the expressible nucleic acid sequence is free of a nucleic acid sequence encoding a leader sequence.
In some embodiments, the self-assembling polypeptide encoded by the first nucleic acid sequence of the expressible nucleic acid sequence of the present disclosure is from Aquifex aeolicus, Helicobacter pylori, Pyrococcus furiosus or Thermotoga maritima. In some embodiments, the self-assembling polypeptide comprises at least 70% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26.
In some embodiments, the viral antigen encoded by the second nucleic acid sequence of the expressible nucleic acid sequence of the present disclosure is an antigen from a retrovirus, flavivirus, Nipah virus, West Nile virus, human papillomavirus, respiratory syncytial virus, filovirus, zaire ebolavirus, sudan ebolavirus, marburgvirus or influenza virus, or any virus disclosed in Table 1. In some embodiments, the viral antigen is an antigen from human immunodeficiency virus-1 (HIV-1). In some embodiments, the viral antigen comprises at least 70% sequence identity to SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67.
In some embodiments, the expressible nucleic acid sequence of the present disclosure further comprises a third nucleic acid sequence encoding a linker domain comprising a linker peptide, said third nucleic acid sequence positioned between the first nucleic acid sequence and the second nucleic acid sequence in the 5′ to 3′ orientation. In some embodiments, the linker peptide comprises at least 70% sequence identity to SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32.
In some embodiments, the expressible nucleic acid sequence of the present disclosure comprises at least 70% sequence identity to SEQ ID NO: 68. In other embodiments, the expressible nucleic acid sequence of the present disclosure encodes a polypeptide comprising at least 70% sequence identity to SEQ ID NO: 69.
In some embodiments, the expressible nucleic acid sequence of the present disclosure is operably linked to one or a plurality of regulatory sequences. In some embodiments, the expressible nucleic acid sequence is comprised in a nucleic acid molecule. In some embodiments, the nucleic acid molecule is a plasmid.
The disclosure further relates to a pharmaceutical composition comprising (i) any of the compositions disclosed herein, and (ii) a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition of the present disclosure comprises any of the disclosed compositions in the amount of from about 1 to about 100 micrograms. In some embodiments, the pharmaceutical composition of the present disclosure comprises any of the disclosed compositions in the amount of from about 1 to about 20 micrograms.
The disclosure also relates to a method of vaccinating a subject in need thereof comprising administering a therapeutically effective amount of any of the pharmaceutical compositions disclosed herein to the subject. In some embodiments, the therapeutically effective amount is from about 20 to about 2000 micrograms of the expressible nucleic acid sequence comprised in any of the pharmaceutical compositions disclosed herein. In some embodiments, the therapeutically effective dose is from about 0.3 micrograms of the composition per kilogram of subject to about 30 micrograms per kilogram of subject. In some embodiments, the subject being vaccinated is a human.
The disclosure further relates to a method of inducing an immune response in a subject in need thereof comprising administering to the subject any of the pharmaceutical compositions disclosed herein. In some embodiments, the administering comprises administering from about 1 to about 2000 micrograms of the expressible nucleic acid sequence comprised in any of the pharmaceutical compositions disclosed herein. In some embodiments, the therapeutically effective dose is from about 0.3 micrograms of the composition per kilogram of subject to about 30 micrograms per kilogram of subject. In some embodiments, the subject is a human. In some embodiments, the immune response being induced is an antigen-specific immune response. In some embodiments, the subject is diagnosed with or suspected of having an HIV-1 infection. In some embodiments, the immune response is an antigen-specific immune response against an HIV-1 antigen.
The disclosure additionally relates to a method of neutralizing one or plurality of viruses in a subject in need thereof comprising administering to the subject any of the pharmaceutical compositions disclosed herein. In some embodiments, the administering comprises administering from about 1 to about 30 micrograms of the expressible nucleic acid sequence comprised in any of the pharmaceutical compositions disclosed herein. In some embodiments, the therapeutically effective dose is from about 0.3 micrograms of the composition per kilogram of subject to about 30 micrograms per kilogram of subject. In some embodiments, the subject is a human.
In some embodiments, the administration of any of the disclosed pharmaceutical compositions in any of the disclosed methods is accomplished by oral administration, parenteral administration, sublingual administration, transdermal administration, rectal administration, transmucosal administration, topical administration, inhalation, buccal administration, intrapleural administration, intravenous administration, intraarterial administration, intraperitoneal administration, subcutaneous administration, intramuscular administration, intranasal administration, intrathecal administration, and intraarticular administration, or a combination thereof.
Also disclosed is a method of stimulating a therapeutically effective antigen-specific immune response against a virus in a mammal in need thereof infected with a virus comprising administering a therapeutically effective amount of any of the pharmaceutical compositions disclosed herein. In some embodiments, the mammal is infected with a HIV virus. In some embodiments, the therapeutically effective amount is from about 0.3 micrograms of the disclosed composition per kilogram of subject to about 30 micrograms per kilogram of subject.
Further disclosed is a method of inducing expression of a self-assembling vaccine in a subject comprising administering any of the pharmaceutical compositions disclosed herein. In some embodiments, any of the disclosed methods are free of administering any polypeptide of the antigen directly to the subject.
The disclosure also relates to a vaccine comprising a polypeptide comprising: a) a scaffold domain comprising a self-assembling polypeptide; and b) an antigen domain comprising a viral antigen, and optionally, wherein the vaccine is free of a leader sequence.
In some embodiments, the self-assembling polypeptide encoded by the first nucleic acid sequence of the expressible nucleic acid sequence of the present disclosure is from Aquifex aeolicus, Helicobacter pylori, Pyrococcus furiosus or Thermotoga maritima. In some embodiments, the self-assembling polypeptide comprises at least 70% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises at least 80% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises at least 85% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises at least 90% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises at least 95% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises at least 96% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises at least 97% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises at least 98% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises at least 99% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the self-assembling polypeptide comprises 100% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26.
In some embodiments, the viral antigen encoded by the second nucleic acid sequence of the expressible nucleic acid sequence of the present disclosure encodes an antigen from a retrovirus, Flavivirus, Nipah virus, West Nile virus, human papillomavirus, respiratory syncytial virus, filovirus, zaire ebolavirus, sudan ebolavirus, marburgvirus or influenza virus, or any virus disclosed in Table 1. In some embodiments, the viral antigen is an antigen from HIV-1. In some embodiments, the viral antigen comprises at least 70% sequence identity to SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67.
In some embodiments, the polypeptide encoded by the expressible nucleic acid sequence of the present disclosure further comprises a linker domain comprising a linker peptide located between the scaffold domain and the antigen domain. In some embodiments, the linker peptide comprises at least 70% sequence identity to SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32. In some embodiments, the polypeptide encoded by the expressible nucleic acid sequence of the present disclosure comprises at least 70% sequence identity to SEQ ID NO: 69.
The disclosure further relates to a DNA vaccine comprising an expressible nucleic acid sequence encoding a polypeptide comprising at least about 70% sequence identity to SEQ ID NO: 69. In some embodiments, the expressible nucleic acid sequence comprised in such DNA vaccines comprises at least about 70% sequence identity to SEQ ID NO: 68. In some embodiments, the DNA vaccine of the present disclosure further comprises a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutically composition further comprises: (i) a second nucleic acid molecule encoding a vaccine adjuvant; and/or (ii) a vaccine adjuvant that is a polypeptide.
The disclosure further related to a composition comprising one or a plurality of any of the expressible nucleic acid sequences disclosed herein, the plurality of expressible nucleic acid sequences comprising a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide and a second nucleic acid sequence encoding an antigen domain comprising a viral antigen, wherein the plurality of expressible nucleic acid sequences is optionally free of a nucleic acid sequence encoding a leader sequence. In some embodiments, the self-assembling polypeptide encoded by the first nucleic acid sequence is from Aquifex aeolicus, Helicobacter pylori, Pyrococcus furiosus or Thermotoga maritima. In some embodiments, the self-assembling polypeptide comprises at least 70% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26. In some embodiments, the viral antigen encoded by the second nucleic acid sequence is an antigen from a retrovirus, flavivirus, Nipah virus, West Nile virus, human papillomavirus, respiratory syncytial virus, filovirus, zaire ebolavirus, sudan ebolavirus, marburgvirus or influenza virus, or any virus disclosed in Table 1. In some embodiments, the viral antigen is an antigen from HIV-1. In some embodiments, the viral antigen comprises at least 70% sequence identity to SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67. In some embodiments, the plurality of expressible nucleic acid sequences further comprise a third nucleic acid sequence encoding a linker domain comprising a linker peptide located between the scaffold domain and the antigen domain. In some embodiments, the linker peptide comprises at least 70% sequence identity to SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32. In some embodiments, the plurality of expressible nucleic acid sequences comprise at least 70% sequence identity to SEQ ID NO: 68, or wherein the plurality of expressible nucleic acid sequences encode a polypeptide comprising at least 70% sequence identity to SEQ ID NO: 69. In some embodiments, at least one of the plurality of expressible nucleic acid sequences is operably linked to at least one regulatory sequence.
The present disclosure also relates to a cell comprising any of the expressible nucleic acid sequences disclosed herein. In some embodiments, the cell of the present disclosure comprises an expressible nucleic acid sequence comprising: a) a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide; and b) a second nucleic acid sequence encoding an antigen domain comprising a viral antigen, and optionally, wherein the expressible nucleic acid sequence is free of a nucleic acid sequence encoding a leader sequence. In some embodiments, the cell is an antigen presenting cell, such as a macrophage or astrocyte.
In some embodiments, the self-assembling polypeptide encoded by the first nucleic acid sequence is from Aquifex aeolicus, Helicobacter pylori, Pyrococcus furiosus or Thermotoga maritima. In some embodiments, the self-assembling polypeptide comprises at least 70% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26.
In some embodiments, the viral antigen encoded by the second nucleic acid sequence encodes an antigen from a retrovirus, flavivirus, Nipah virus, West Nile virus, human papillomavirus, respiratory syncytial virus, filovirus, zaire ebolavirus, sudan ebolavirus, marburgvirus or influenza virus, or any virus disclosed in Table 1. In some embodiments, the viral antigen is an antigen from HIV-1. In some embodiments, the viral antigen comprises at least 70% sequence identity to SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67.
In some embodiments, the expressible nucleic acid sequence comprised in the cell of the present disclosure further comprises a third nucleic acid sequence encoding a linker domain comprising a linker peptide, said third nucleic acid sequence positioned between the first nucleic acid sequence and the second nucleic acid sequence in the 5′ to 3′ orientation. In some embodiments, the linker peptide comprises at least 70% sequence identity to SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32.
In some embodiments, the expressible nucleic acid sequence comprised in the cell of the present disclosure comprises at least 70% sequence identity to SEQ ID NO: 68. In some embodiments, the expressible nucleic acid sequence comprised in the cell of the present disclosure encodes a polypeptide comprising at least 70% sequence identity to SEQ ID NO: 69.
In some embodiments, the expressible nucleic acid sequence comprised in the cell of the present disclosure is operably linked to one or a plurality of regulatory sequences. In some embodiments, the expressible nucleic acid sequence is comprised within a nucleic acid molecule. In some embodiments, the nucleic acid molecule is a plasmid. In some embodiments, the disclosure relates to a plasmid comprising at least one, two, three, four or more expressible nucleic acid sequences, at least a first nucleic acid sequence comprising or consisting of: a) a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide; and b) a second nucleic acid sequence encoding an antigen domain comprising a viral antigen, and optionally, wherein the expressible nucleic acid sequence is free of a nucleic acid sequence encoding a leader sequence. In some embodiments, the cell is an antigen presenting cell, such as a macrophage or astrocyte. In some embodiments, each composition comprises at least a first expressible nucleic acid sequence further comprises a immunoglobulin leader sequence, such as an IgE leader or a IgG leader sequence.
The disclosure further relates to a pharmaceutical composition comprising: (i) any of the compositions or cells disclosed herein, and (ii) a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition further comprises a nucleic acid sequence that encodes an adjuvant or a protein adjuvant. In some embodiments, the pharmaceutical composition comprises from about 1 to about 100 micrograms of the disclosed expressible nucleic acid sequence. In some embodiments, the pharmaceutical composition comprises from about 1 to about 20 micrograms of the disclosed expressible nucleic acid sequence.
Further disclosed is a method of vaccinating a subject in need thereof against viral infection comprising administering a therapeutically effective amount of any of the pharmaceutical compositions disclosed herein. A method of inducing an immune response to a viral antigen in a subject in need thereof comprising administering a therapeutically effective amount of any of the pharmaceutical composition disclosed herein is also disclosed. In some embodiments, the viral infection being vaccinated against is an infection of retrovirus, flavivirus, Nipah Virus, West Nile virus, human papillomavirus, respiratory syncytial virus, filovirus, zaire ebolavirus, sudan ebolavirus, marburgvirus or influenza virus. In some embodiments, the administering is accomplished by oral administration, parenteral administration, sublingual administration, transdermal administration, rectal administration, transmucosal administration, topical administration, inhalation, buccal administration, intrapleural administration, intravenous administration, intraarterial administration, intraperitoneal administration, subcutaneous administration, intramuscular administration, intranasal administration, intrathecal administration, and intraarticular administration, or combinations thereof. In some embodiments, the therapeutically effective amount is from about 20 to about 2000 micrograms of the disclosed expressible nucleic acid sequence. In some embodiments, the therapeutically effective amount is from about 0.3 micrograms of the disclosed expressible nucleic acid sequence per kilogram of subject to about 30 micrograms of the disclosed expressible nucleic acid sequence per kilogram of subject. In some embodiments, the subject is a human. In some embodiments, the immune response is an antigen-specific immune response against a viral antigen. In some embodiments, the immune response is a therapeutically effective antigen-specific immune response against a viral antigen that includes a CD8+ and CD4+ immune response.
The disclosure further provides a nanoparticle comprising: (i) from about 7 to about 120 monomers, each monomer comprising at least about 70% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 26, or SEQ ID NO: 31, or a functional fragment thereof; and (ii) a CD40L polypeptide. In some embodiments, the nanoparticle further comprises a polypeptide that is a viral antigen or cancer antigen. Also disclosed is a nucleic acid molecule comprising an expressible nucleic acid sequence encoding: (i) a nanoparticle monomer from lumen synthase or a functional fragment or variant thereof comprising at least about 70% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 26, or SEQ ID NO: 31; and (ii) a CD40L polypeptide. The disclosure also relates to a nucleic acid molecule comprising an expressible nucleic acid sequence encoding: (i) a self-assembling nanoparticle monomer or a functional fragment or variant thereof comprising at least about 70% sequence identity to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15; and (ii) a CD40L polypeptide. In some embodiments, any of the disclosed nucleic acid molecules is an RNA, DNA or RNA/DNA plasmid, cosmid, or viral vector. In some embodiments, the expressible nucleic acid sequence comprised in any of the disclosed nucleic acid molecules further comprises a nucleic acid sequence encoding a viral antigen or cancer antigen. The disclosure further provides a composition comprising an expressible nucleic acid sequence comprising: a) a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide; and b) a second nucleic acid sequence encoding a CD40L polypeptide. In some embodiments, the disclosed composition further comprises a third nucleic acid sequence encoding a protein of interest. In some embodiments, the protein of interest is a viral antigen or a cancer antigen.
In some embodiments, the CD40L polypeptide comprised in any of the disclosed nanoparticles, nucleic acid molecules and compositions comprises at least 70% sequence identity to SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, or SEQ ID NO: 111, or a functional fragment thereof. In some embodiments, the CD40L polypeptide is encoded by a nucleic acid sequence comprising at least 70% sequence identity to SEQ ID NO: 102 or SEQ ID NO: 107, or a functional fragment thereof that comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 102 or SEQ ID NO: 107. In some embodiments, any of the disclosed nucleic acid molecules or expressible nucleic acid sequences comprises a nucleic acid sequence comprising at least 70% sequence identity to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof that comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15. In some embodiments, any of the disclosed nucleic acid molecules or expressible nucleic acid sequences encodes a scaffold domain comprising at least about 70% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 26, or SEQ ID NO: 31, or a functional fragment thereof. In some embodiments, the nucleic acid sequences encoding the CD40L polypeptide and the monomer are contiguously connected by a nucleic acid sequence encoding a linker.
Further disclosed is a cell comprising any of the nanoparticles and nucleic acid molecules disclosed herein. In some embodiments, the cell is a eukaryotic cell. In some embodiments, the cell is an antigen presenting cell.
The disclosure also provides a pharmaceutical composition comprising a therapeutically effective amount of one or a plurality of any of the nanoparticles, nucleic acid molecules or cells disclosed herein and a pharmaceutically acceptable carrier. Also disclosed is a method of inducing an immune response in a subject comprising administering the disclosed pharmaceutical composition to the subject. The disclosure also provides a method of treating and/or preventing a viral infection or cancer in a subject in need thereof comprising administering a therapeutically effective amount of the pharmaceutical composition disclosed herein to the subject. A method of vaccinating a subject in need thereof comprising administering a therapeutically effective amount of the disclosed pharmaceutical composition to the subject is also provided. Further disclosed is a method of activating and/or enhancing an antigen-specific immune response of a vaccine in a subject in need thereof comprising administering a therapeutically effective amount of the disclosed pharmaceutical composition to the subject.
The disclosure also relates to a vaccine or vaccine adjuvant comprising a therapeutically effective amount of any of the disclosed pharmaceutical composition.
The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several embodiments of the disclosed method and compositions and together with the description, serve to explain the principles of the disclosed method and compositions.
The disclosed method and compositions may be understood more readily by reference to the following detailed description of particular embodiments and the examples included therein and to the figures and their previous and following description.
It is to be understood that the disclosed method and compositions are not limited to specific synthetic methods, specific analytical techniques, or to particular reagents unless otherwise specified, and, as such, may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
It is understood that the disclosed method and compositions are not limited to the particular methodology, protocols, and reagents described as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present disclosure which will be limited only by the appended claims.
It must be noted that as used herein and in the appended claims, the singular forms “a”, “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to “a nucleic acid sequence” includes a plurality of nucleotides that are formed, reference to “the nucleic acid sequence” is a reference to one or more nucleic acid sequences and equivalents thereof known to those skilled in the art, and so forth.
Ranges may be expressed herein as from “about” one particular value, and/or to “about” another particular value. When such a range is expressed, also specifically contemplated and considered disclosed is the range from the one particular value and/or to the other particular value unless the context specifically indicates otherwise. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another, specifically contemplated embodiment that should be considered disclosed unless the context specifically indicates otherwise. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint unless the context specifically indicates otherwise. The term “about” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20%, ±10%, ±5%, ±1%, ±0.5%, or ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.
As used herein, the terms “activate,” “stimulate,” “enhance” “increase” and/or “induce” (and like terms) are used interchangeably to generally refer to the act of improving or increasing, either directly or indirectly, a concentration, level, function, activity, or behavior relative to the natural, expected, or average, or relative to a control condition. “Activate” in context of an immunotherapy refers to a primary response induced by ligation of a cell surface moiety. For example, in the context of receptors, such stimulation entails the ligation of a receptor and a subsequent signal transduction event. Further, the stimulation event may activate a cell and upregulate or downregulate expression or secretion of a molecule. Thus, indirect or direct ligation of cell surface moieties, even in the absence of a direct signal transduction event, may result in the reorganization of cytoskeletal structures, or in the coalescing of cell surface moieties, each of which could serve to enhance, modify, or alter subsequent cellular responses. As used herein, the terms “activating CD8+ T cells” or “CD8+ T cell activation” refer to a process (e.g., a signaling event) causing or resulting in one or more cellular responses of a CD8+ T cell (CTL), selected from: proliferation, differentiation, cytokine secretion, cytotoxic effector molecule release, cytotoxic activity, and expression of activation markers. As used herein, an “activated CD8+ T cell” refers to a CD8+ T cell that has received an activating signal, and thus demonstrates one or more cellular responses, selected from proliferation, differentiation, cytokine secretion, cytotoxic effector molecule release, cytotoxic activity, and expression of activation markers. Suitable assays to measure CD8+ T cell activation are known in the art and are described herein.
The term “combination therapy” as used herein is meant to refer to administration of one or more therapeutic agents in a sequential manner, that is, wherein each therapeutic agent is administered at a different time, as well as administration of these therapeutic agents, or at least two of the therapeutic agents, in a substantially simultaneous manner. Substantially simultaneous administration can be accomplished, for example, by administering to the subject a single dose having a fixed ratio of each therapeutic agent or in multiple, individual doses for each of the therapeutic agents. For example, one combination of the present disclosure may comprise a pooled sample of one or more nucleic acid molecules comprising one or a plurality of expressible nucleic acid sequences and an adjuvant and/or an anti-viral agent administered at the same or different times. In some embodiments, the pharmaceutical composition of the disclosure can be formulated as a single, co-formulated pharmaceutical composition comprising one or more nucleic acid molecules comprising one or a plurality of expressible nucleic acid sequences and one or more adjuvants and/or one or more anti-viral agents. As another example, a combination of the present disclosure (e.g., DNA vaccines and anti-viral agent) may be formulated as separate pharmaceutical compositions that can be administered at the same or different time. As used herein, the term “simultaneously” is meant to refer to administration of one or more agents at the same time. For example, in certain embodiments, antiviral vaccine or immunogenic composition and antiviral agents are administered simultaneously). Simultaneously includes administration contemporaneously or immediately sequentially, that is during the same period of time. In certain embodiments, the one or more agents are administered simultaneously in the same hour, or simultaneously in the same day. Sequential or substantially simultaneous administration of each therapeutic agent can be effected by any appropriate route including, but not limited to, oral routes, intravenous routes, sub-cutaneous routes, intramuscular routes, direct absorption through mucous membrane tissues (e.g., nasal, mouth, vaginal, and rectal), and ocular routes (e.g., intravitreal, intraocular, etc.). The therapeutic agents can be administered by the same route or by different routes. For example, one component of a particular combination may be administered by intravenous injection while the other component(s) of the combination may be administered intramuscularly only. The components may be administered in any therapeutically effective sequence. A “combination” embraces groups of compounds or non-small chemical compound therapies useful as part of a combination therapy. In some embodiments, the therapeutic agent is an anti-retroviral therapy, (such as one or a combination of efavirenz, lamivudine and tenofovir disoproxil fumarate) or anti-flu therapy (such as TamiFlu®). In some embodiments, the therapeutic agent is one or a combiantion of: abacavir/dolutegravir/lamivudine (Triumeq), dolutegravir/rilpivirine (Juluca), elvitegravir/cobicistat/emtricitabine/tenofovir disoproxil fumarate (Stribild), elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide (Genvoya), efavirenz/emtricitabine/tenofovir disoproxil fumarate (Atripla), emtricitabine/rilpivirine/tenofovir disoproxil fumarate (Complera), emtricitabine/rilpivirine/tenofovir alafenamide (Odefsey), bictegravir, emtricitabine, and tenofovir alafenamide (Biktarvy). In some embodiments, the therapeutic agent is one or a combination of a reverse transcrioptase inhibitor of a retrovirus such as: efavirenz (Sustiva), etravirine (Intelence), nevirapine (Viramune), nevirapine extended-release (Viramune XR), rilpivirine (Edurant), delavirdine mesylate (Rescriptor). In some embodiments, the therapeutic agent is one or a combination of a protease inhibitor of a retrovirus, such as: atazanavir/cobicistat (Evotaz), darunavir/cobicistat (Prezcobix), lopinavir/ritonavir (Kaletra), ritonavir (Norvir), atazanavir (Reyataz), darunavir (Prezista), fosamprenavir (Lexiva), tipranavir (Aptivus).
As used herein, “expression” refers to the process by which a polynucleotide is transcribed from a DNA template (such as into and mRNA or other RNA transcript) and/or the process by which a transcribed mRNA (or administered mRNA) is translated into peptides, polypeptides, or proteins. Transcripts and encoded polypeptides may be collectively referred to as “gene product.” If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell. In some embodiments, the at least first expressible nucleic acid sequence comprises only DNA nucleotides, RNA nucleotides or comprises both RNA and DNA nucleotides. In some embodiments, the at least first expressible nucleic acid consist of RNA. In some embodiments, the at least first expressible nucleic acid consist of DNA.
The terms “functional fragment” means any portion of a polypeptide or nucleic acid sequence from which the respective full-length polypeptide or nucleic acid relates that is of a sufficient length and has a sufficient structure to confer a biological affect that is at least similar or substantially similar to the full-length polypeptide or nucleic acid upon which the fragment is based. In some embodiments, a functional fragment is a portion of a full-length or wild-type nucleic acid sequence that encodes any one of the nucleic acid sequences disclosed herein, and said portion encodes a polypeptide of a certain length and/or structure that is less than full-length but encodes a domain that still biologically functional as compared to the full-length or wild-type protein. In some embodiments, the functional fragment may have a reduced biological activity, about equivalent biological activity, or an enhanced biological activity as compared to the wild-type or full-length polypeptide sequence upon which the fragment is based (such wild-type or full length sequences “reference sequences” or each individually a “reference sequence”). In some embodiments, the functional fragment is derived from the sequence of an organism, such as a human. In such embodiments, the functional fragment may retain about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% sequence identity to the wild-type human sequence upon which the sequence is derived. In some embodiments, the functional fragment may retain about 85%, 80%, 75%, 70%, 65%, or 60% sequence identity to the wild-type sequence upon which the sequence is derived.
By “fragment” is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, preferably, at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or about 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain about 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more nucleotides or amino acids.
“Optional” or “optionally” means that the subsequently described event, circumstance, or material may or may not occur or be present, and that the description includes instances where the event, circumstance, or material occurs or is present and instances where it does not occur or is not present.
The phrase “and/or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Other elements may optionally be present other than the elements specifically identified by the “and/or” clause, whether related or unrelated to those elements specifically identified unless clearly indicated to the contrary. Thus, as a non-limiting example, a reference to “A and/or B,” when used in conjunction with open-ended language such as “comprising” can refer, in some embodiments, to A without B (optionally including elements other than B); in another embodiments, to B without A (optionally including elements other than A); in yet another embodiments, to both A and B (optionally including other elements); etc.
As used herein in the specification and in the claims, “or” should be understood to have the same meaning as “and/or” as defined above. For example, when separating items in a list, “or” or “and/or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of” or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e. “one or the other but not both”) when preceded by terms of exclusivity, “cither,” “one of,” “only one of,” or “exactly one of.” “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law.
As used herein an “antigen” is meant to refer to any substance that elicits an immune response.
As used herein, the term “a CD40 ligand,” “CD40L” or “CD40L polypeptide” refers to a protein that is primarily expressed on activated T cells and is a member of the TNF superfamily of molecules. It binds to CD40 protein on antigen-presenting cells (APC), which leads to many effects depending on the target cell type. In some embodiments, the CD40L polypeptide is a human CD40 ligand comprising the amino acid sequence of SEQ ID NO: 103 encoded by the nucleic acid sequence of SEQ ID NO: 102.
In some embodiments, the CD40L polypeptide is a fragment of the human CD40 ligand comprising the amino acid sequence of SEQ ID NO: 104, SEQ ID NO: 105, or SEQ ID NO: 106.
In some embodiments, the CD40L polypeptide is a mouse CD40 ligand comprising the amino acid sequence of SEQ ID NO: 108 encoded by the nucleic acid sequence of SEQ ID NO: 107.
In some embodiments, the CD40L polypeptide is a fragment of the mouse CD40 ligand comprising the amino acid sequence of SEQ ID NO: 109, SEQ ID NO: 110, or SEQ ID NO: 111.
In some embodiments, the “CD40L” or “CD40L polypeptide,” as used herein, comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, or SEQ ID NO: 111. In some embodiments, the “CD40L” or “CD40L polypeptide,” as used herein, is encoded by a nucleic acid comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 102 or SEQ ID NO: 107. In some embodiments, the “CD40L” or “CD40L polypeptide,” as used herein, refers to a CD40L polypeptide comprising at least about 1 N-linked glycan. In some embodiments, the “CD40L” or “CD40L polypeptide,” as used herein, refers to a CD40L polypeptide comprising at least about 2 N-linked glycan. In some embodiments, the “CD40L” or “CD40L polypeptide,” as used herein, refers to a CD40L polypeptide comprising at least about 3 N-linked glycan. In some embodiments, the “CD40L” or “CD40L polypeptide,” as used herein, refers to a CD40L polypeptide comprising at least about 4 N-linked glycan. In some embodiments, the “CD40L” or “CD40L polypeptide,” as used herein, refers to a CD40L polypeptide comprising at least about 5 N-linked glycan. In some embodiments, the “CD40L” or “CD40L polypeptide,” as used herein, refers to a CD40L polypeptide comprising more than about 5 N-linked glycan.
As used herein, the term “protein of interest” refers to any protein. In some embodiments, the term “protein of interest” refers to any protein that can be expressed in any of the constructs disclosed herein. In some embodiments, the “protein of interest” is a viral antigen. In some embodiments, the “protein of interest” is any of the viral antigens disclosed herein. In some embodiments, the “protein of interest” is a cancer antigen. In some embodiments, the “protein of interest” is a cancer antigen disclosed herein. In some embodiments, the “protein of interest” is any of the protein antigens disclosed herein.
As used herein, the term “electroporation,” “electro-permeabilization,” or “electro-kinetic enhancement” (“EP”), are used interchangeably and are meant to refer to the use of a transmembrane electric field pulse to induce microscopic pathways (pores) in a bio-membrane; their presence allows biomolecules such as plasmids, oligonucleotides, siRNA, drugs, ions, and/or water to pass from one side of the cellular membrane to the other. In some of the disclosed methods of treatment or prevention, the method comprises a step of electroporation of a subject's tissue for a sufficient time and with a sufficient electrical field capable of inducing uptake of the pharmaceutical compositions disclosed herein into the antigen-presenting cells. In some embodiments, the cells are antigen presenting cells.
The term “pharmaceutically acceptable excipient,” “pharmaceutically acceptable carrier” or “pharmaceutically acceptable diluent” as used herein is meant to refer to an excipient, carrier or diluent that can be administered to a subject, together with an agent or the pharmaceutical compositions disclosed herein, and which is inert or fails to eliminate the pharmacological activity of the active agent of the pharmaceutical composition. In some embodiments, the pharmaceutically acceptable carrier does fails to destroy or is incapable of eliminating the pharmacological activity of an active agent/vaccine and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the active agent. The term “pharmaceutically acceptable salt” of nucleic acids as used herein may be an acid or base salt that is generally considered in the art to be suitable for use in contact with the tissues of human beings or animals without excessive toxicity, irritation, allergic response, or other problem or complication. Such salts include mineral and organic acid salts of basic residues such as amines, as well as alkali or organic salts of acidic residues such as carboxylic acids. Specific pharmaceutical salts include, but are not limited to, salts of acids such as hydrochloric, phosphoric, hydrobromic, malic, glycolic, fumaric, sulfuric, sulfamic, suifanilic, formic, toluenesulfonic, methanesulfonic, benzene sulfonic, ethane disulfonic, 2-hydroxyethyl sulfonic, nitric, benzoic, 2-acetoxybenzoic, citric, tartaric, lactic, stearic, salicylic, glutamic, ascorbic, pamoic, succinic, fumaric, maleic, propionic, hydroxymaleic, hydroiodic, phenyiacetic, alkanoic such as acetic, HOOC—(CH2)n-COOH where n is 0-4, and the like. Similarly, pharmaceutically acceptable cations include, but are not limited to sodium, potassium, calcium, aluminum, lithium and ammonium. Those of ordinary skill in the art will recognize from this disclosure and the knowledge in the art that further pharmaceutically acceptable salts for the pooled viral specific antigens or polynucleotides provided herein, including those listed by Remington's Pharmaceutical Sciences, 17th ed., Mack Publishing Company, Easton, PA, p. 1418 (1985). In general, a pharmaceutically acceptable acid or base salt can be synthesized from a parent compound that contains a basic or acidic moiety by any conventional chemical method. Briefly, such salts can be prepared by reacting the free acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in an appropriate solvent.
As used herein, the terms “prevent,” “preventing,” “prevention,” “prophylactic treatment,” and the like, are meant to refer to reducing the probability of developing a disease or condition in a subject, who does not have, but is at risk of or susceptible to developing a disease or condition.
As used herein, the term “purified” means that the polynucleotide or polypeptide or fragment, variant, or derivative thereof is substantially free of other biological material with which it is naturally associated, or free from other biological materials derived, e.g., from a recombinant host cell that has been genetically engineered to express the polypeptide of the present disclosure. That is, e.g., a purified polypeptide of the present disclosure is a polypeptide that is at least from about 70 to 100% pure, i.e., the polypeptide is present in a composition wherein the polypeptide constitutes from about 70 to about 100% by weight of the total composition. In some embodiments, the purified polypeptide of the present disclosure is from about 75% to about 99% by weight pure, from about 80% to about 99% by weight pure, from about 90 to about 99% by weight pure, or from about 95% to about 99% by weight pure.
As used herein, the terms “subject,” “individual,” “host,” and “patient,” are used interchangeably herein and refer to a vertebrate individual, including but not limited to a mammal or human, for whom diagnosis, treatment or therapy is desired, particularly humans. Mammals include, but are not limited to, murines, simians, humans, farm animals, cows, pigs, goats, sheep, horses, dogs, sport animals, and pets. Tissues, cells and their progeny obtained in vivo or cultured in vitro are also encompassed by the definition of the term “subject.” The methods described herein are applicable to both human therapy and veterinary applications. In some instances in the description of the present disclosure, the term “patient” refers to human patients suffering from a particular disease or disorder. In some embodiments, the subject may be a human suspected of having or being identified as at risk to develop a viral infection. In some embodiments, the subject may be diagnosed as having human immunodeficiency virus-1 (HIV-1) and of having or being identified as at risk to develop autoimmune deficiency syndrome or AIDS. In some embodiments, the subject is a mammal, and, in other embodiments, the subject is a human.
The term “therapeutic effect” as used herein is meant to refer to some extent of relief of one or more of the symptoms of a disorder (e.g., HIV infection) or its associated pathology. A “therapeutically effective amount” as used herein is meant to refer to an amount of an agent which is effective, upon single or multiple dose administration (such as a first, second and/or third booster) to the cell or subject, in prolonging the survivability of the patient with such a disorder, reducing one or more signs or symptoms of the disorder, preventing or delaying, and the like beyond that expected in the absence of such treatment. A “therapeutically effective amount” is intended to qualify the amount required to achieve a therapeutic effect. A physician or veterinarian having ordinary skill in the art can readily determine and prescribe the “therapeutically effective amount” (e.g., ED50) of the pharmaceutical composition required. For example, the physician or veterinarian could start doses of the compounds of the present disclosure employed in a pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved.
The terms “treat,” “treated,” “treating,” “treatment,” and the like as used herein are meant to refer to reducing or ameliorating a disorder and/or symptoms associated therewith (e.g., a viral infection). “Treating” can refer to administration of the DNA vaccines described herein to a subject after the onset, or suspected onset, of a viral infection. “Treating” includes the concepts of “alleviating,” which refers to lessening the frequency of occurrence or recurrence, or the severity, of any symptoms or other ill effects related to a virus and/or the side effects associated with viral therapy. The term “treating” also encompasses the concept of “managing” which refers to reducing the severity of a particular disease or disorder in a patient or delaying its recurrence, e.g., lengthening the period of remission in a patient who had suffered from the disease. It is appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition, or symptoms associated therewith be completely eliminated.
For any therapeutic agent described herein the therapeutically effective amount may be initially determined from preliminary in vitro studies and/or animal models. A therapeutically effective dose may also be determined from human data. The applied dose can be adjusted based on the relative bioavailability and potency of the administered agent. Adjusting the dose to achieve maximal efficacy based on the methods described above and other well-known methods is within the capabilities of the ordinarily skilled artisan. General principles for determining therapeutic effectiveness, which may be found in Chapter 1 of Goodman and Gilman's The Pharmacological Basis of Therapeutics, 10th Edition, McGraw-Hill (New York) (2001), incorporated herein by reference, are summarized below. Pharmacokinetic principles provide a basis for modifying a dosage regimen to obtain a desired degree of therapeutic efficacy with a minimum of unacceptable adverse effects. In situations where the drug's plasma concentration can be measured and related to the therapeutic window, additional guidance for dosage modification can be obtained. Drug products are considered to be pharmaceutical equivalents if they contain the same active ingredients and are identical in strength or concentration, dosage form, and route of administration. Two pharmaceutically equivalent drug products are considered to be bioequivalent when the rates and extents of bioavailability of the active ingredient in the two products are not significantly different under suitable test conditions.
The terms “polynucleotide,” “oligonucleotide” and “nucleic acid” are used interchangeably throughout and include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), analogs of the DNA or RNA generated using nucleotide analogs (e.g., peptide nucleic acids and non-naturally occurring nucleotide analogs), and hybrids thereof. Thus, ther term “expressible nucleic acid” or “expressible nucleic acid sequence” as used herein refers to expressible DNA or RNA molecules or expressible DNA or RNA sequences.
The nucleic acid molecule and/or sequences of each embodiment can be single-stranded or double-stranded. In some embodiments, the nucleic acid molecules of the disclosure comprise a contiguous open reading frame encoding an antibody, or a fragment thereof, as described herein. “Nucleic acid” or “oligonucleotide” or “polynucleotide” as used herein may mean at least two nucleotides covalently linked together. The depiction of a single strand also defines the sequence of the complementary strand. Thus, a nucleic acid also encompasses the complementary strand of a depicted single strand. Many variants of a nucleic acid may be used for the same purpose as a given nucleic acid. Thus, a nucleic acid also encompasses substantially identical nucleic acids and complements thereof. A single strand provides a probe that may hybridize to a target sequence under stringent hybridization conditions. Thus, a nucleic acid also encompasses a probe that hybridizes under stringent hybridization conditions. Nucleic acids may be single stranded or double stranded, or may contain portions of both double stranded and single stranded sequence. The nucleic acid may be DNA, both genomic and cDNA, RNA, or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine and isoguanine. Nucleic acids may be obtained by chemical synthesis methods or by recombinant methods. A nucleic acid will generally contain phosphodiester bonds, although nucleic acid analogs maybe included that may have at least one different linkage, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or o-methylphosphoroamidite linkages and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506, which are incorporated by reference in their entireties. Nucleic acids containing one or more non-naturally occurring or modified nucleotides are also included within one definition of nucleic acids. The modified nucleotide analog may he located for example at the 5′-end and/or the 3′-end of the nucleic acid molecule. Representative examples of nucleotide analogs may be selected from sugar- or backbone-modified ribonucleotides. It should be noted, however, that also nucleobase-modified ribonucleotides, i.e. ribonucleotides, containing a non-naturally occurring nucleobase instead of a naturally occurring nucleobase such as uridines or cytidines modified at the 5-position, e.g. 5-(2-amino)propyl uridine, 5-bromo uridine; adenosines and guanosines modified at the 8-position, e.g. 8-bromo guanosine; deaza nucleotides, e.g. 7-deaza-adenosine; 0- and N-alkylated nucleotides, e.g. N6-methyl adenosine are suitable. The 2′-OH-group may be replaced by a group selected from H, OR, R, halo, SH, SR, NH2, NHR, N2 or CN, wherein R is C1-C6 alkyl, alkenyl or alkynyl and halo is F, Cl, Br or I. Modified nucleotides also include nucleotides conjugated with cholesterol through, e.g., a hydroxyprolinol linkage as described in Krutzfeldt et al., Nature (Oct. 30, 2005), Soutschek et al., Nature 432:173-178 (2004), and U.S. Patent Publication No. 20050107325, which are incorporated herein by reference in their entireties. Modified nucleotides and nucleic acids may also include locked nucleic acids (LNA), as described in U.S. Pat. No. 20020115080, which is incorporated herein by reference. Additional modified nucleotides and nucleic acids are described in U.S. Patent Publication No. 20050182005, which is incorporated herein by reference in its entirety. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments, to enhance diffusion across cell membranes, or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs may be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made. In some embodiments, the expressible nucleic acid sequence is in the form of DNA. In some embodiments, the expressible nucleic acid is in the form of RNA with a sequence that encodes the polypeptide sequences disclosed herein and, in some embodiments, the expressible nucleic acid sequence is an RNA/DNA hybrid molecule that encodes any one or plurality of polypeptide sequences disclosed herein.
As used herein, the term “nucleic acid molecule” is a molecule that comprises one or more nucleotide sequences that encode one or more proteins. In some embodiments, a nucleic acid molecule comprises initiation and termination signals operably linked to regulatory elements including a promoter and polyadenylation signal capable of directing expression in the cells of the individual to whom the nucleic acid molecule is administered. In some embodiments, the nucleic acid molecule also includes a plasmid containing one or more nucleotide sequences that encode one or a plurality of viral antigens. In some embodiments, the disclosure relates to a pharmaceutical composition comprising a first, second, third or more nucleic acid molecule, each of which encoding one or a plurality of viral antigens and at least one of each plasmid comprising one or more of the compositions disclosed herein. In some embodiments, the compositions can comprise a nucleic acid molecule that comprises a first, second, third or more expressible nucleic acid sequences, wherein at least one of the first, second or third expressible nucleic acid sequences comprise the domains disclosed herein.
The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-natural amino acids or chemical groups that are not amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. As used herein the term “amino acid” includes natural and/or unnatural or synthetic amino acids, including glycine and both the D or L optical isomers, and amino acid analogs and peptidomimetics.
The “percent identity” or “percent homology” of two polynucleotide or two polypeptide sequences is determined by comparing the sequences using the GAP computer program (a part of the GCG Wisconsin Package, version 10.3 (Accelrys, San Diego, Calif.)) using its default parameters. “Identical” or “identity” as used herein in the context of two or more nucleic acids or amino acid sequences, may mean that the sequences have a specified percentage of residues that are the same over a specified region. The percentage may be calculated by optimally aligning the two sequences, comparing the two sequences over the specified region, determining the number of positions at which the identical residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the specified region, and multiplying the result by 100 to yield the percentage of sequence identity. In cases where the two sequences are of different lengths or the alignment produces one or more staggered ends and the specified region of comparison includes only a single sequence, the residues of single sequence are included in the denominator but not the numerator of the calculation. When comparing DNA and RNA, thymine (T) and uracil (U) may be considered equivalent. Identity may he performed manually or by using a computer sequence algorithm such as BLAST or BLAST 2.0. Briefly, the BLAST algorithm, which stands for Basic Local Alignment Search Tool is suitable for determining sequence similarity. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (ncbi.nlm.nih.gov). This algorithm involves first identifying high scoring sequence pair (HSPs) by identifying short words of length Win the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extension for the word hits in each direction are halted when: 1) the cumulative alignment score falls off by the quantity X from its maximum achieved value; 2) the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or 3) the end of either sequence is reached. The Blast algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The Blast program uses as defaults a word length (W) of 11, the BLOSUM62 scoring matrix (see Henikoff et al., Proc. Natl. Acad. Sci. USA, 1992, 89, 10915-10919, which is incorporated herein by reference in its entirety) alignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparison of both strands. The BLAST algorithm (Karlin et al., Proc. Natl. Acad. Sci. USA, 1993, 90, 5873-5787, which is incorporated herein by reference in its entirety) and Gapped BLAST perform a statistical analysis of the similarity between two sequences. One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide sequences would occur by chance. For example, a nucleic acid is considered similar to another if the smallest sum probability in comparison of the test nucleic acid to the other nucleic acid is less than about 1, less than about 0.1, less than about 0.01, and less than about 0.001. Two single-stranded polynucleotides are “the complement” of each other if their sequences can be aligned in an anti-parallel orientation such that every nucleotide in one polynucleotide is opposite its complementary nucleotide in the other polynucleotide, without the introduction of gaps, and without unpaired nucleotides at the 5′ or the 3′ end of either sequence. A polynucleotide is “complementary” to another polynucleotide if the two polynucleotides can hybridize to one another under moderately stringent conditions. Thus, a polynucleotide can be complementary to another polynucleotide without being its complement.
The term “hybridization” or “hybridizes” as used herein refers to the formation of a duplex between nucleotide sequences that are sufficiently complementary to form duplexes via Watson-Crick base pairing. Two nucleotide sequences are “complementary” to one another when those molecules share base pair organization homology. “Complementary” nucleotide sequences will combine with specificity to form a stable duplex under appropriate hybridization conditions. For instance, two sequences are complementary when a section of a first sequence can bind to a section of a second sequence in an anti-parallel sense wherein the 3′-end of each sequence binds to the 5′-end of the other sequence and each A, T(U), G and C of one sequence is then aligned with a T(U), A, C and G, respectively, of the other sequence. RNA sequences can also include complementary G=U or U=G base pairs. Thus, two sequences need not have perfect homology to be “complementary.” Usually two sequences are sufficiently complementary when at least about 90% (preferably at least about 95%) of the nucleotides share base pair organization over a defined length of the molecule.
By “substantially identical” is meant nucleic acid molecule (or polypeptide) exhibiting at least about 50% identity to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein). Preferably, such a sequence is at least about 60%, more preferably about 80% or 85%, and more preferably about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or even 99% identical at the amino acid level or nucleic acid level to the sequence used for comparison.
A nucleotide sequence is “operably linked” to a regulatory sequence if the regulatory sequence affects the expression (e.g., the level, timing, or location of expression) of the nucleotide sequence. A “regulatory sequence” is a nucleic acid that affects the expression (e.g., the level, timing, or location of expression) of a nucleic acid to which it is operably linked. The regulatory sequence can, for example, exert its effects directly on the regulated nucleic acid, or through the action of one or more other molecules (e.g., polypeptides that bind to the regulatory sequence and/or the nucleic acid). Examples of regulatory sequences include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Further examples of regulatory sequences are described in, for example, Goeddel, 1990, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. and Baron et al., 1995, Nucleic Acids Res. 23:3605-06.
A “vector” is a nucleic acid that can be used to introduce another nucleic acid linked to it into a cell. One type of vector is a “plasmid,” which refers to a linear or circular double stranded DNA molecule into which additional nucleic acid segments can be ligated. Another type of vector is a viral vector (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), comprising additional, exogenous DNA, RNA or hybrid DNA or RNA molecules that can be introduced into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors comprising a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. An “expression vector” is a type of vector that can direct the expression of a chosen polynucleotide. The disclosure relates to any one or plurality of vectors that comprise nucleic acid sequences encoding any one or plurality of amino acid sequence disclosed herein. In some embodiments, the expression vector includes from about 30 to about 100,000 nucleotides (e.g., from about 30 to about 50, from 30 to 100, from 30 to 250, from 30 to 500, from 30 to 1,000, from 30 to 1,500, from 30 to 3,000, from 30 to 5,000, from 30 to 7,000, from 30 to 10,000, from 30 to 25,000, from 30 to 50,000, from 30 to 70,000, from 100 to 250, from 100 to 500, from 100 to 1,000, from 100 to 1,500, from 100 to 3,000, from 100 to 5,000, from 100 to 7,000, from 100 to 10,000, from 100 to 25,000, from 100 to 50,000, from 100 to 70,000, from 100 to 100,000, from 500 to 1,000, from 500 to 1,500, from 500 to 2,000, from 500 to 3,000, from 500 to 5,000, from 500 to 7,000, from 500 to 10,000, from 500 to 25,000, from 500 to 50,000, from 500 to 70,000, from 500 to 100,000, from 1,000 to 1,500, from 1,000 to 2,000, from about 1,000 to about 3,000, from 1,000 to 5,000, from 1,000 to 7,000, from 1,000 to 10,000, from 1,000 to 25,000, from 1,000 to 50,000, from 1,000 to 70,000, from 1,000 to 100,000, from 1,500 to 3,000, from 1,500 to 5,000, from 1,500 to 7,000, from 1,500 to 10,000, from 1,500 to 25,000, from 1,500 to 50,000, from 1,500 to 70,000, from 1,500 to 100,000, from 2,000 to 3,000, from 2,000 to 5,000, from 2,000 to 7,000, from 2,000 to 10,000, from 2,000 to 25,000, from 2,000 to 50,000, from about 2,000 to about 70,000, and from 2,000 to 100,000).
The term “vaccine” as used herein is meant to refer to a composition for generating immunity for the prophylaxis and/or treatment of diseases (e.g., viral infections). Accordingly, vaccines are medicaments which comprise antigens in protein and/or nucleic acid forms and are in animals for generating specific defense and protective substance by vaccination. A “vaccine composition” or a “DNA vaccine composition” can include a pharmaceutically acceptable excipient, carrier or diluent. A “DNA vaccine composition” as used herein can comprise a DNA vaccine, a RNA vaccine or a combination thereof.
“Variants” are intended to mean substantially similar sequences. For nucleic acid molecules, a variant comprises a nucleic acid molecule having deletions (i.e., truncations) at the 5′ and/or 3′ end; deletion and/or addition of one or more nucleotides at one or more internal sites in the native polynucleotide; and/or substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a “native” nucleic acid molecule or polypeptide comprises a naturally occurring or endogenous nucleotide sequence or amino acid sequence, respectively. For nucleic acid molecules, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the polypeptides of the disclosure. Variant nucleic acid molecules also include synthetically derived nucleic acid molecules, such as those generated, for example, by using site-directed mutagenesis but which still encode a protein of the disclosure. Generally, variants of a particular nucleic acid molecule of the disclosure will have at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters as described elsewhere herein. Variants of a particular nucleic acid molecule of the disclosure (i.e., the reference DNA sequence) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant nucleic acid molecule and the polypeptide encoded by the reference nucleic acid molecule. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of nucleic acid molecule of the disclosure is evaluated by comparison of the percent sequence identity shared by the two polypeptides that they encode, the percent sequence identity between the two encoded polypeptides is at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity. In some embodiments, the term “variant” protein is intended to mean a protein derived from the native protein by deletion (so-called truncation) of one or more amino acids at the N-terminal and/or C-terminal end of the native protein; deletion and/or addition of one or more amino acids at one or more internal sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Variant proteins encompassed by the present disclosure are biologically active, that is they continue to possess the desired biological activity of the native protein as described herein. Such variants may result from, for example, genetic polymorphism or from human manipulation. Biologically active variants of a protein of the disclosure will have at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native protein as determined by sequence alignment programs and parameters described elsewhere herein. A biologically active variant of a protein of the disclosure may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue. The proteins or polypeptides of the disclosure may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants and fragments of the proteins can be prepared by mutations in the nucleic acid sequence that encode the amino acid sequence recombinantly.
Finally, it should be understood that all of the individual values and sub-ranges of values contained within an explicitly disclosed range are also specifically contemplated and should be considered disclosed unless the context specifically indicates otherwise. The foregoing applies regardless of whether in particular cases some or all of these embodiments are explicitly disclosed.
Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of skill in the art to which the disclosed method and compositions belong. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present method and compositions, the particularly useful methods, devices, and materials are as described. Publications cited herein and the material for which they are cited are hereby specifically incorporated by reference. Nothing herein is to be construed as an admission that the present disclosure is not entitled to antedate such disclosure by virtue of prior disclosure. No admission is made that any reference constitutes prior art. The discussion of references states what their authors assert, and applicants reserve the right to challenge the accuracy and pertinency of the cited documents. It will be clearly understood that, although a number of publications are referred to herein, such reference does not constitute an admission that any of these documents forms part of the common general knowledge in the art.
Throughout the description and claims of this specification, the word “comprise” and variations of the word, such as “comprising” and “comprises,” means “including but not limited to,” and is not intended to exclude, for example, other additives, components, integers or steps. In particular, in methods stated as comprising one or more steps or operations it is specifically contemplated that each step comprises what is listed (unless that step includes a limiting term such as “consisting of”), meaning that each step is not intended to exclude, for example, other additives, components, integers or steps that are not listed in the step.
Disclosed are expressible nucleic acid sequences, nucleic acid molecules comprising one or plurality of such expressible nucleic acid sequences, and compositions comprising one or plurality of such expressible nucleic acid sequences and/or nucleic acid molecules. The expressible nucleic acid sequence according to the present disclosure comprises a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide, and a second nucleic acid sequence encoding an antigen domain comprising a viral antigen, and optionally, wherein the expressible nucleic acid sequence is free of a nucleic acid sequence encoding a leader sequence. In some embodiments, the expressible nucleic acid sequence further comprises a third nucleic acid sequence encoding a linker domain comprising a linker peptide, wherein the third nucleic acid sequence is positioned between the first nucleic acid sequence and the second nucleic acid sequence in the 5′ to 3′ orientation. Thus, also disclosed are compositions comprising an expressible nucleic acid sequence comprising a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide, a second nucleic acid sequence encoding an antigen domain comprising a viral antigen, and a third nucleic acid sequence encoding a linker domain comprising a linker peptide, wherein the third nucleic acid sequence is positioned between the first nucleic acid sequence and the second nucleic acid sequence in the 5′ to 3′ orientation, and optionally, wherein the expressible nucleic acid sequence is free of a nucleic acid sequence encoding a leader sequence. In some embodiments, the expressible nucleic acid is operably linked to at least one regulatory sequence and/or forms part of a nucleic acid molecule, such as a plasmid.
In some embodiments, compositions of the disclosure relate to a composition comprising one or a plurality of expressible nucleic acid sequences disclosed herein. In some embodiments, the self-assembling polypeptide is a self-assembling peptide that is expressed to envelope an antigen. Transformed or transfected cells exposed to the vaccine can produce the self-assembling peptide that envelopes the viral antigens, thereby stimulating an antigen-specific immune response against the antigen. In some embodiments, the antigen-specific immune response is a therapeutically effective immune response against the virus from which the antigen amino acid sequence is derived.
The disclosure relates to an expressible nucleic acid sequence comprising a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide. Self-assembling polypeptide are polypeptides capable of undergoing spontaneous assembling into ordered nanostructures. Effectively self-assembling polypeptides can act as building blocks to form the scaffold domain of the present disclosure. Any self-assembling polypeptide can be used. In some embodiments, the self assembling polypeptide is from Aquifex aeolicus, Helicobacter pylori, Pyrococcus furiosus or Thermotoga maritima.
A non-limiting example of a self-assembling polypeptide is the lumazine synthase of hyperthermophilic bacterium Aquifex aeolicus having the amino acid sequence of SEQ ID NO: 7 (LS scaffold) encoded by the nucleic acid sequence of SEQ ID NO: 2.
Another non-limiting example of a self-assembling polypeptide is ferritin from Helicobacter pylori having the amino acid sequence of SEQ ID NO: 23 (3BVE scaffold) encoded by the nucleic acid sequence of SEQ ID NO: 13.
A yet another non-limiting example of a self-assembling polypeptide is PfV viral cage from Pyrococcus furiosus (2e0z) having the amino acid sequence of SEQ ID NO: 31 (RBE scaffold) encoded by the nucleic acid sequence of SEQ ID NO: 14.
A further non-limiting example of a self-assembling polypeptide is the self-assembling polypeptide from Thermotoga maritima having the amino acid sequence of SEQ ID NO: 26 (13 scaffold) encoded by the nucleic acid sequence of SEQ ID NO: 15.
Accordingly, in some embodiments, the self-assembling polypeptide encoded by the expressible nucleic acid sequence of the present disclosure comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 26, or SEQ ID NO: 31, or a functional fragment thereof. In some embodiments, the self-assembling polypeptide comprises the amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 26, or SEQ ID NO: 31, or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the self-assembling polypeptide comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the self-assembling polypeptide comprises the nucleotide sequence of SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof. In other embodiments, the nucleic acid sequence encoding the self-assembling polypeptide comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to a nucleic acid sequence that is complementary to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the self-assembling polypeptide comprises a nucleic acid sequence that is complementary to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof.
In some embodiments, the compostions or pharmaceutical compositions of the disclosure comprises a nucleic acid molecule comprising an expressible nucleic acid that encodes a self-assembling polypeptide that is 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof; or an expressible nucleic acid that encodes a self-assembling polypeptide that is 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to the complementary sequence of SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof. In some embodiments, composition or pharmaceutical composition of the disclosure relate to a vector or a nucleic acid molecule comprising an expressible RNA sequence that encodes a self-assembling polypeptide that is optionally in sequence with one or more additional expressible RNA sequences that encode a viral antigen. In some embodiments, the expressible DNA or RNA sequence that encodes a self-assembling polypeptide is from about 300 to 500 nucletides in length. In some embodiments, the expressible DNA or RNA sequence that encodes a self-assembling polypeptide is from about 350 to 480 nucletides in length. In some embodiments, the expressible DNA or RNA sequence that encodes a self-assembling polypeptide is from about 350 to 460 nucletides in length. In some embodiments, the expressible DNA or RNA sequence that encodes a self-assembling polypeptide is from about 300 to 500 nucletides in length. In some embodiments, the expressible DNA or RNA sequence that encodes a self-assembling polypeptide is from about 400 to 500 nucletides in length. In some embodiments, the expressible DNA or RNA sequence that encodes a self-assembling polypeptide is from about 390 to 410 nucletides in length. In some embodiments, the expressible DNA or RNA sequence that encodes a self-assembling polypeptide is from about 300 to 410 nucletides in length. In some embodiments, the expressible DNA or RNA sequence that encodes a self-assembling polypeptide is from about 300 to 500 nucletides in length.
The disclose relates to an expressible nucleic acid sequence comprising a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide, and a second nucleic acid sequence encoding an antigen domain comprising a viral antigen. In some embodiments, the nucleic acid molecule encodes a fusion peptide comprising one or a plurality of self-assembling peptides and one or a plurality of viral antigens. In some embodiments, upon administration to a subject, the composition comprising a nucleic acid comprising the expressible nucleic acid sequence of the present disclosure is transfected or transduced into an antigen presenting cell which encodes the expressible nucleic acid sequence. Upon expression, the self-assembling peptides assemble into a nanoparticle comprising the one or plurality of viral antigens. Antigen presenting cells expressing the one or plurality of viral antigens can elicit a therapeutically effective antigen-specific immune response against the virus in a subject. Any viral antigen may be used. In some embodiments, the viral antigen can be an antigen from a retrovirus, flavivirus, Nipah virus, West Nile virus, human papillomavirus, respiratory syncytial virus, filovirus, zaire ebolavirus, sudan ebolavirus, marburgvirus or influenza virus, or any virus disclosed in Table 1 below. For example, in some embodiments, the viral antigen can be an antigen from human immunodeficiency virus-1 (HIV-1). In other embodiments, the viral antigen can be an antigen from influenza virus.
Viral antigens are known for several genera of viruses and viral strains. A non-limiting example of a viral antigen is a fragment of gp120 having the amino acid sequence of SEQ ID NO: 9 (GT8) encoded by the nucleic acid sequence of SEQ ID NO: 4.
Other non-limiting examples of viral antigens are provided in Table 1.
Influenza HA protein (from past patent US20180344842A1, which is incorporated by reference in its entirety)
The accession numbers are as follows: GQ323579.1 (ACS72657.1), GQ323564.1 (ACS72654.1), GQ323551.1 (ACS72652.1), GQ323530.1 (ACS72651.1), GQ323520.1 (ACS72650.1), GQ323495.1 (ACS72648.1), GQ323489.1 (ACS72647.1), GQ323486.1 (ACS72646.1), GQ323483.1 (ACS72645.1), GQ323455.1 (ACS72641.1), GQ323451.1 (ACS72640.1), GQ323443.1 (ACS72638.1), GQ293077.1 (ACS68822.1), GQ288372.1 (ACS54301.1), GQ287625.1 (ACS54262.1), GQ287627.1 (ACS54263.1), GQ287623.1 (ACS54261.1), GQ287621.1 (ACS54260.1), GQ286175.1 (ACS54258.1), GQ283488.1 (ACS50088.1), GQ280797.1 (ACS45035.1), GQ280624.1 (ACS45017.1), GQ280121.1 (ACS45189.1), GQ261277.1 (ACS34968.1), GQ253498.1 (ACS27787.1), GQ323470.1 (ACS72643.1), GQ253492.1 (ACS27780.1), FJ981613.1 (ACQ55359.1), FJ971076.1 (ACP52565.1), FJ969540.1 (ACP44189.1), FJ969511.1 (ACP44150.1), FJ969509.1 (ACP44147.1), GQ255900.1 (ACS27774.1), GQ255901.1 (ACS27775.1), FJ966974.1 (ACP41953.1), GQ261275.1 (ACS34967.1), FJ966960.1 (ACP41935.1), FJ966952.1 (ACP41926.1), FJ966082.1 (ACP41105.1), GQ255897.1 (ACS27770.1), CY041645.1 (ACS27249.1), CY041637.1 (ACS27239.1), CY041629 (ACS27229.1), GQ323446.1 (ACS72639.1), CY041597.1 (ACS27189.1), CY041581.1 (ACS14726.1), CY040653.1 (ACS14666.1), CY041573.1 (ACS14716.1), CY041565.1 (ACS14706.1), CY041541.1 (ACS14676.1), GQ258462.1 (ACS34667.1), CY041557.1 (ACS14696.1), CY041549.1 (ACS14686.1), GQ283484.1 (ACS50084.1), GQ283493.1 (ACS50095.1), GQ303340.1 (ACS71656.1), GQ287619.1 (ACS54259.1), GQ267839.1 (ACS36632.1), GQ268003.1 (ACS36645.1), CY041621.1 (ACS27219.1), CY041613.1 (ACS27209.1), CY041605.1 (ACS27199.1), FJ966959.1 (ACP41934.1), FJ966982.1 (ACP41963.1), CY039527.2 (ACQ45338.1), FJ981612.1 (ACQ55358.1), FJ981615.1 (ACQ55361.1), FJ982430.1 (ACQ59195.1), FJ998208.1 (ACQ73386.1), GQ259909.1 (ACS34705.1), GQ261272.1 (ACS34966.1), GQ287621.1 (ACS54260.1), GQ290059.1 (ACS66821.1), GQ323464.1 (ACS72642.1), GQ323473.1 (ACS72644.1), GQ323509.1 (ACS72649.1). GQ323560.1 (ACS72653.1). GQ323574.1 (ACS72655.1), and GQ323576.1 (ACS72656.1).
Filoviruses (from US20180344840A1. which is incorporated by reference in its entirety)
Accordingly, in some embodiments, the viral antigen encoded by the expressible nucleic acid sequence of the present disclosure comprises at least about 60%. 65%. 70%. 75%. 80%. 85%. 90%, 95%. or 99% sequence identity to SEQ ID NO: 9. SEQ ID NO: 45. SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67, or a functional fragment thereof. In some embodiments, the viral antigen comprises the amino acid sequence of SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67, or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the viral antigen comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 4, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52 or SEQ ID NO: 54 or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the viral antigen comprises the nucleotide sequence of SEQ ID NO: 4, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52 or SEQ ID NO: 54 or a functional fragment thereof. In other embodiments, the nucleic acid sequence encoding the viral antigen comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to a nucleic acid sequence that is complementary to SEQ ID NO: 4, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52 or SEQ ID NO: 54 or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the viral antigen comprises a nucleic acid sequence that is complementary to SEQ ID NO: 4, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52 or SEQ ID NO: 54 or a functional fragment thereof. In some embodiments, the antigens for the present disclosure comprise at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to any antigen sequences disclosed in the Examples disclosed herein, particularly Examples 8-11.
In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1100 to 1300 nucletides in length. In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1100 to 1200 nucletides in length. In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1100 to 1300 nucletides in length.
In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1200 to 1210 nucletides in length. In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1180 to 1220 nucletides in length. In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1180 to 1215 nucletides in length. In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1180 to 1210 nucletides in length. In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1180 to 1200 nucletides in length. In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1220 to 1230 nucletides in length.
In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1100 to 1300 nucletides in length. In some embodiments, the composition or pharmaceutical composition of the disclosure comprises an expressible DNA or RNA sequence that encodes a viral antigen is from about 1100 to 1300 nucletides in length.
The disclosure relates, in some embodiments, to an expressible nucleic acid sequence comprising, in addition to the first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide and the second nucleic acid sequence encoding an antigen domain comprising a viral antigen described above, a third nucleic acid sequence encoding a linker domain comprising a linker peptide, wherein the third nucleic acid sequence is positioned between the first nucleic acid sequence and the second nucleic acid sequence in the 5′ to 3′ orientation. Any type of linker or linker peptide can be used. The term “linker” or “linker peptide” is used interchangeable herein.
In some embodiments, each linker or linker peptide is independently selectable from about 0 to about 25, about 1 to about 25, about 2 to about 25, about 3 to about 25, about 4 to about 25, about 5 to about 25, about 6 to about 25, about 7 to about 25, about 8 to about 25, about 9 to about 25, about 10 to about 25, about 11 to about 25, about 12 to about 25, about 13 to about 25, about 14 to about 25, about 15 to about 25, about 16 to about 25, about 17 to about 25, about 18 to about 25, about 19 to about 25, about 20 to about 25, about 21 to about 25, about 22 to about 25, about 23 to about 25, about 24 to about 25 natural or non-natural amino acids in length.
In some embodiments, each linker or linker peptide is about 0, about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25 natural or non-natural amino acids in length. In some embodiments, each linker or linker peptide is independently selectable from a linker or linker peptide that is about 0, about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25 natural or non-natural amino acids in length. In some embodiments, each linker or linker peptide is about 21 natural or non-natural amino acids in length.
In some embodiments, the length of each linker or linker peptide is different. For example, in some embodiments, the length of a first linker or linker peptide is about 0, about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25 natural or non-natural amino acids in length, and the length of a second linker is about 0, about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25 natural or non-natural amino acids in length, where the length of the first linker is different from the length of the second linker. Various configurations can be envisioned by the present disclosure, where the linker domain comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more linkers or linker peptides wherein the linkers or linker peptides are of similar or different lengths.
In some embodiments, two linkers or linker peptides can be used together. Accordingly, in some embodiments, the first linker or linker peptide is independently selectable from about 0 to about 25 natural or non-natural amino acids in length, about 0 to about 25, about 1 to about 25, about 2 to about 25, about 3 to about 25, about 4 to about 25, about 5 to about 25, about 6 to about 25, about 7 to about 25, about 8 to about 25, about 9 to about 25, about 10 to about 25, about 11 to about 25, about 12 to about 25, about 13 to about 25, about 14 to about 25, about 15 to about 25, about 16 to about 25, about 17 to about 25, about 18 to about 25, about 19 to about 25, about 20 to about 25, about 21 to about 25, about 22 to about 25, about 23 to about 25, about 24 to about 25 natural or non-natural amino acids in length. In some embodiments, the second linker or linker peptide is independently selectable from about 0 to about 25, about 1 to about 25, about 2 to about 25, about 3 to about 25, about 4 to about 25, about 5 to about 25, about 6 to about 25, about 7 to about 25, about 8 to about 25, about 9 to about 25, about 10 to about 25, about 11 to about 25, about 12 to about 25, about 13 to about 25, about 14 to about 25, about 15 to about 25, about 16 to about 25, about 17 to about 25, about 18 to about 25, about 19 to about 25, about 20 to about 25, about 21 to about 25, about 22 to about 25, about 23 to about 25, about 24 to about 25 natural or non-natural amino acids in length. In some embodiments, the first linker or linker peptide is independently selectable from a linker or linker peptide that is about 0, about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25 natural or non-natural amino acids in length. In some embodiments, the second linker or linker peptide is independently selectable from a linker or linker peptide that is about 0, about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25 natural or non-natural amino acids in length.
A non-limiting example of a linker peptide may comprise the amino acid sequence of GGSGGSGGSGGSGGG (SEQ ID NO: 8) encoded by the nucleic acid sequence of GGAGGCTCCGGAGGATCTGGAGGGAGTGGAGGCTCAGGAGGAGGC (SEQ ID NO: 3).
A linker or lilnker peptide can be either flexible or rigid or a combination thereof. An example of a flexible linker is a GGS repeat. In some embodiments, the GGS can be repeated about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times. Non-limiting examples of such linker peptides may comprise the amino acid sequence of GGSGGSGGS (SEQ ID NO: 22), GGSGGSGGSGGS (SEQ ID NO: 27), or GGSGGSGGSGGSGGGGSGGGSGGG (SEQ ID NO: 32). An example of a rigid linker is 4QTL-115 Angstroms, single chain 3-helix bundle represented by the sequence:
Other non-limiting examples of linker peptides may be encoded by the nucleic acid sequence of:
Accordingly, in some embodiments, the linker peptide encoded by the expressible nucleic acid sequence of the present disclosure comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32, or a functional fragment thereof. In some embodiments, the linker peptide comprises the amino acid sequence of SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32, or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the linker peptide comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 3, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19 or SEQ ID NO: 29, or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the linker peptide comprises the nucleotide sequence of SEQ ID NO: 3, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19 or SEQ ID NO: 29, or a functional fragment thereof. In other embodiments, the nucleic acid sequence encoding the linker peptide comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to a nucleic acid sequence that is complementary to SEQ ID NO: 3, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19 or SEQ ID NO: 29, or a functional fragment thereof. In some embodiments, the nucleic acid sequence encoding the linker peptide comprises a nucleic acid sequence that is complementary to SEQ ID NO: 3, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19 or SEQ ID NO: 29, or a functional fragment thereof.
The expressible nucleic acid sequence of the present disclosure is optionally free of a nucleic acid sequence encoding a leader sequence. A “leader sequence” may be from time to time refers to a “signal peptide” and thus, the terms “leader sequence” and “signal peptide” are used interchangeably herein and refer to an amino acid sequence that can be linked at the amino terminus of a protein set forth herein. Signal peptides/leader sequences typically direct localization of a protein. Signal peptides/leader sequences used herein preferably facilitate secretion of the protein from the cell in which it is produced. Signal peptides/leader sequences are often cleaved from the remainder of the protein, often referred to as the mature protein, upon secretion from the cell. Signal peptides/leader sequences, when present, are linked at the N terminus of the protein.
Although the expressible nucleic acid sequence of the present disclosure is optionally free of a nucleic acid sequence encoding a leader sequence, if the presence of such a leader sequence is required for proper secretion of the protein produced by the cell, it may nonetheless be included in the polypeptide encoded by the expressible nucleic acid sequence of the present disclosure.
A non-limiting example of the leader sequence is the amino acid sequence of MDWTWILFLVAAATRVHS (SEQ ID NO: 6) encoded by the nucleic acid sequence of atggactggacctggattctgttcctggtggccgccgccacaagggtgcacagc (SEQ ID NO: 1).
Another non-limiting example of the leader sequence is the amino acid sequence of MDWTWRILFLVAAATGTHA (SEQ ID NO: 40) encoded by the nucleic acid sequence of atggactggacctggagaatcctgttcctggtggccgccgccaccggcacacacgccgatacacacttccccatctgcatcttttg ctgtggctgttgccataggtccaagtgtgggatgtgctgcaaaact (SEQ ID NO: 39).
A yet another non-limiting example of the leader sequence is the amino acid sequence of MRRMQLLLLIALSLALVTNS (SEQ ID NO: 101).
Thus, in some embodiments when the leader sequence is present, the leader sequence may comprise at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 6, SEQ ID NO: 40, or SEQ ID NO: 101, or a functional fragment thereof. In some embodiments when the leader sequence is present, the leader sequence may comprise the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 40, or SEQ ID NO: 101, or a functional fragment thereof. In some embodiments when the leader sequence is present, the leader sequence may be encoded by a nucleic acid sequence comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 1 or SEQ ID NO: 39, or a functional fragment thereof. In some embodiments when the leader sequence is present, the leader sequence may be encoded by the nucleic acid sequence of SEQ ID NO: 1 or SEQ ID NO: 39, or a functional fragment thereof. In other embodiments when the leader sequence is present, the leader sequence may be encoded by a nucleic acid sequence comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to a nucleic acid sequence that is complementary to SEQ ID NO: 1 or SEQ ID NO: 39, or a functional fragment thereof. In some embodiments when the leader sequence is present, the leader sequence may be encoded by a nucleic acid sequence that is complementary to SEQ ID NO: 1 or SEQ ID NO: 39, or a functional fragment thereof.
In some embodiments, the expressible nucleic acid sequence can be operably linked to one or a plurality of regulatory sequences. Examples of regulatory sequences include, but not limited to, promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Further examples of regulatory sequences are described in, for example, Goeddel, 1990, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. and Baron et al., 1995, Nucleic Acids Res. 23:3605-06.
In some embodiments, the expressible nucleic acid sequence comprised in the composition of the present disclosure is an RNA molecule or RNA transcript. In such embodiments therefore, the expressible nucleic acid sequence comprises a first RNA sequence encoding a scaffold domain comprising any of the self-assembling polypeptides disclosed herein and a second RNA sequence encoding one or more of any of the viral antigens disclosed herein, and optionally, wherein the expressible RNA sequence is free of a RNA sequence encoding a leader sequence. In some embodiments, the expressible RNA sequence may comprise a third RNA sequence encoding a linker domain comprising any of the linker peptides disclosed herein, wherein the third RNA sequence is positioned between the first RNA sequence and the second RNA sequence in the 5′ to 3′ orientation.
In some embodiments, the first RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a complement thereof. In some embodiments, the first RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence comprising SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a complement thereof. In some embodiments, the first RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence encoding a self-assembling polypeptide comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26, or a functional fragment thereof. In some embodiments, the first RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence encoding a self-assembling polypeptide comprising SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26, or a functional fragment thereof.
In some embodiments, the second RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 4, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52 or SEQ ID NO: 54 or a complement thereof. In some embodiments, the second RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence comprising SEQ ID NO: 4, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52 or SEQ ID NO: 54 or a complement thereof. In some embodiments, the second RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence encoding a viral antigen comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67, or a functional fragment thereof. In some embodiments, the second RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence encoding a viral antigen comprising SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67, or a functional fragment thereof.
In some embodiments, the third RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 3, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19 or SEQ ID NO: 29, or a complement thereof. In some embodiments, the third RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence comprising SEQ ID NO: 3, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19 or SEQ ID NO: 29, or a complement thereof. In some embodiments, the third RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence encoding a linker peptide comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32, or a functional fragment thereof. In some embodiments, the third RNA sequence of the expressible RNA sequence of the present disclosure comprises an RNA sequence encoding a linker peptide comprising SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32, or a functional fragment thereof.
In some embodiments, the expressible RNA sequence of the present disclosure comprises an RNA sequence comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97 or SEQ ID NO: 99, or a complement thereof. In some embodiments, the expressible RNA sequence of the present disclosure comprises an RNA sequence comprising SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97 or SEQ ID NO: 99, or a complement thereof. In some embodiments, the expressible RNA sequence of the present disclosure comprises an RNA sequence encoding a polypeptide comprising at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 69, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98 or SEQ ID NO: 100, or a functional fragment thereof. In some embodiments, the expressible RNA sequence of the present disclosure comprises an RNA sequence encoding a polypeptide comprising SEQ ID NO: 69, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98 or SEQ ID NO: 100, or a functional fragment thereof.
In one aspect, the present disclosure also relates to a nucleic acid molecule that comprises any of the disclosed expressible nucleic acid sequences. For example, the expressible nucleic acid sequence disclosed herein can be part of a plasmid and thus the nucleic acid molecule is a plasmid comprising such an expressible nucleic acid sequence. Provided herein is a vector or plasmid that is capable of expressing at least a monomer of a self-assembling nanoparticle and a viral antigen construct or constructs in the cell of a mammal in a quantity effective to elicit an immune response in the mammal. The vector or plasmid may comprise heterologous nucleic acid encoding the one or more viral antigens (such as HIV-1 antigens). The vector may be a plasmid. The plasmid may be useful for transfecting cells with nucleic acid encoding a viral antigen, which the transformed host cell is cultured and maintained under conditions wherein expression of the viral antigen takes place and wherein the structure of the nanoparticle with the antigen elicits an immune response of a magnitude greater than and/or more therapeutically effective than the immune response elicited by the antigen alone. The plasmid may further comprise an initiation codon, which may be upstream of the expressible sequence, and a stop codon, which may be downstream of the coding sequence. The initiation and termination codon may be in frame with the expressible sequence.
The plasmid may also comprise a promoter that is operably linked to the coding sequence. The promoter operably linked to the coding sequence may be a promoter from simian virus 40 (SV40), a mouse mammary tumor virus (MMTV) promoter, a human immunodeficiency virus (HIV) promoter such as the bovine immunodeficiency virus (BIV) long terminal repeat (LTR) promoter, a Moloney virus promoter, an avian leukosis virus (ALV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter, Epstein Barr virus (EBV) promoter, or a Rous sarcoma virus (RSV) promoter. The promoter may also be a promoter from a human gene such as human actin, human myosin, human hemoglobin, human muscle creatine, or human metalothionein. The promoter may also be a tissue specific promoter, such as a muscle or skin specific promoter, natural or synthetic. Examples of such promoters are described in US patent application publication no. US20040175727, the contents of which are incorporated herein in its entirety. The plasmid may also comprise a polyadenylation signal, which may be downstream of the coding sequence. The polyadenylation signal may be a SV40 polyadenylation signal, LTR polyadenylation signal, bovine growth hormone (bGH) polyadenylation signal, human growth hormone (hGH) polyadenylation signal, or human β-globin polyadenylation signal. The SV40 polyadenylation signal may be a polyadenylation signal from a pCEP4 plasmid (Invitrogen, San Diego, CA).
The plasmid may also comprise an enhancer upstream of the coding sequence. The enhancer may be human actin, human myosin, human hemoglobin, human muscle creatine or a viral enhancer such as one from CMV, FMDV, RSV or EBV. Polynucleotide function enhancers are described in U.S. Pat. Nos. 5,593,972, 5,962,428, and WO94/016737, the contents of each are fully incorporated by reference. The plasmid may also comprise a mammalian origin of replication in order to maintain the plasmid extrachromosomally and produce multiple copies of the plasmid in a cell. The plasmid may be pVAX1, pCEP4 or pREP4 from ThermoFisher Scientific (San Diego, CA), which may comprise the Epstein Barr virus origin of replication and nuclear antigen EBNA-1 coding region, which may produce high copy episomal replication without integration.
In some embodiments, the vector can be pVAX1 or a pVax1 variant with changes such as the variant plasmid described herein. The variant pVax1 plasmid is a 2998 basepair variant of the backbone vector plasmid pVAX1 (Invitrogen, Carlsbad CA). The CMV promoter is located at bases 137-724. The T7 promoter/priming site is at bases 664-683. Multiple cloning sites are at bases 696-811. Bovine GH polyadenylation signal is at bases 829-1053. The Kanamycin resistance gene is at bases 1226-2020. The pUC origin is at bases 2320-2993. The vaccine may comprise the consensus antigens and plasmids at quantities of from about 1 nanogram to 100 milligrams; about 1 microgram to about 10 milligrams; or preferably about 0.1 microgram to about 10 milligrams; or more preferably about 1 milligram to about 2 milligram. In some embodiments, pharmaceutical compositions according to the present disclosure comprise from about 1 nanogram to about 1000 micrograms of DNA. The nucleic acid sequence for the pVAX1 backbone sequence is as follows:
Other vectors or plasmids that can be used herein to produce the vaccine of the present disclosure include, but not limited to, pcDNA3.1(+), pCI mammalian expression vector, pSI vector, pZeoSV2(+), phCMV1, pTCP and pIRES with their respective backbone sequence as follows.
The pcDNA3.1(+) backbone sequence:
The pCI mammalian expression vector backbone sequence:
The pSI vector backbone sequence:
The pZeoSV2(+) backbone sequence:
The phCMV1 backbone sequence:
The pTCP backbone sequence:
The pIRES backbone sequence:
In some embodiments therefore, the disclosure relates to a composition comprising a nucleic acid molecule comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof. In some embodiments, the disclosure relates to a composition comprising a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof. In some embodiments, the disclosure relates to a composition comprising a nucleic acid molecule that is a pVax variant.
In some embodiments, the disclosure relates to a composition comprising a nucleic acid molecule or a plasmid comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence comprising a first nucleic acid sequence encoding a scaffold domain comprising any of the self-assembling polypeptides disclosed herein and a second nucleic acid sequence encoding an antigen domain comprising any of the viral antigens disclosed herein. In some embodiments therefore, the composition of the present disclosure comprises a nucleic acid molecule or a plasmid comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence comprising a first nucleic acid sequence comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof, and a second nucleic acid sequence comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 4, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52 or SEQ ID NO: 54 or a functional fragment thereof. In some embodiments, the composition of the present disclosure comprises a nucleic acid molecule or a plasmid comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence comprising a first nucleic acid sequence encoding a self-assembling polypeptide comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26, or a functional fragment thereof, and a second nucleic acid sequence encoding a viral antigen comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67, or a functional fragment thereof.
In some embodiments, the expressible nucleic acid sequences comprised in such nucleic acid molecules or plasmids further comprise a third nucleic acid sequence encoding a linker domain comprising any of the linker peptides disclosed herein. In some embodiments therefore, the composition of the present disclosure comprises a nucleic acid molecule or a plasmid comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence comprising a first nucleic acid sequence comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15, or a functional fragment thereof, a second nucleic acid sequence comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 4, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52 or SEQ ID NO: 54, or a functional fragment thereof, and a third nucleic acid sequence comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 3, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19 or SEQ ID NO: 29, or a functional fragment thereof. In some embodiments, the composition of the present disclosure comprises a nucleic acid molecule or a plasmid comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence comprising a first nucleic acid sequence encoding a self-assembling polypeptide comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26, or a functional fragment thereof, a second nucleic acid sequence encoding a viral antigen comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67, or a functional fragment thereof, and a third nucleic acid sequence encoding a linker comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32, or a functional fragment thereof.
In some embodiments, the expressible nucleic acid sequences comprised in such nucleic acid molecules or plasmids are free of a nucleic acid sequence encoding a leader sequence.
In some embodiments, the expressible nucleic acid sequence comprised in the nucleic acid molecule or plasmid of the present disclosure comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97 or SEQ ID NO: 99, or a functional fragment thereof. In some embodiments, the expressible nucleic acid sequence of the present disclosure comprises the nucleic acid sequence of SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97 or SEQ ID NO: 99, or a functional fragment thereof. In some embodiments, the expressible nucleic acid sequence comprised in the nucleic acid molecule or plasmid of the present disclosure encodes a polypeptide comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 69, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98 or SEQ ID NO: 100, or a functional fragment thereof. In some embodiments, the expressible nucleic acid sequence of the present disclosure encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 69, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98 or SEQ ID NO: 100, or a functional fragment thereof.
In some embodiments, the disclosure relates to a composition comprising a nucleic acid molecule or a plasmid comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97 or SEQ ID NO: 99, or a functional fragment thereof. In some embodiments, the disclosure relates to a composition comprising a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97 or SEQ ID NO: 99, or a functional fragment thereof. In some embodiments, the disclosure relates to a composition comprising a nucleic acid molecule comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence encoding a polypeptide comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 69, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98 or SEQ ID NO: 100, or a functional fragment thereof. In some embodiments, the disclosure relates to a composition comprising a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 56, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:80, SEQ ID NO: 81 or SEQ ID NO: 82, or a functional fragment thereof, and an expressible nucleic acid sequence encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 69, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98 or SEQ ID NO: 100, or a functional fragment thereof.
In some embodiments, the disclosure relates to nucleic acid molecules comprising a plasmid comprising a regulatory sequence operably linked one or more expressible nucleic acid sequences, wherein the expressible nucleic acid sequences comprise at least a first nucleic acid sequence encoding a scaffold domain comprising a self-assembling polypeptide, and a second nucleic acid sequence encoding an antigen domain comprising any one or plurality of viral antigens disclosed herein. In some embodiments, the first and second nucleic acids are linked by a linker peptide disclosed herein. In some embodiments, the first and second nucleic acids are in a 5′ to 3′ orientation and free of an IgE or IgG linker positioned 5′ of the 5′ end of the first and/or second nucleic acid sequence. In some embodiments, the disclosure relates to a composition comprising a nucleic acid molecule comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56, or a functional fragment thereof, and positioned within a multiple cloning site are one or more expressible nucleic acid sequences of the present disclosure.
In some embodiments, the disclosed compositions can be vectors comprising a DNA backbone with an expressible insert comprising one or more of the nucleic acid sequences encoding a self-assembling polypeptide, linker and one or a plurality of viral antigens. In some embodiments, the disclosure relates to a viral vector comprising a DNA or RNA sequence that comprises one or more of the nucleic acid sequences encoding a self-assembling polypeptide, linker and one or a plurality of viral antigens.
Disclosed are the polypeptide sequences encoded by the disclosed nucleic acid sequences. In some embodiments, the disclosure relates to compositions comprising polypeptide sequences encoded by the expressible nucleic acid molecule of the present disclosure comprising a scaffold domain comprising a self-assembling polypeptide and an antigen domain comprising a viral antigen, and optionally comprising a linker domain comprising a linker peptide. The disclosure also relates to cells expressing one or more such polypeptides disclosed herein.
In some embodiments, the polypeptide encoded by the expressible nucleic acid molecule of the present disclosure comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97% or 99% sequence identity to SEQ ID NO: 69, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98 or SEQ ID NO: 100, or a functional fragment thereof. In some embodiments, the polypeptide encoded by the expressible nucleic acid molecule of the present disclosure comprises the amino acid sequence of SEQ ID NO: 69, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98 or SEQ ID NO: 100, or a functional fragment thereof. The sequences of SEQ ID NO: 68 and SEQ ID NO: 69 also refer to in the present disclosure as GT8_180 mer_pVAX or DLnano_PfV_GT8.
In some embodiments, the self-assembling polypeptide comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97% or 99% sequence identity to SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26, or a functional fragment thereof. In some embodiments, the self-assembling polypeptide comprises the amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 23, SEQ ID NO: 31 or SEQ ID NO: 26, or a functional fragment thereof.
In some embodiments, the viral antigen encoded by the expressible nucleic acid sequence of the present disclosure comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67, or a functional fragment thereof. In some embodiments, the viral antigen comprises the amino acid sequence of SEQ ID NO: 9, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 65, SEQ ID NO: 66 or SEQ ID NO: 67, or a functional fragment thereof.
In some embodiments, the linker peptide encoded by the expressible nucleic acid sequence of the present disclosure comprises at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32, or a functional fragment thereof. In some embodiments, the linker peptide comprises the amino acid sequence of SEQ ID NO: 8, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 27 or SEQ ID NO: 32, or a functional fragment thereof.
tcaagctgctgaacgaacaggtgaacaaagagatgcagtctagcaacctgtacatgtccatgagctcctggtgctatacccactctctg
gacggagcaggcctgttcctgtttgatcacgccgccgaggagtacgagcacgccaagaagctgatcatcttcctgaatgagaacaat
gtgcccgtgcagctgacctctatcagcgcccctgagcacaagttcgagggcctgacacagatctttcagaaggcctacgagcacgag
cagcacatctccgagtctatcaacaatatcgtggaccacgccatcaagtccaaggatcacgccacattcaactttctgcagtggtacgtg
gccgagcagcacgaggaggaggtgctgtttaaggacatcctggataagatcgagctgatcggcaatgagaaccacgggctgtacct
ggcagatcagtatgtcaagggcatcgctaagtcaaggaaaagctgataa
YTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKA
YEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENH
GLYLADQYVKGIAKSRKS
agccaaagcagaggaagcagcacggaagatggaagaactgttcaagaagcacaagatcgtggccgtgctgagggccaactccgt
ggaggaggccaagaagaaggccctggccgtgttcctgggcggcgtgcacctgatcgagatcacctttacagtgcccgacgccgata
ccgtgatcaaggagctgtctttcctgaaggagatgggagcaatcatcggagcaggaaccgtgacaagcgtggagcagtgcagaaag
gccgtggagagcggcgccgagtttatcgtgtcccctcacctggacgaggagatctctcagttctgtaaggagaagggcgtgttttacat
gccaggcgtgatgacccccacagagctggtgaaggccatgaagctgggccacacaatcctgaagctgttccctggcgaggtggtgg
gcccacagtttgtgaaggccatgaagggccccttccctaatgtgaagtttgtgcccaccggcggcgtgaacctggataacgtgtgcga
gtggttcaaggcaggcgtgctggcagtgggcgtgggcagcgccctggtgaagggcacacccgtggaagtcgctgagaaggcaaa
ggcattcgtggaaaagattagggggtgtactgagtgataa
NSVEEAKKKALAVFLGGVHLIEITFTVPDADTVIKELSFLKEMGAIIGAGTVTSVEQC
VVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPVEV
AEKAKAFVEKIRGCTE
aaaccctacaccaaagaggaactgatggagattctgagactggctattatcgctgagctggacgccatcaacctgtacgagcagatgg
cccggtattctgaggacgagaatgtgcgcaagatcctgctggatgtggccagggaggagaaggcacacgtgggagagttcatggcc
ctgctgctgaacctggaccccgagcaggtgaccgagctgaagggcggctttgaggaggtgaaggagctgacaggcatcgaggccc
acatcaacgacaataagaaggaggagagcaacgtggagtatttcgagaagctgagatccgccctgctggatggcgtgaataagggc
aggagcctgctgaagcacctgcctgtgaccaggatcgagggccagagcttcagagtggacatcatcaagtttgaggatggcgtgcg
cgtggtgaagcaggagtacaagcccatccctctgctgaagaagaagttctacgtgggcatcagggagctgaacgacggcacctacg
atgtgagcatcgccacaaaggccggcgagctgctggtgaaggacgaggagtccctggtcatccgcgagatcctgtctacagagggc
atcaagaagatgaagctgagctcctgggacaatccagaggaggccctgaacgatctgatgaatgccctgcaggaggcatctaacgc
aagcgccggaccattcggcctgatcatcaatcccaagagatacgccaagctgctgaagatctatgagaagtccggcaagatgctggt
ggaggtgctgaaggagatcttccggggcggcatcatcgtgaccctgaacatcgatgagaacaaagtgatcatctttgccaacacccct
gccgtgctggacgtgotggtgggacaggatgtgacactgcaggagctgggaccagagggcgacgatgtggcctttctggtgtccga
ggccatcggcatcaggatcaagaatccagaggcaatcgtggtgctggag
ggcggctctggcggaagtggcggaagtgggggaa
gtggaggcggcggaagcgggggaggcagcgggggaggg
gacaccatcacactgccatgccgccctgcaccacctccacattgt
ARYSEDENVRKILLDVAREEKAHVGEFMALLLNLDPEQVTELKGGFEEVKELTGIEA
HINDNKKEESNVEYFEKLRSALLDGVNKGRSLLKHLPVTRIEGQSFRVDIIKFEDGVR
VVKQEYKPIPLLKKKFYVGIRELNDGTYDVSIATKAGELLVKDEESLVIREILSTEGIK
KMKLSSWDNPEEALNDLMNALQEASNASAGPFGLIINPKRYAKLLKIYEKSGKMLV
EVLKEIFRGGIMQDIFIEDLNIDENKVIIFANTPAVLDVVVGQDVTLQELGPEGDDVAF
LVSEAIGIRIKNPEAIVVLE
GGSGGSGGSGGSGGGGSGGGSGGG
DTITLPCRPAPPPHC
The present disclosure further relates to one or a plurality of cells that comprise any of the disclosed expressible nucleic acid sequences and/or any of the disclosed nucleic acid molecules or plasmids. In some embodiments, the cells of the present disclosure are cultured cells comprising one or more of the disclosed expressible nucleic acid sequences and/or one or more of the disclosed nucleic acid molecules or plasmids. In such embodiments, the cells may include, but not limited to, bacterial cells, fungal cells, insect cells, mammalian cells, or human cells. Any method routinely used by one of ordinary skill in the art for transforming or transfecting cells and maintaining transformed or transfected cells can be used to generate the cells of the present disclosure. In some embodiments, the cells of the present disclosure are cells present in a living subject which has been adminstered with a composition comprising one or a plurality of the disclosed expressible nucleic acid sequences and/or one or more of the disclosed nucleic acid molecules or plasmids.
Disclosed are pharmaceutical compositions comprising any one or more of the disclosed compositions and a pharmaceutically acceptable carrier.
In some embodiments, any of the disclosed compositions is from about 1 to about 30 micrograms. For example, any of the disclosed compositions can be from about 1 to about 5 micrograms. In some preferred embodiments, the pharmaceutical compositions contain from about 5 nanograms to about 800 micrograms of DNA. In some preferred embodiments, the pharmaceutical compositions contain about 25 to about 250 micrograms, from about 100 to about 200 microgram, from about 1 nanogram to 100 milligrams; from about 1 microgram to about 10 milligrams; from about 0.1 microgram to about 10 milligrams; from about 1 milligram to about 2 milligram, from about 5 nanogram to about 1000 micrograms, from about 10 nanograms to about 800 micrograms, from about 0.1 to about 500 micrograms, from about 1 to about 350 micrograms, from about 25 to about 250 micrograms, from about 100 to about 200 microgram of the consensus antigen or plasmid thereof. The pharmaceutical compositions can comprise from about 5 nanograms to about 10 mg of the vaccine DNA. In some embodiments, pharmaceutical compositions according to the present disclosure comprise from about 25 nanogram to about 5 mg of vaccine DNA. In some embodiments, the pharmaceutical compositions contain from about 50 nanograms to about 1 mg of DNA. In some embodiments, the pharmaceutical compositions contain about from about 0.1 to about 500 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain from about 1 to about 350 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain from about 5 to about 250 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain from about 10 to about 200 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain from about 15 to about 150 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain about 20 to about 100 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain about 25 to about 75 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain about 30 to about 50 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain about 35 to about 40 micrograms of DNA. In some embodiments, the pharmaceutical compositions contain about 100 to about 200 microgram DNA. In some embodiments, the pharmaceutical compositions comprise about 10 microgram to about 100 micrograms of DNA. In some embodiments, the pharmaceutical compositions comprise about 20 micrograms to about 80 micrograms of DNA. In some embodiments, the pharmaceutical compositions comprise about 25 micrograms to about 60 micrograms of DNA. In some embodiments, the pharmaceutical compositions comprise about 30 nanograms to about 50 micrograms of DNA. In some embodiments, the pharmaceutical compositions comprise about 35 nanograms to about 45 micrograms of DNA. In some preferred embodiments, the pharmaceutical compositions contain about 0.1 to about 500 micrograms of DNA. In some preferred embodiments, the pharmaceutical compositions contain about 1 to about 350 micrograms of DNA. In some preferred embodiments, the pharmaceutical compositions contain about 1 to about 250 micrograms of DNA. In some preferred embodiments, the pharmaceutical compositions contain about 2 to about 200 microgram DNA.
In some embodiments, pharmaceutical compositions according to the present disclosure comprise at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 nanograms of DNA of the vaccine. In some embodiments, the pharmaceutical compositions can comprise at least about 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 305, 310, 315, 320, 325, 330, 335, 340, 345, 350, 355, 360, 365, 370, 375, 380, 385, 390, 395, 400, 405, 410, 415, 420, 425, 430, 435, 440, 445, 450, 455, 460, 465, 470, 475, 480, 485, 490, 495, 500, 605, 610, 615, 620, 625, 630, 635, 640, 645, 650, 655, 660, 665, 670, 675, 680, 685, 690, 695, 700, 705, 710, 715, 720, 725, 730, 735, 740, 745, 750, 755, 760, 765, 770, 775, 780, 785, 790, 795, 800, 805, 810, 815, 820, 825, 830, 835, 840, 845, 850, 855, 860, 865, 870, 875, 880, 885, 890, 895. 900, 905, 910, 915, 920, 925, 930, 935, 940, 945, 950, 955, 960, 965, 970, 975, 980, 985, 990, 995 or 1000 micrograms of DNA of the vaccine. In some embodiments, the pharmaceutical composition can comprise at least 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 mg or more of DNA of the vaccine.
In other embodiments, the pharmaceutical composition can comprise up to and including about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 nanograms of DNA of the vaccine. In some embodiments, the pharmaceutical composition can comprise up to and including about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 305, 310, 315, 320, 325, 330, 335, 340, 345, 350, 355, 360, 365, 370, 375, 380, 385, 390, 395, 400, 405, 410, 415, 420, 425, 430, 435, 440, 445, 450, 455, 460, 465, 470, 475, 480, 485, 490, 495, 500, 605, 610, 615, 620, 625, 630, 635, 640, 645, 650, 655, 660, 665, 670, 675, 680, 685, 690, 695, 700, 705, 710, 715, 720, 725, 730, 735, 740, 745, 750, 755, 760, 765, 770, 775, 780, 785, 790, 795, 800, 805, 810, 815, 820, 825, 830, 835, 840, 845, 850, 855, 860, 865, 870, 875, 880, 885, 890, 895. 900, 905, 910, 915, 920, 925, 930, 935, 940, 945, 950, 955, 960, 965, 970, 975, 980, 985, 990, 995, or 1000 micrograms of DNA of the vaccine. In some embodiments, the pharmaceutical composition can comprise up to and including about 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or about 10 mg of DNA of the vaccine. The pharmaceutical composition can further comprise other agents for formulation purposes according to the mode of administration to be used. In cases where pharmaceutical compositions are injectable pharmaceutical compositions, they are sterile, pyrogen free and particulate free. An isotonic formulation is preferably used. Generally, additives for isotonicity can include sodium chloride, dextrose, mannitol, sorbitol and lactose. In some cases, isotonic solutions such as phosphate buffered saline are preferred. Stabilizers include gelatin and albumin. In some embodiments, a vasoconstriction agent is added to the formulation.
The vaccine can further comprise a pharmaceutically acceptable excipient. The pharmaceutically acceptable excipient can be functional molecules as vehicles, adjuvants, carriers, or diluents. The pharmaceutically acceptable excipient can be a transfection facilitating agent, which can include surface active agents, such as immune-stimulating complexes
(ISCOMS), Freunds incomplete adjuvant, LPS analog including monophosphoryl lipid A, muramyl peptides, quinone analogs, vesicles such as squalene and squalene, hyaluronic acid, lipids, liposomes, calcium ions, viral proteins, polyanions, polycations, or other known transfection facilitating agents. In some embodiments, the vaccine is a composition comprising a plasmid DNA molecule, RNA molecule or DNA/RNA hybrid molecule encoding an expressible nucleic acid sequence, the expressible nucleic acid sequence comprising a first nucleic acid encoding a self-assembling nanoparticle comprising a viral antigen, optionally encoding a leader sequence disclosed herein.
The transfection facilitating agent is a polyanion, polycation, including poly-L-glutamate (LGS), or lipid. The transfection facilitating agent is poly-L-glutamate, and more preferably, the poly-L-glutamate is present in the vaccine at a concentration less than 6 mg/ml. The transfection facilitating agent can also include surface active agents such as immune-stimulating complexes (ISCOMS), Freunds incomplete adjuvant, LPS analog including monophosphoryl lipid A, muramyl peptides, quinone analogs and vesicles such as squalene and squalene, and hyaluronic acid can also be used administered in conjunction with the genetic construct. In some embodiments, the DNA vector vaccines can also include a transfection facilitating agent such as lipids, liposomes, including lecithin liposomes or other liposomes known in the art, as a DNA-liposome mixture (see for example WO9324640), calcium ions, viral proteins, polyanions, polycations, or nanoparticles, or other known transfection facilitating agents. Preferably, the transfection facilitating agent is a polyanion, polycation, including poly-L-glutamate (LGS), or lipid. Concentration of the transfection agent in the vaccine is less than 4 mg/ml, less than 2 mg/ml, less than 1 mg/ml, less than 0.750 mg/ml, less than 0.500 mg/ml, less than 0.250 mg/ml, less than 0.100 mg/ml, less than 0.050 mg/ml, or less than 0.010 mg/ml.
The pharmaceutically acceptable excipient can be an adjuvant. The adjuvant can be other genes that are expressed in alternative plasmid or are deneurological systemed as proteins in combination with the plasmid above in the vaccine. The adjuvant can be selected from the group consisting of: α-interferon(IFN-α), β-interferon (IFN-β), γ-interferon, platelet derived growth factor (PDGF), TNFα, TNFβ, GM-CSF, epidermal growth factor (EGF), cutaneous T cell-attracting chemokine (CTACK), epithelial thymus-expressed chemokine (TECK), mucosae-associated epithelial chemokine (MEC), IL-12, IL-15, MHC, CD80,CD86 including IL-15 having the signal sequence deleted and optionally including the signal peptide from IgE. The adjuvant can be IL-12, IL-15, IL-28, CTACK, TECK, platelet derived growth factor (PDGF), TNFα, TNFβ, GM-CSF, epidermal growth factor (EGF), IL-1, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-18, or a combination thereof. In an exemplary embodiment, the adjuvant is IL-12.
Other genes which can be useful adjuvants include those encoding: MCP-1, MIP-1a, MIP-1p, IL-8, RANTES, L-selectin, P-selectin, E-selectin, CD34, GlyCAM-1, MadCAM-1, LFA-1, VLA-1, Mac-1, p150.95, PECAM, ICAM-1, ICAM-2, ICAM-3, CD2, LFA-3, M-CSF, G-CSF, IL-4, mutant forms of IL-18, CD40, CD40L, vascular growth factor, fibroblast growth factor, IL-7, nerve growth factor, vascular endothelial growth factor, Fas, TNF receptor, Fit, Apo-1, p55, WSL-1, DR3, TRAMP, Apo-3, AIR, LARD, NGRF, DR4, DR5, KILLER, TRAIL-R2, TRICK2, DR6, Caspase ICE, Fos, c-jun, Sp-1, Ap-1, Ap-2, p38, p65Rel, MyD88, IRAK, TRAF6, IkB, Inactive NIK, SAP K, SAP-1, JNK, interferon response genes, NFkB, Bax, TRAIL, TRAILrec, TRAILrecDRC5, TRAIL-R3, TRAIL-R4, RANK, RANK LIGAND, Ox40, Ox40 LIGAND, NKG2D, MICA, MICB, NKG2A, NKG2B, NKG2C, NKG2E, NKG2F, TAP1, TAP2 and functional fragments thereof or a combination thereof.
In some embodiments, adjuvant may be one or more proteins and/or nucleic acid molecules that encode proteins selected from the group consisting of: CCL-20, IL-2, IL-6, IL-7, IL-12, single-chain IL-12, IL-15, IL-27, IL-28, CTACK, TECK, MEC or RANTES. Examples of IL-12 constructs and sequences are disclosed in PCT application no. PCT/US1997/019502 and corresponding U.S. application Ser. No. 08/956,865, and U.S. Provisional Application Ser. No. 61/569,600 filed Dec. 12, 2011, which are each incorporated herein by reference in their entireties. Examples of IL-15 constructs and sequences are disclosed in PCT application no. PCT/US04/18962 and corresponding U.S. application Ser. No. 10/560,650, and in PCT application no. PCT/US07/00886 and corresponding U.S. application Ser. No. 12/160,766, and in PCT Application Serial No. PCT/US10/048827, which are each incorporated herein by reference in their entireties. Examples of IL-28 constructs and sequences are disclosed in PCT application no. PCT/US09/039648 and corresponding U.S. application Ser. No. 12/936,192, which are each incorporated herein by reference in their entireties. Examples of RANTES and other constructs and sequences are disclosed in PCT application no. PCT/US 1999/004332 and corresponding U.S. Application Serial No. and Ser. No. 09/622,452, which are each incorporated herein by reference in their entireties. Other examples of RANTES constructs and sequences are disclosed in PCT Application Serial No. PCT/US Ser. No. 11/024,098, which is incorporated herein by reference. Examples of RANTES and other constructs and sequences are disclosed in PCT Application Serial No. PCT/US 1999/004332 and corresponding U.S. application Ser. No. 09/622,452, which are each incorporated herein by reference. Other examples of RANTES constructs and sequences are disclosed in PCT application no. PCT/U.S. Ser. No. 11/024,098, which is incorporated herein by reference in its entirety. Examples of chemokines CTACK, TECK and MEC constructs and sequences are disclosed in PCT Application Serial No. PCT/US2005/042231 and corresponding U.S. application Ser. No. 11/719,646, which are each incorporated herein by reference in their entireties. Examples of OX40 and other immunomodulators are disclosed in U.S. application Ser. No. 10/560,653, which is incorporated herein by reference in its entirety. Examples of DR5 and other immunomodulators are disclosed in U.S. application Ser. No. 09/622,452, which is incorporated herein by reference in its entirety. In some embodiments, adjuvant may be a protein comprising at least 70%, 80%, 85%, 90%, 95%, 99% or more sequence identity to any proteins disclosed in any of the aforementioned patent applications incorporated by reference herein. In some embodiments, adjuvant may be a nucleic acid encoding a cytokine or chemokine comprising at least 70%, 80%, 85%, 90%, 95%, 99% or more sequence identity to any proteins disclosed in any of the aforementioned patent applications incorporated by reference herein.
The pharmaceutical composition may be formulated according to the mode of administration to be used. An injectable vaccine pharmaceutical composition may be sterile, pyrogen free and particulate free. An isotonic formulation or solution may be used. Additives for isotonicity may include sodium chloride, dextrose, mannitol, sorbitol, and lactose. The vaccine may comprise a vasoconstriction agent. The isotonic solutions may include phosphate buffered saline. Vaccine may further comprise stabilizers including gelatin and albumin. The stabilizing may allow the formulation to be stable at room or ambient temperature for extended periods of time such as LGS or polycations or polyanions to the vaccine formulation.
The vaccine can be a DNA or RNA vaccine. In some embodiments, the vaccine is a DNA vaccine. DNA vaccines are disclosed in U.S. Pat. Nos. 5,593,972, 5,739,118, 5,817,637, 5,830,876, 5,962,428, 5,981,505, 5,580,859, 5,703,055, and 5,676,594, which are incorporated herein fully by reference. The DNA vaccine can further comprise elements or reagents that inhibit it from integrating into the chromosome. Examples of attenuated live vaccines, those using recombinant vectors to foreign antigens, subunit vaccines and glycoprotein vaccines are described in U.S. Pat. Nos. 4,510,245; 4,797,368; 4,722,848; 4,790,987; 4,920,209; 5,017,487; 5,077,044; 5,110,587; 5,112,749; 5,174,993; 5,223,424; 5,225,336; 5,240,703; 5,242,829; 5,294,441; 5,294,548; 5,310,668; 5,387,744; 5,389,368; 5,424,065; 5,451,499; 5,453,364; 5,462,734; 5,470,734; 5,474,935; 5,482,713; 5,591,439; 5,643,579; 5,650,309; 5,698,202; 5,955,088; 6,034,298; 6,042,836; 6,156,319 and 6,589,529, which are each incorporated herein by reference in their entireties.
In some embodiments, the vaccine is an LNP comprising one or a modified RNA molecule. In some embodiments, the vaccine comprises a modified mRNA. Modified polynucleotides (such as, but not limited to, primary constructs), formulations and compositions comprising modified polynucleotides, and methods of making, using and administering modified polynucleotides are described in co-pending U.S. Provisional Patent Application No. 61/618,862, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Biologics; U.S. Provisional Patent Application No. 61/681,645, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Biologics; U.S. Provisional Patent Application No. 61/737,130, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Biologics; U.S. Provisional Patent Application No. 61/618,866, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Antibodies; U.S. Provisional Patent Application No. 61/681,647, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Antibodies; U.S. Provisional Patent Application No. 61/737,134, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Antibodies; U.S. Provisional Patent Application No. 61/618,868, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Vaccines; U.S. Provisional Patent Application No. 61/681,648, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Vaccines; U.S. Provisional Patent Application No. 61/737,135, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Vaccines; U.S. Provisional Patent Application No. 61/618,873, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Secreted Proteins; U.S. Provisional Patent Application No. 61/681,650, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Secreted Proteins; U.S. Provisional Patent Application No. 61/737,147, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Secreted Proteins; U.S. Provisional Patent Application No. 61/618,878, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Plasma Membrane Proteins; U.S. Provisional Patent Application No. 61/681,654, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Plasma Membrane Proteins; U.S. Provisional Patent Application No. 61/737,152, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Plasma Membrane Proteins; U.S. Provisional Patent Application No. 61/618,885, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Cytoplasmic and Cytoskeletal Proteins; U.S. Provisional Patent Application No. 61/681,658, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Cytoplasmic and Cytoskeletal Proteins; U.S. Provisional Patent Application No. 61/737,155, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Cytoplasmic and Cytoskeletal Proteins; U.S. Provisional Patent Application No. 61/618,896, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Intracellular Membrane Bound Proteins; U.S. Provisional Patent Application No. 61/668,157, filed Jul. 5, 2012, entitled Modified Polynucleotides for the Production of Intracellular Membrane Bound Proteins; U.S. Provisional Patent Application No. 61/681,661, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Intracellular Membrane Bound Proteins; U.S. Provisional Patent Application No. 61/737,160, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Intracellular Membrane Bound Proteins; U.S. Provisional Patent Application No. 61/618,911, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Nuclear Proteins; U.S. Provisional Patent Application No. 61/681,667, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Nuclear Proteins; U.S. Provisional Patent Application No. 61/737,168, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Nuclear Proteins; U.S. Provisional Patent Application No. 61/618,922, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Proteins; U.S. Provisional Patent Application No. 61/681,675, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Proteins; U.S. Provisional Patent Application No. 61/737,174, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Proteins; U.S. Provisional Patent Application No. 61/618,935, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; U.S. Provisional Patent Application No. 61/681,687, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; U.S. Provisional Patent Application No. 61/737,184, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; U.S. Provisional Patent Application No. 61/618,945, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; U.S. Provisional Patent Application No. 61/681,696, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; U.S. Provisional Patent Application No. 61/737,191, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; U.S. Provisional Patent Application No. 61/618,953, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; U.S. Provisional Patent Application No. 61/681,704, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; U.S. Provisional Patent Application No. 61/737,203, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; International Application No PCT/US2013/030062, filed Mar. 9, 2013, entitled Modified Polynucleotides for the Production of Biologics and Proteins Associated with Human Disease; International Application No. PCT/US2013/030064, entitled Modified Polynucleotides for the Production of Secreted Proteins; International Application No PCT/US2013/030059, filed Mar. 9, 2013, entitled Modified Polynucleotides for the Production of Membrane Proteins; International Application No. PCT/US2013/030066, filed Mar. 9, 2013, entitled Modified Polynucleotides for the Production of Cytoplasmic and Cytoskeletal Proteins; International Application No. PCT/US2013/030067, filed Mar. 9, 2013, entitled Modified Polynucleotides for the Production of Nuclear Proteins; International Application No. PCT/US2013/030060, filed Mar. 9, 2013, entitled Modified Polynucleotides for the Production of Proteins; International Application No. PCT/US2013/030061, filed Mar. 9, 2013, entitled Modified Polynucleotides for the Production of Proteins Associated with Human Disease; in co-pending U.S. Provisional Patent Application No. 61/681,720, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Cosmetic Proteins and Peptides; U.S. Provisional Patent Application No. 61/737,213, filed Dec. 14, 2012, entitled Modified Polynucleotides for the Production of Cosmetic Proteins and Peptides; U.S. Provisional Patent Application No. 61/681,742, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Oncology-Related Proteins and Peptides; International Application No. PCT/US2013/030070, filed Mar. 9, 2013, entitled Modified Polynucleotides for the Production of Oncology-Related Proteins and Peptides; in co-pending International Application No. PCT/US2013/030068, filed Mar. 9, 2013, entitled Modified Polynucleotides for the Production of Cosmetic Proteins and Peptides; in co-pending U.S. Provisional Patent Application No. 61/618,870, filed Apr. 2, 2012, entitled Modified Polynucleotides for the Production of Therapeutic Proteins and Peptides; in co-pending U.S. Provisional Patent Application No. 61/681,649, filed Aug. 10, 2012, entitled Modified Polynucleotides for the Production of Therapeutic Proteins and Peptides; in co-pending U.S. Provisional Patent Application No. 61/737,139, filed Dec. 14, 2012, Modified Polynucleotides for the Production of Therapeutic Proteins and Peptides; in co-pending International Application No PCT/US2013/030063, filed Mar. 9, 2013, entitled Modified Polynucleotides; and in co-pending International Application No PCT/US2013/031821, filed Mar. 15, 2013, entitled In Vivo Production of Proteins; the contents of each of which are herein incorporated by reference in their entireties. Any of the recited polypeptides of the modified polynucleotides of the foregoing are considered useful as a polypeptide of interest or antigen of the LNPs of the present invention.
The genetic construct can also be part of a genome of a recombinant viral vector, including recombinant adenovirus, recombinant adenovirus associated virus and recombinant vaccinia. The genetic construct can be part of the genetic material in attenuated live microorganisms or recombinant microbial vectors which live in cells.
The disclosure relates to a genetic construct or composition comprising any of the expressible nucleic acid molecules disclosed herein. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 1. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 2. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 3. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 4. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 5. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 6. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 7. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 8. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 9. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 10. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 11. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 12, In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 13. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 14. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 15. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 16. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 17. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 18. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 19. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 20. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 21. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 22. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 23. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 24. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 25. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 26. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 27. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 28. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 29. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 30. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 31. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 32. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 33. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 34. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 35. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 36. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 37. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 38. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 39. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 40. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 41. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 42. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 43. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 44. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 45. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 46. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 47. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 48. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 49. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 50. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 51. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 52. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 53. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 54. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 55. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 56. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 57. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 58. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 59. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 60. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 61. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 62. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 63. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 64. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 65. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 66. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 67. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 68. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 69. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 70. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 71. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 72. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 73. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 74. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 75. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 76. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 77. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 78. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 79. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 80. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 81. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 82. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 83. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 84. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 85. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 86. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 87. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 88. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 89. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 90. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 91. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 92. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 93. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 94. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 95. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 96. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 97. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 98. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 99. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 100. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 101. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 102. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 103. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 104. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 105. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 106. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 107. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 108. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 109. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 110. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 111. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 112. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 113. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 114. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 115. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 116. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 117. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 118. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 119. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 120. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 121. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 122. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 123. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 124. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 125. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 126. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 127. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 128. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 129. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 130. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 131. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 132. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 133. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 134. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 135. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 136. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 137. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 138. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 139. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 140. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 141. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 142. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 143. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 144. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 145. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 146. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 147. In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence comprising (or encoding an amino acid sequence comprising) at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 148.
In some embodiments, the disclosure relates to a composition comprising any of the self-assembling polypeptides disclosed herein, or the corresponding coding nucleic acid, in combination with any of the viral antigens disclosed herein, or the corresponding coding nucleic acid. In some embodiments, such composition further comprises any of the leader sequences disclosed herein, or the corresponding coding nucleic acid, and/or any of the linkers disclosed herein, or the corresponding coding nucleic acid. In some embodiments, when in form of a nucleic acid, such composition is present in any of the DNA backbonds disclosed herein.
In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 9 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 45 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 47 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 49 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 51 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 53 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 55 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 65 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 66 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 67 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 9 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 45 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 47 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 49 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 51 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 53 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 55 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 65 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 66 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 67 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 9 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 45 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 47 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 49 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 51 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 53 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 55 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 65 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 66 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 67 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 9 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 45 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 47 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 49 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 51 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 53 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 55 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 65 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 66 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 67 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 6 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 40 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 101 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 8 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 18 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 22 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 27 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 32 (or a variant thereof), or the corresponding coding nucleic acid.
In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 103 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 104 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 105 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 106 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 108 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 109 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 110 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 7 (or a variant thereof) in combination with SEQ ID NO: 111 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 103 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 104 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 105 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 106 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 108 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 109 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 110 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 23 (or a variant thereof) in combination with SEQ ID NO: 111 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 103 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 104 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 105 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 106 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 108 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 109 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 110 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 26 (or a variant thereof) in combination with SEQ ID NO: 111 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 103 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 104 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 105 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 106 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 108 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 109 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 110 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, the disclosure relates to a composition comprising SEQ ID NO: 31 (or a variant thereof) in combination with SEQ ID NO: 111 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 9 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 45 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 47 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 49 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 51 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 53 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 55 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 65 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 66 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 67 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 6 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 40 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 101 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 8 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 18 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 22 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 27 (or a variant thereof), or the corresponding coding nucleic acid. In some embodiments, any of the aforementioned compositions further comprises SEQ ID NO: 32 (or a variant thereof), or the corresponding coding nucleic acid.
In some embodiments, any of the aforementioned coding nucleic acids in the disclosed compositions further comprises SEQ ID NO: 56 (or a variant thereof). In some embodiments, any of the aforementioned coding nucleic acids in the disclosed compositions further comprises SEQ ID NO: 76 (or a variant thereof). In some embodiments, any of the aforementioned coding nucleic acids in the disclosed compositions further comprises SEQ ID NO: 77 (or a variant thereof). In some embodiments, any of the aforementioned coding nucleic acids in the disclosed compositions further comprises SEQ ID NO: 78 (or a variant thereof). In some embodiments, any of the aforementioned coding nucleic acids in the disclosed compositions further comprises SEQ ID NO: 79 (or a variant thereof). In some embodiments, any of the aforementioned coding nucleic acids in the disclosed compositions further comprises SEQ ID NO: 80 (or a variant thereof). In some embodiments, any of the aforementioned coding nucleic acids in the disclosed compositions further comprises SEQ ID NO: 81 (or a variant thereof). In some embodiments, any of the aforementioned coding nucleic acids in the disclosed compositions further comprises SEQ ID NO: 82 (or a variant thereof). As used herein, the term “variant” comprised in any of the disclosed compositions is a polypeptide or a nucleic acid that comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the parent polypeptide or the parent nucleic acid as determined by sequence alignment programs and parameters described elsewhere herein.
In some embodiments, the disclosure relates to a DNA vector pVAX1 comprising any one or more of the expressible nucliec acid sequences disclosed herein or an RNA transcript thereof. In some embodiments, the disclosure relates to a pharmaceutical composition comprising a nucleic acid sequence that includes one or a plurality of expressible nucleic acid sequences disclosed herein or an RNA transcript thereof; and a pharmaceutically acceptable carrier.
Disclosed are methods of vaccinating a subject comprising administering a therapeutically effective amount of any of the disclosed nucleic acid molecules, compositions, cells or pharmaceutical compositions to the subject. In some embodiments, the vaccination is against viral infection. In some embodiments, the viral infection is an infection of retroviridae. In some embodiments, the viral infection is an infection of a retrovirus. In some embodiments, the viral infection is an infection of a flavivirus. In some embodiments, the viral infection is an infection of Nipah virus. In some embodiments, the viral infection is an infection of West Nile virus. In some embodiments, the viral infection is an infection of human papillomavirus. In some embodiments, the viral infection is an infection of respiratory syncytial virus. In some embodiments, the viral infection is an infection of filovirus. In some embodiments, the viral infection is an infection of zaire ebolavirus. In some embodiments, the viral infection is an infection of sudan ebolavirus. In some embodiments, the viral infection is an infection of marburgvirus. In some embodiments, the viral infection is an infection of influenza virus. In some embodiments, the viral infection is an infection of HIV-1.
Disclosed are methods of inducing an immune response in a subject comprising administering to the subject any of the disclosed pharmaceutical compositions. In some embodiments, the methods are for inducing an immune response to a viral antigen in the subject. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a retroviridae. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a retrovirus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a flavivirus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a Nipah virus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a West Nile virus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a human papillomavirus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a respiratory syncytial virus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a filovirus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a zaire ebolavirus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a sudan ebolavirus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from a marburgvirus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from an influenza virus. In some embodiments, the immune response induced by the disclosed methods is against a viral antigen from HIV-1.
Disclosed are methods of neutralizing one or a plurality of viruses in a subject comprising administering to the subject any of the disclosed pharmaceutical compositions. In some embodiments, the virus being neutralized by the disclosed method is retroviridae. In some embodiments, the virus being neutralized by the disclosed method is a retrovirus. In some embodiments, the virus being neutralized by the disclosed method is flavivirus. In some embodiments, the virus being neutralized by the disclosed method is Nipah virus. In some embodiments, the virus being neutralized by the disclosed method is West Nile virus. In some embodiments, the virus being neutralized by the disclosed method is human papillomavirus. In some embodiments, the virus being neutralized by the disclosed method is respiratory syncytial virus. In some embodiments, the virus being neutralized by the disclosed method is filovirus. In some embodiments, the virus being neutralized by the disclosed method is zaire ebolavirus. In some embodiments, the virus being neutralized by the disclosed method is sudan ebolavirus. In some embodiments, the virus being neutralized by the disclosed method is marburgvirus. In some embodiments, the virus being neutralized by the disclosed method is influenza virus. In some embodiments, the virus being neutralized by the disclosed method is HIV-1.
Disclosed are methods of neutralizing infection of one or a plurality of viruses in a subject comprising administering to the subject any of the disclosed pharmaceutical compositions. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of retroviridae. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of a retrovirus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of flavivirus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of Nipah virus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of West Nile virus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of human papillomavirus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of respiratory syncytial virus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of filovirus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of zaire ebolavirus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of sudan ebolavirus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of marburgvirus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of influenza virus. In some embodiments, the viral infection being neutralized by the disclosed method is an infection of HIV-1.
Disclosed are methods of stimulating a therapeutically effective antigen-specific immune response against a virus in a mammal infected with the virus comprising administering any of the disclosed pharmaceutical compositions. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against retroviridae. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against a retrovirus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against flavivirus. In some embodiments, In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against Nipah virus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against West Nile virus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against human papillomavirus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against respiratory syncytial virus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against a filovirus. In some embodiments, the disclosed method is against zaire ebolavirus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against sudan ebolavirus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune responses against marburgvirus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against influenza virus. In some embodiments, the disclosed method is a method of stimulating a therapeutically effective antigen-specific immune response against HIV-1.
Disclosed are methods of inducing expression of a self-assembling vaccine in a subject comprising administering any of the disclosed pharmaceutical compositions. Also disclosed are methods of treating a subject having a viral infection or susceptible to becoming infected with a virus comprising administering to the subject a therapeutically effective amount of any of the disclosed pharmaceutical compositions. In some embodiments, the viral infection is an infection of retroviridae. In some embodiments, the viral infection is an infection of a retrovirus. In some embodiments, the viral infection is an infection of flavivirus. In some embodiments, the viral infection is an infection of Nipah virus. In some embodiments, the viral infection is an infection of West Nile virus. In some embodiments, the viral infection is an infection of human papillomavirus. In some embodiments, the viral infection is an infection of respiratory syncytial virus. In some embodiments, the viral infection is an infection of filovirus. In some embodiments, the viral infection is an infection of zaire ebolavirus. In some embodiments, the viral infection is an infection of sudan ebolavirus. In some embodiments, the viral infection is an infection of marburgvirus. In some embodiments, the viral infection is an infection of influenza virus. In some embodiments, the viral infection is an infection of HIV-1.
The disclosed pharmaceutical compositions may be administered by any route of administration. Accordingly, in some embodiments, the administering can be accomplished by oral administration. In some embodiments, the administering can be accomplished by parenteral administration. In some embodiments, the administering can be accomplished by sublingual administration. In some embodiments, the administering can be accomplished by transdermal administration. In some embodiments, the administering can be accomplished by rectal administration. In some embodiments, the administering can be accomplished by transmucosal administration. In some embodiments, the administering can be accomplished by topical administration. In some embodiments, the administering can be accomplished by inhalation. In some embodiments, the administering can be accomplished by buccal administration. In some embodiments, the administering can be accomplished by intrapleural administration. In some embodiments, the administering can be accomplished by intravenous administration. In some embodiments, the administering can be accomplished by intraarterial administration. In some embodiments, the administering can be accomplished by intraperitoneal administration. In some embodiments, the administering can be accomplished by subcutaneous administration. In some embodiments, the administering can be accomplished by intramuscular administration. In some embodiments, the administering can be accomplished by intranasal administration. In some embodiments, the administering can be accomplished by intrathecal administration. In some embodiments, the administering can be accomplished by intraarticular administration. In some embodiments, the administering can be accomplished by intradermal administration. In some embodiments, the above modes of action are accomplished by injection of the pharmaceutical compositions disclosed herein.
In some embodiments, the therapeutically effective dose can be from about 1 to about 30 micrograms of expressible nucleic acid sequence. In some embodiments, the therapeutically effective dose can be from about 0.001 micrograms of the composition per kilogram of subject to about 0.050 micrograms per kilogram of subject.
In some embodiments, any of the disclosed methods can be free of activating any mannose-binding lectin or complement process. In some embodiments, any of the disclosed methods may be performed without inducing the MBL-complement pathway.
In some embodiments, the subject can be a human. In some embodiments, the subject is diagnosed with or suspected of having a viral infection. For example, the subject can be diagnosed with or suspected of having an HIV-1 infection. In other embodiments, the subject can be diagnosed with or suspected of having a retrovirus infection. In some embodiments, the subject can be diagnosed with or suspected of having a flavivirus infection. In some embodiments, the subject can be diagnosed with or suspected of having a Nipah virus infection. In some embodiments, the subject can be diagnosed with or suspected of having a West Nile virus infection. In some embodiments, the subject can be diagnosed with or suspected of having a human papillomavirus infection. In some embodiments, the subject can be diagnosed with or suspected of having a respiratory syncytial virus infection. In some embodiments, the subject can be diagnosed with or suspected of having a filovirus infection. In some embodiments, the subject can be diagnosed with or suspected of having a zaire ebolavirus infection. In some embodiments, the subject can be diagnosed with or suspected of having a sudan ebolavirus infection. In some embodiments, the subject can be diagnosed with or suspected of having a marburgvirus infection. In some embodiments, the subject can be diagnosed with or suspected of having a influenza virus infection. In other embodiments, the subject can be diagnosed with or suspected of having an retrovirus infection. In some embodiments, the subject can be diagnosed with or suspected of having an flavivirus infection.
In some embodiments of the methods of inducing an immune response, the immune response can be an antigen-specific immune response. For example, the antigen-specific immune response can be an antigen-specific HIV-1 antigen immune response. In some embodiments, the antigen-specific immune response can be a therapeutically effective CD-4+ antigen-specific HIV-1 immune response. In some embodiments, the antigen-specific immune response can be a therapeutically effective CD-8+ antigen-specific HIV-1 immune response. In some embodiments, the antigen-specific immune response can be a therapeutically effective CD-4+ and CD-8+ antigen-specific HIV-1 immune response.
In some embodiments, the methods are free of administering any polypeptide directly to the subject.
In some embodiments, methods of inducing an immune response can include inducing a humoral or cellular immune response. A humoral immune response mainly refers to antibody production. A cellular immune response can include activation of CD4+ T-cells and activation CD8+ cells and associated cytotoxic activity. In one aspect, the present disclosure features a method of inducing an immune response in a subject, the method comprising administering to the subject in need thereof a pharmaceutically effective amount of any of the nucleic acid molecule comprising any one or plurality of the nucleic acid sequences or embodiments herein, or any one of the pharmaceutical compositions of any one of the aspects and embodiments herein. In one aspect, the present disclosure features a method of inducing a CD8+ T cell immune response in a subject, the method comprising administering to the subject in need thereof a pharmaceutically effective amount of any of the nucleic acid molecules of any one of the aspects or embodiments herein, or any one of the pharmaceutical compositions of any one of the aspects and embodiments herein.
In one aspect, the present disclosure features a method of enhancing an immune response in a subject, the method comprising administering to the subject in need thereof a pharmaceutically effective amount of any of the nucleic acid molecules of any one of the aspects or embodiments herein, or any one of the pharmaceutical compositions of any one of the aspects and embodiments herein.
In one aspect, the present disclosure features a method of enhancing a CD8+ T cell immune response in a subject, the method comprising administering to the subject in need thereof a pharmaceutically effective amount of any of the nucleic acid molecules of any one of the aspects or embodiments herein, or any one of the pharmaceutical compositions of any one of the aspects and embodiments herein.
In some embodiments, the subject has a viral infection and is in need of therapy for the viral infection. In some embodiments, the viral infection is an infection of retroviridae. In some embodiments, the viral infection is an infection of flavivirus. In some embodiments, the viral infection is an infection of Nipah Virus. In some embodiments, the viral infection is an infection of West Nile virus. In some embodiments, the viral infection is an infection of human papillomavirus. In some embodiments, the viral infection is an infection of respiratory syncytial virus. In some embodiments, the viral infection is an infection of filovirus. In some embodiments, the viral infection is an infection of zaire ebolavirus. In some embodiments, the viral infection is an infection of sudan ebolavirus. In some embodiments, the viral infection is an infection of marburgvirus. In some embodiments, the viral infection is an infection of influenza virus.
In some embodiments, the subject has previously been treated, and not responded to anti-viral therapy. In some embodiments, the nucleic acid molecule and/or expressible sequence is administered to the subject by electroporation.
The vaccine may be administered by different routes including orally, parenterally, sublingually, transdermally, rectally, transmucosally, topically, via inhalation, via buccal administration, intrapleurally, intravenous, intraarterial, intraperitoneal, subcutaneous, intramuscular, intranasal intrathecal, and intraarticular or combinations thereof. For veterinary use, the composition may be administered as a suitably acceptable formulation in accordance with normal veterinary practice. The veterinarian can readily determine the dosing regimen and route of administration that is most appropriate for a particular animal. The vaccine may be administered by traditional syringes, needleless injection devices, “microprojectile bombardment gone guns”, or other physical methods such as electroporation (“EP”), “hydrodynamic method”, or ultrasound.
The plasmid of the vaccine may be delivered to the mammal by several well-known technologies including DNA injection (also referred to as DNA vaccination) with and without in vivo electroporation, liposome mediated, nanoparticle facilitated, recombinant vectors such as recombinant adenovirus, recombinant adenovirus associated virus and recombinant vaccinia. The consensus antigen may be delivered via DNA injection and along with in vivo electroporation.
The vaccine or pharmaceutical composition can be administered by electroporation. Administration of the vaccine via electroporation of the plasmids of the vaccine may be accomplished using electroporation devices that can be configured to deliver to a desired tissue of a mammal a pulse of energy effective to cause reversible pores to form in cell membranes, and preferable the pulse of energy is a constant current similar to a preset current input by a user. The electroporation device may comprise an electroporation component and an electrode assembly or handle assembly. The electroporation component may include and incorporate one or more of the various elements of the electroporation devices, including: controller, current waveform generator, impedance tester, waveform logger, input element, status reporting element, communication port, memory component, power source, and power switch. The electroporation can be accomplished using an in vivo electroporation device, for example CELLECTRA® EP system (Inovio Pharmaceuticals, Inc., Blue Bell, PA) or Elgen electroporator (Inovio Pharmaceuticals, Inc.) to facilitate transfection of cells by the plasmid.
The electroporation component may function as one element of the electroporation devices, and the other elements are separate elements (or components) in communication with the electroporation component. The electroporation component may function as more than one element of the electroporation devices, which may be in communication with still other elements of the electroporation devices separate from the electroporation component. The elements of the electroporation devices existing as parts of one electromechanical or mechanical device may not limited as the elements can function as one device or as separate elements in communication with one another. The electroporation component may be capable of delivering the pulse of energy that produces the constant current in the desired tissue, and includes a feedback mechanism. The electrode assembly may include an electrode array having a plurality of electrodes in a spatial arrangement, wherein the electrode assembly receives the pulse of energy from the electroporation component and delivers same to the desired tissue through the electrodes. At least one of the plurality of electrodes is neutral during delivery of the pulse of energy and measures impedance in the desired tissue and communicates the impedance to the electroporation component. The feedback mechanism may receive the measured impedance and can adjust the pulse of energy delivered by the electroporation component to maintain the constant current.
A plurality of electrodes may deliver the pulse of energy in a decentralized pattern. The plurality of electrodes may deliver the pulse of energy in the decentralized pattern through the control of the electrodes under a programmed sequence, and the programmed sequence is input by a user to the electroporation component. The programmed sequence may comprise a plurality of pulses delivered in sequence, wherein each pulse of the plurality of pulses is delivered by at least two active electrodes with one neutral electrode that measures impedance, and wherein a subsequent pulse of the plurality of pulses is delivered by a different one of at least two active electrodes with one neutral electrode that measures impedance.
The feedback mechanism may be performed by either hardware or software. The feedback mechanism may be performed by an analog closed-loop circuit. The feedback occurs every 50 μs, 20 μs, 10 μs or 1 μs, but is preferably a real-time feedback or instantaneous (i.e., substantially instantaneous as determined by available techniques for determining response time). The neutral electrode may measure the impedance in the desired tissue and communicates the impedance to the feedback mechanism, and the feedback mechanism responds to the impedance and adjusts the pulse of energy to maintain the constant current at a value similar to the preset current. The feedback mechanism may maintain the constant current continuously and instantaneously during the delivery of the pulse of energy.
Examples of electroporation devices and electroporation methods that may facilitate delivery of the DNA vaccines of the present disclosure, include those described in U.S. Pat. No. 7,245,963 by Draghia-Akli, et al., U.S. Patent Pub. 2005/0052630 submitted by Smith, et al., the contents of which are hereby incorporated by reference in their entirety. Other electroporation devices and electroporation methods that may be used for facilitating delivery of the DNA vaccines include those provided in co-pending and co-owned U.S. patent application Ser. No. 11/874,072, filed Oct. 17, 2007, which claims the benefit under 35 USC 119(c) to U.S. Provisional Application Ser. No. 60/852,149, filed Oct. 17, 2006, and 60/978,982, filed Oct. 10, 2007, all of which are hereby incorporated in their entirety.
U.S. Pat. No. 7,245,963 by Draghia-Akli, et al. describes modular electrode systems and their use for facilitating the introduction of a biomolecule into cells of a selected tissue in a body or plant. The modular electrode systems may comprise a plurality of needle electrodes; a hypodermic needle; an electrical connector that provides a conductive link from a programmable constant-current pulse controller to the plurality of needle electrodes; and a power source. An operator can grasp the plurality of needle electrodes that are mounted on a support structure and firmly insert them into the selected tissue in a body or plant. The biomolecules are then delivered via the hypodermic needle into the selected tissue. The programmable constant-current pulse controller is activated and constant-current electrical pulse is applied to the plurality of needle electrodes. The applied constant-current electrical pulse facilitates the introduction of the biomolecule into the cell between the plurality of electrodes. The entire content of U.S. Pat. No. 7,245,963 is hereby incorporated by reference in its entirety.
U.S. Patent Pub. 2005/0052630 submitted by Smith, et al. describes an electroporation device which may be used to effectively facilitate the introduction of a biomolecule into cells of a selected tissue in a body or plant. The electroporation device comprises an electro-kinetic device (“EKD device”) whose operation is specified by software or firmware. The EKD device produces a series of programmable constant-current pulse patterns between electrodes in an array based on user control and input of the pulse parameters, and allows the storage and acquisition of current waveform data. The electroporation device also comprises a replaceable electrode disk having an array of needle electrodes, a central injection channel for an injection needle, and a removable guide disk. The entire content of U.S. Patent Pub. 2005/0052630 is hereby incorporated by reference in its entirety. The electrode arrays and methods described in U.S. Pat. No. 7,245,963 and U.S. Patent Pub. 2005/0052630 may be adapted for deep penetration into not only tissues such as muscle, but also other tissues or organs. Because of the configuration of the electrode array, the injection needle (to deliver the biomolecule of choice) is also inserted completely into the target organ, and the injection is administered perpendicular to the target issue, in the area that is pre-delineated by the electrodes The electrodes described in U.S. Pat. No. 7,245,963 and U.S. Patent Pub. 2005/005263 are preferably 20 mm long and 21 gauge. Additionally, contemplated in some embodiments that incorporate
electroporation devices and uses thereof, there are electroporation devices that are those described in the following patents: U.S. Pat. No. 5,273,525 issued Dec. 28, 1993, U.S. Pat. No. 6,110,161 issued Aug. 29, 2000, U.S. Pat. No. 6,261,281 issued Jul. 17, 2001, and U.S. Pat. No. 6,958,060 issued Oct. 25, 2005, and U.S. Pat. No. 6,939,862 issued Sep. 6, 2005. Furthermore, patents covering subject matter provided in U.S. Pat. No. 6,697,669 issued Feb. 24, 2004, which concerns delivery of DNA using any of a variety of devices, and U.S. Pat. No. 7,328,064 issued Feb. 5, 2008, drawn to a method of injecting DNA are contemplated herein. The above-patents are incorporated by reference in their entireties.
Methods of preparing the nucleic acid sequences are disclosed. In some embodiments, plasmid sequences with one or more multiple clining sites my be purchased from commercially available vendors and the expressible nucleic acid sequences disclosed herein may be ligated into the plasmids after a digestion with a known restriction enzyme needed to cute the plasmid DNA. In another alternative embodiment, membrane-based purification methods disclosed herein offer reduced cost, high binding capacity, and high flow rates, resulting in a superior purification process. The purification process is further demonstrated to produce plasmid products substantially free of genomic DNA, RNA, protein, and endotoxin.
In some embodiments, all of the described aspects of the present disclosure are advantageously combined to provide an integrated process for preparing substantially purified cellular components of interest from cells in bioreactors. Again, the cells are most preferably plasmid-containing cells, and the cellular components of interest are most preferably plasmids. The substantially purified plasmids are suitable for various uses, including, but not limited to, gene therapy, plasmid-mediated therapy, as DNA vaccines for human, veterinary, or agricultural use, or for any other application that requires large quantities of purified plasmid. In this aspect, all of the advantages described for individual aspects of the present disclosure accrue to the complete, integrated process, providing a highly advantageous method that is rapid, scalable, and inexpensive. Enzymes and other animal-derived or biologically sourced products are avoided, as are carcinogenic, mutagenic, or otherwise toxic substances. Potentially flammable, explosive, or toxic organic solvents are similarly avoided.
One aspect of the present disclosure is an apparatus for isolating plasmid DNA from a suspension of cells having both plasmid DNA and genomic DNA. An embodiment of the apparatus comprises a first tank and second tank in fluid communication with a mixer. The first tank is used for holding the suspension cells and the second tank is used for holding a lysis solution. The suspension of cells from the first tank and the lysis solution from the second tank are both allowed to flow into the mixer forming a lysate mixture or lysate fluid. The mixer comprises a high shear, low residence-time mixing device with a residence time of equal to or less than about 1 second. In a preferred embodiment, the mixing device comprises a flow through, rotor/stator mixer or emulsifier having linear flow rates from about 0.1 L/min to about 20 L/min. The lysate-mixture flows from the mixer into a holding coil for a period of time sufficient to lyse the cells and forming a cell lysate suspension, wherein the lysate-mixture has resident time in the holding coil in a range of about 2-8 minutes with a continuous linear flow rate.
The cell lysate suspension is then allowed to flow into a bubble-mixer chamber for precipitation of cellular components from the plasmid DNA. In the bubble mixer chamber, the cell lysate suspension and a precipitation solution or a neutralization solution from a third tank are mixed together using gas bubbles, which forms a mixed gas suspension comprising a precipitate and an unclarified lysate or plasmid containing fluid. The precipitate of the mixed gas suspension is less dense than the plasmid containing fluid, which facilitates the separation of the precipitate from the plasmid containing fluid. The precipitate is removed from the mixed gas suspension to give a clarified lysate having the plasmid DNA, and the precipitate having cellular debris and genomic DNA.
In some embodiments, the bubble mixer-chamber comprises a closed vertical column with a top, a bottom, a first, and a second side with a vent proximal to the top of the column. A first inlet port of the bubble mixer-chamber is on the first side proximal to the bottom of the column and in fluid communication with the holding coil. A second inlet port of the bubble mixer-chamber is proximal to the bottom on a second side opposite of the first inlet port and in fluid communication with a third tank, wherein the third tank is used for holding a precipitation or a neutralization solution. A third inlet port of the bubble mixer-chamber is proximal to the bottom of the column and about in the middle of the first and second inlets and is in fluid communication with a gas source the third inlet entering the bubble-mixer-chamber. A preferred embodiment utilizes a sintered sparger inside the closed vertical column of the third inlet port. The outlet port exiting the bubble mixing chamber is proximal to the top of the closed vertical column. The outlet port is in fluid communication with a fourth tank, wherein the mixed gas suspension containing the plasmid DNA is allowed to flow from the bubble-mixer-chamber into the fourth tank. The fourth tank is used for separating the precipitate of the mixed gas suspension having a plasmid containing fluid, and can also include an impeller mixer sufficient to provide uniform mixing of fluid without disturbing the precipitate. A fifth tank is used for a holding the clarified lysate or clarified plasmid containing fluid. The clarified lysate is then filtered at least once. A first filter has a particle size limit of about 5-10 μm and the second filter has a cut of about 0.2 μm. Although gravity, pressure, vacuum, or a mixture thereof can be used for transporting: suspension of cells; lysis solutions; precipitation solutions; neutralization solutions; or mixed gas suspensions from any of the tanks to mixers, holding coils or different tanks, pumps are utilized in a preferred embodiments. In a more preferred embodiment, at least one pump having a linear flow rate from about 0.1 to about 1 ft/second is used.
In another specific embodiment, a Y-connector having a having a first bifurcated branch, a second bifurcated branch and an exit branch is used to contact the cell suspension and the lysis solutions before they enter the high shear, low residence-time mixing device. The first tank holding the cell suspension is in fluid communication with the first bifurcated branch of the Y-connector through the first pump and the second tank holding the lysis solution is in fluid communication with the second bifurcated branch of the Y-connector through the second pump. The high shear, low residence-time mixing device is in fluid communication with an exit branch of the Y-connector, wherein the first and second pumps provide a linear flow rate of about 0.1 to about 2 ft/second for a contacted fluid exiting the Y-connector.
Another specific aspect of the present disclosure is a method of substantially separating plasmid DNA and genomic DNA from a bacterial cell lysate. The method comprises: delivering a cell lysate into a chamber; delivering a precipitation fluid or a neutralization fluid into the chamber; mixing the cell lysate and the precipitation fluid or a neutralization fluid in the chamber with gas bubbles forming a gas mixed suspension, wherein the gas mixed suspension comprises the plasmid DNA in a fluid portion (i.e. an unclarified lysate) and the genomic DNA is in a precipitate that is less dense than the fluid portion; floating the precipitate on top of the fluid portion; removing the fluid portion from the precipitate forming a clarified lysate, whereby the plasmid DNA in the clarified lysate is substantially separated from genomic DNA in the precipitate. In preferred embodiments: the chamber is the bubble mixing chamber as described above; the lysing solution comprises an alkali, an acid, a detergent, an organic solvent, an enzyme, a chaotrope, or a denaturant; the precipitation fluid or the neutralization fluid comprises potassium acetate, ammonium acetate, or a mixture thereof; and the gas bubbles comprise compressed air or an inert gas. Additionally, the decanted-fluid portion containing the plasmid DNA is preferably further purified with one or more purification steps selected from a group consisting of: ion exchange, hydrophobic interaction, size exclusion, reverse phase purification, endotoxin depletion, affinity purification, adsorption to silica, glass, or polymeric materials, expanded bed chromatography, mixed mode chromatography, displacement chromatography, hydroxyapatite purification, selective precipitation, aqueous two-phase purification, DNA condensation, thiophilic purification, ion-pair purification, metal chelate purification, filtration through nitrocellulose, or ultrafiltration.
In some embodiments, a method for isolating a plasmid DNA from cells comprising: mixing a suspension of cells having the plasmid DNA and genomic DNA with a lysis solution in a high-shear-low-residence-time-mixing-device for a first period of time forming a cell lysate fluid; incubating the cell lysate fluid for a second period of time in a holding coil forming a cell lysate suspension; delivering the cell lysate suspension into a chamber; delivering a precipitation/neutralization fluid into the chamber; mixing the cell lysate suspension and the a precipitation/neutralization fluid in the chamber with gas bubbles forming a gas mixed suspension, wherein the gas mixed suspension comprises an unclarified lysate containing the plasmid DNA and a precipitate containing the genomic DNA, wherein the precipitate is less dense than the unclarified lysate; floating the precipitate on top of the unclarified lysate; removing the precipitate from the unclarified lysate forming a clarified lysate, whereby the plasmid DNA is substantially separated from genomic DNA; precipitating the plasmid DNA from the clarified lysate forming a precipitated plasmid DNA; and resuspending the precipitated plasmid DNA in an aqueous solution.
The disclosure also relates to a method of treating and/or preventing viral infection in a subject comprising administering to the subject a therapeutically and/or prophylactically effective amount (as applicable) of a pharmaceutical composition comprising at least one expressible nucleic acid sequence, the expressible nucleic acid sequence comprising in 5′ to 3′ orientation a first, second and third nucleic acid sequence; wherein the first nucleic acid sequence encodes a leader sequence, the second nucleic acid sequence encodes a self-assembling polypeptide, and the third nucleic acid sequence encodes a viral antigen. In some embodiments, the first, second and third nucleic acid sequences are contiguous. In some embodiments, the first, second, third nucleic acid sequence are non-contiguous and are separated by one or a plurality of other independently selectable nucleic acids encoding the same or different viral antigens. In some embodiments, the first, second, third nucleic acid sequence are non-contiguous and are separated by one or a plurality of other independently selectable nucleic acids encoding the same or different self-assembling peptides.
Disclosed are vaccines comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 69, or a functional fragment thereof. In some embodiment, the vaccines disclosed herein comprises the amino acid sequence of SEQ ID NO: 69, or a functional fragment thereof.
Also disclosed are DNA vaccines comprising an expressible nucleic acid sequence encoding a polypeptide comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 69, or a functional fragment thereof. In some embodiment, the DNA vaccines disclosed herein encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 69, or a functional fragment thereof. In some embodiment, the DNA vaccines disclosed herein comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 68, or a functional fragment thereof. In some embodiment, the DNA vaccines disclosed herein comprises the nucleic acid sequence of SEQ ID NO: 68, or a functional fragment thereof. In some embodiments, the disclosed DNA vaccine further comprises a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutically acceptable excipient is an adjuvant.
Also disclosed are vaccines comprising at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to any of the sequences disclosed in Examples 8-11.
In some embodiments, the vaccine comprises a lipid nanoparticle (LNP) comprising one or a plurality of nucleic acid molecules disclosed herein. In some embodiments, delivery to a target cell is enhanced in vitro, while in other aspects, delivery to a target cell is enhanced in vivo. When administered in vivo, in one embodiment, target cell target cell delivery LNPs demonstrate enhanced delivery of agents to the liver and spleen when compared to reference LNPs. In some aspects, the target cell, e.g., a liver cell (e.g., a hepatocyte) or splenic cell, is contacted with the LNP in vitro. In some aspects, the target cell is contacted with the LNP in vivo by administering the LNP to a subject, e.g., a human subject. In one embodiment, the subject is one that would benefit from modulation of protein expression of a target protein, e.g., in a target cell. In some aspects, the LNP is administered intravenously. In some aspects, the LNP is administered intramuscularly. In some aspects, the LNP is administered by a route selected from the group consisting of subcutaneously, intranodally and intratumorally.
In some embodiments, the agent may comprise or consist of a nucleic acid molecule. In some aspects, the nucleic acid molecule is selected from the group consisting of RNA, mRNA, RNAi, dsRNA, siRNA, antisense RNA, ribozyme, CRISPR/Cas9, ssDNA and DNA. In some aspects, the nucleic acid molecule is RNA selected from the group consisting of a shortmer, an antagomir, an antisense, a ribozyme, a small interfering RNA (siRNA), an asymmetrical interfering RNA (aiRNA), a microRNA (miRNA or miR), a Dicer-substrate RNA (dsRNA), a small hairpin RNA (shRNA), a messenger RNA (mRNA), and mixtures thereof. In some embodiments, the nucleic acid molecule is an siRNA molecule. In some embodiments, the nucleic acid molecule is a miR. In some embodiments, the nucleic acid molecule is an antagomir. In some aspects, the nucleic acid molecule is DNA. In some aspects, the nucleic acid molecule is mRNA.
Accordingly, in one aspect the disclosure relates to a target cell delivery lipid nanoparticle (LNP) comprising:
The materials described above as well as other materials can be packaged together in any suitable combination as a kit useful for performing, or aiding in the performance of, the disclosed method. It is useful if the kit components in a given kit are designed and adapted for use together in the disclosed method. For example disclosed are kits comprising any of the elements of the disclosed nucleic acid compositions. For example, disclosed are kits comprising nucleic acid sequences comprising a leader sequence, a linker sequence, a nucleic acid sequence encoding a self-assembling polypeptide, and/or a nucleic acid sequence encoding a viral antigen. In some embodiments, the kits can further comprise a plasmid backbone.
We were informed by our prior findings that synthetic DNA and electroporation (DNA/EP) can be used to deliver in vivo biologics such as antibodies and enzymes, and sought to determine in this study whether more complex structures such as macromolecular nanoparticle assemblies can also be delivered by DNA/EP. Nano-vaccines have historically been shown to induce more potent humoral responses than their monomeric counterparts but may be challenging to produce on a large scale. Therefore, a method to simplify the process by producing these nano-vaccines in the hosts may be relevant. Sample sizes in the study were pre-determined by power analyses with results from another set of the pilot studies. All the collected datapoints were included in the final analyses except for a single guinea pig in the DLmono_GT8 group which showed pre-existing antibody titers to GT8. All data were collected in at least technical duplicates, and except for the guinea pig and the challenge experiment, all findings were replicated successfully at least once in the study. Animals were randomly allocated to cages at the initiation of the study and were not further randomized. Data collection and analyses were not blinded. Detailed sample sizes are provided in the brief description of the drawings.
The nanoparticle structures for ferritin (PDB ID: 3BVE), lumazine synthase (PDB ID: 1HQK) and PfV (2E0Z) were used to seed the modeling simulations. The structure of eOD-GT8 (PDB ID: 5IDL) and HAI (PDB ID: 3GBN) were used to decorate the nanoparticles. N-linked glycans with missing density were added using glycan modeling modules of Rosetta [66]. Next, we wrote a new algorithm (simpleNanoparticleModeling) in the Molecular Software Library [67]. Briefly, we aligned the appropriate number of immunogens at the nanoparticle surface using coordinate frames constructed by 3 C-α atoms of the terminal positions of each protein. Immunogens were then tilted by random rotations around the x- and y-axes up to 30 degrees for the first ¾ of the simulation and up to 75 degrees for the last ¼ of the simulation, with a 120-degree rotation allowed for the z-axis. The immunogens were also translated by 10 Å to 200 Å along an axis projected away from the nanoparticle surface. Clashes were detected at each iteration and the models with the lowest number of clashes at each translation was written out as a potential structural model. The models were manually inspected and utilized to construct linkers as glycine-serine repeats using 30 Å per 9 linker residues as a guide. The sequence of the HA isolate H1 NC99 (A/New Caledonia/30/1999 (H1N1)) from residues 65-276 was used to construct the flu nanoparticle.
Protein sequences for IgE Leader Sequence and eOD-GT8-60mer were as previously reported[34, 68] and disclosed herein as SEQ ID NO: 6 and 9, respectively. Protein sequences for 3BVE-ferritin, PfV and HA_CA09 were obtained from UniProt (accession numbers: Q9ZLI1, 16U7J4, and C3W5X2). Protein sequence for HAI_NC99 was obtained from GenBank (accession number AY289929.1). DNA encoding protein sequences were codon and RNA optimized as previously described [34]. The optimized transgenes were synthesized de novo (GenScript, Piscataway, NJ) and cloned into a modified pVAX-1 backbone under the control of the human CMV promoter and bovine growth hormone poly-adenylation signal. All the plasmid maxi-preps were produced commercially (GenScript, Piscataway, NJ; Aldevron, Fargo, ND), with low endotoxin level (<0.005EU/μg). Production of His-tagged GT8-monomer and recombinant protein DLnanos
Expi293F cells were transfected with pVAX plasmid vector carrying the DLnano or His-tagged GT8-monomer transgene with PEI/OPTI-MEM and harvested 6 days post-transfection. Transfection supernatant was first purified with affinity chromatography using the AKTA pure 25 system and an IMAC Nickel column (for His-tagged GT8) and gravity flow columns filled with GNL Lectin beads (for DLnanos). The eluate fractions from the affinity purification were pooled, concentrated and dialyzed into 1×PBS buffer before being loaded onto the SEC column and then purified with size exclusion chromatography, for which the Superdex 75 10/300 GL column was used to purify His-tagged GT8-monomer and the Superose 6 Increase 10/300 GL column was used for DLnanos (run at 0.5 mL/min). Identified eluate fractions were then collected and concentrated to 1 mg/mL in PBS.
All mouse experiments were carried out in accordance with animal protocols 1127760 and 112782 approved by the Wistar Institute Institutional Animal Care and Use Committee (IACUC) (Philadelphia, PA). For DNA-based immunization, 6-8 week old female C57BL/6, BALB/c and CDI mice or 6-8 week old male BALB/c mice purchased from Jackson Laboratory or Charles River Laboratories were immunized one to three times (three-weeks apart) with DLmono_GT8, DLmono_HA_NC99, DLmono_HA_CA09, DNA-encoded LS_HA_CA09, DL_GT8_IMX313P or DLnano_LS_GT8, DLnano_CD4MutLS_GT8, DLnano_3 BVE_GT8, DLnano_PfV_GT8, DLnano_LS_HA_NC99 and DLnano_3 BVE_HA_CA09 via intramuscular injections into the tibialis anterior muscles (over two sites), followed by intramuscular electroporation with the CELLECTRA 3P device (Inovio Pharmaceuticals). For electroporation, 2 sets of 2 pulses (at 0.1 Amps) were delivered. Each set of 2 pulses lasts 52 milliseconds with a 1 second delay. For all DNA-encoded GT8-based immunizations (except for dosing studies), 25 μg of plasmid DNA was used, a standard DNA dose as in prior study [69]. For the control experiment to assess the importance of antigen decoration on nanoparticle, balb/c mice were immunized with 1:1 co-formulated (25 μg each) DLmono_GT8 with pVAX, DLmono_GT8 with DLnano_LS (core), and DLnano_LS_GT8 with pVAX and followed for seven d.p.i for sero-conversion. For all DNA-encoded HA-based immunizations, doses of 1 μg were used for each immunization for studies of humoral responses and 10 μg for studies of cellular responses. MBL knockout mice (B6.129S4-Mbl1tm1Kata Mbl2tm1Kata/J) and CR2 knockout mice (B6.129S7(NOD)-Cr2tm1Hmo/J) purchased from Jackson Laboratory were immunized in the same fashion.
For protein-based immunization, 6-8 week old female C57BL/6, MBL knockout and CR2 knockout mice were immunized subcutaneously over two sites with a high dose of 10 μg of recombinant eOD-GT8-60mer protein in 50 μL co-formulated with 50 μL Sigma adjuvant system (SigmaAldrich); the protein dose was 2.7-times higher than a prior study [26].
Female Hartley guinea pigs (8-10 weeks old) purchased from Charles River Laboratories (Wilmington, MA) were group housed and handled at AccuLab (San Diego, CA) with ad libitum access to food and water according to the standards of the Institutional Animal Care and Use Committee (IACUC) protocol CalMI2-043. Following acclimation, each guinea pig was given a single immunization of 50 μg of DLnano_LS_GT8 or DLmono_GT8 over 2 sites on the flank followed by intradermal EP with CELLECTRA 3P device. The animals were then bled at the indicated time points for humoral analyses.
Corning 96-well half area plates were coated at room temperature for 6 hours with 1 μg/mL MonoRab anti-His antibody (GenScript), followed by overnight blocking with solution containing 1×PBS, 5% skim milk, 10% goat serum, 1% BSA, 1% FBS, and 0.2% Tween-20. The plates were then incubated with 2 μg/mL of his-tagged GT8-monomer at room temperature for 2 hours, followed by addition of mice sera serially diluted with PBS with 1% FBS and 0.1% Tween and incubation at 37° C. for 2 hours. The plates were then incubated at room temperature for 1 hour with Peroxidase AffiniPure Goat Anti-Mouse IgG, Fcγ fragment specific at 1:5,000 dilution (Jackson Immunoresearch) or AffiniPure Goat Anti-Mouse IgM, u chain specific, (Jackson Immunoresearch) at 1:5000 dilution followed by addition of TMB substrates (ThermoFisher) and then quenched with IM H2SO4. Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader. Endpoint titer is defined as the highest dilution at which the OD of the post-immune sera exceeds the cut-off (mean OD of naïve animals plus standard deviations of the OD in the naïve sera multiplied with standard deviation multiplier f at the 99% confidence level).
The plates were coated, and blocked, followed by addition with GT8-his as described in the last section. Serially diluted mice sera were then incubated with the plates at 37° C. for 1 hour, followed by addition of purified VRC01 antibody (NIH AIDS Reagent) for an additional 1 hour at room temperature. The plates were then incubated with anti-human Fc (cross-adsorbed against rabbits and mice) (Jackson Immunoresearch) at 1:10,000 dilution for 1 hour, followed by addition of TMB substrate for detection. Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader.
The plates were coated with 5 μg/mL recombinant mouse MBL protein (R&D system) in 0.1 M CaCl2 at room temperature for 6 hours, followed by blocking with 1% BSA in 0.1 M CaCl2 in PBS overnight at 4° ° C. Transfection supernatant or muscle homogenates containing DLmono_GT8 or DLnano_LS_GT8 were then added to the plates for 2 hour incubation at 37° C., followed by Week 5 sera of BALB/c mice previously immunized twice with 25 μg DLnano_LS_GT8. The plates were then incubated with anti-mouse IgG H+L (cross-adsorbed against human) HRP (Jackson Immunoresearch) at 1:10,000 dilution, followed by addition of TMB substrates. Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader.
ELISA format as described in the MBL binding ELISA section except that the recombinant MBL used in the coating step is replaced by 5 μg/mL of VRC01 (NIH AIDS Reagent). Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader. Antigenic profile characterization of designed GT8-nano-vaccines
Corning half-area 96-well plates were coated with 2 μg/mL of GT8-monomer, or 3BVE_GT8-24mer, eOD-GT8-60mer, CD4Mut_LS_GT8-60mer and PfV_GT8-180mer at 4° C. overnight. The plates were then blocked with the buffer as described in the GT8-binding ELISA section for 2 hours at room temperature, followed by incubation with serially diluted VRC01 at room temperature for 2 hours. The plates were then incubated with anti-human Fc (cross-adsorbed against rabbits and mice) (Jackson Immunoresearch) at 1:10,000 dilution for 1 hour, followed by addition of TMB substrate for detection. Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader.
Corning 96-well half area plates were coated at 4° C. overnight with 2 μg/mL of recombinant HA(ΔTM)(H1N1/A/New Caledonia/20/1999) or HA(ΔTM)(A/California/04/2009)(H1N1) (Immune Technology), and blocked at room temperature for 2 hour with the buffer as described in the GT8-binding ELISA section. The plates were subsequently incubated with serially diluted mouse sera in PBS with 1% FBS and 0.1% Tween at 37° C. for 2 hours, followed by 1-hour incubation with anti-mouse IgG H+L HRP (Bethyl) at 1:20,000 dilution at room temperature and development with the use of TMB substrate. Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader. HAI assay
Mice sera were treated with receptor-destroying enzyme (RDE, 1:3 ratio) at 37° C. overnight for 18-20 hours followed by complement and enzyme inactivation at 56° C. for 45 minutes. RDE-treated sera were subsequently cross-adsorbed with 10% rooster red blood cells (Lampire Biologicals) in PBS at 4° ° C. for 1 hour. The cross-adsorbed sera were then serially diluted with PBS in a 96-well V-bottom microtiter plates (Corning). Four hemagglutinating doses (HAD) of A/Solomon Islands/03/06 virus, A/New Caledonia/20/99, or A/California/07/2009 (BEI) were added to each well and the serum-virus mixture was incubated at room temperature for 1 hour and then incubated with 50 μl 0.5% v/v rooster red blood cells in 0.9% saline for 30 minutes at room temperature. The HAI antibody titer was scored with the dot method, and the reciprocal of the highest dilution that did not exhibit agglutination of the rooster red blood cells was recorded.
For lymph node staining, 7 days after BALB/c mice were immunized with 80 μg DNA co-formulated with 12U Hyaluronidase (Sigma) encoding GT8-monomer or DLnano_LS_GT8, tibialis anterior muscles of the mice were injected with 5 μg of anti-mouse CD35 BV421 (BD-Bioscience) for in situ labelling of follicular dendritic cells 16 hours prior to harvest. Ipsilateral iliac lymph nodes from the mice were harvested the next day and preserved in O.C.T medium (Fisher) for cryo-sectioning. The sections were fixed with 4% paraformaldehyde, then blocked in 3% BSA/PBS for 1 hour at room temperature, followed by overnight staining with 6 μg/mL VRC01. The sections were then washed and stained with anti-human Alexa Fluor 488 antibody and imaged with Leica SP5 confocal microscopes.
For muscle staining, four days after BALB/c mice were immunized with 80 μg DNA encoding GT8-monomer, DLnano_LS_GT8, DLnano_3 BVE_GT8 or DLnano_PfV_GT8 co-formulated with 12U Hyaluronidase in the tibialis anterior muscles of the mice were harvested and preserved in 4% PFA/PBS for 2 hours at room temperature and then stored overnight in 70% EtOH/H2O at 4° C. The tissues were then serially dehydrated and blocked in 3% BSA/PBS for 1 hour at room temperature, followed by overnight staining with 6 μg/mL VRC01. The sections were then washed, and stained with anti-human Alexa Fluor 488 antibody, counterstained with 0.5 μg/mL DAPI and imaged with Leica SP5 confocal microscopes.
For transfected cells, HEK293T cells were cultured in poly-lysine coated glass chambers overnight, and then transfected with DNA encoding GT8-monomer or eOD-GT8-60mer with GeneJammer (Agilent). The cells were harvested 48 hours post transfection, fixed with 4% paraformaldehyde, permeabilized with 0.5% Triton X-100/PBS, blocked and stained as in the section describing muscle immunofluorescence staining.
For immunohistochemistry staining of muscle sections, BALB/C mice were immunized with 80 μg DLmono_GT8 or DLnano_LS_GT8 co-formulated with 12U hyaluronidase (Sigma). Transfected muscles were harvested seven days post immunization, cryo-sectioned, fixed, permeabilized, and blocked as described in the Immunofluorescence section. The muscle sections were then stained with goat anti-mouse MBL at 1:200 dilution in 1% BSA/PBS (R&D system) overnight, and then with secondary Rabbit anti-goat (H+L) HRP conjugated at 1:500 dilution (BioRad) and DAB substrates for development.
Tibialis anterior muscles from BALB/c mice immunized with 80 μg DLmono_GT8 or DLnano_LS_GT8 co-formulated with 12U hyaluronidase were collected seven d.p.i. The muscles were then fixed in 2.5% glutaraldehyde, serially dehydrated in acetone/ethanol solvents, and then embedded in epoxy and LR white resin. The resin was then sectioned to a thickness of 70 nm and deposited onto a metal grid, blocked overnight in 3% BSA/PBS, followed by staining with 60 μg/mL VRC01 (diluted in 3% BSA/PBS) overnight, and with 1:200 anti-human 6 nm gold nanoparticles (Jackson Immunoresearch) for 1 hour. The sections were then washed with 0.1% Tween in PBS, and water, followed by post-staining fixation with 2.5% glutaraldehyde in PBS for 5 minutes at room temperature followed by staining with 2% Uranyl acetate for 1 hour. The grids were subsequently imaged with JEOL JEM 1010 transmission electron microscope. For quantitative analyses, total number of gold-labeled clusters, and order of each cluster were manually counted. Frequency of a cluster of a particular order in a field of view was normalized relative to the total number of clusters observed.
The nanoparticles were produced in Expi293 cells, purified using Agarose bound lectin beads (Agarose Galanthus Nivalis Lectin, Vector Laboratories) followed by size exclusion chromatography (GE Healthcare) using the Superose 6 Increase 10/300 GL column. The proteins were further dialyzed into Tris-buffered saline (TBS). A total of 3 μL of purified proteins was adsorbed onto glow discharged carbon-coated Cu400 EM grids. The grids were then stained with 3 μL of 2% uranyl acetate, blotted, and stained again with 3 μL of the stain followed by a final blot. Image collection and data processing was performed on a FEI Tecnai T12 microscope equipped with an Oneview Gatan camera at 90,450× magnification at the camera and a pixel size of 1.66 Å.
Spleens from immunized mice were collected 5 weeks post the first immunization (2 weeks post the second) and homogenized into single cell suspension with a tissue stomacher in 10% FBS/1% Penicillin-streptomycin in RPMI 1640. Red blood cells were subsequently lysed with ACK lysing buffer (ThermoFisher) and percentage of viable cells were determined with Trypan Blue exclusion. 200,000 cells were then plated in each well in the mouse IFNγ ELISpot plates (MabTech), followed by addition of peptide pools that span both the lumazine synthase, GT8 or HA domains at 5 μg/mL of final concentration for each peptide (GenScript). The cells were then stimulated at 37° C. for 16-18 hours, followed by development according to the manufacturer's instructions. Spots for each well were then imaged and counted with ImmunoSpot Macro Analyzer.
Single cell suspension from spleens of immunized animals were prepared as described in the previous section and stimulated with 5 μg/mL of peptides spanning both the lumazine synthase, GT8 or HA domains(GenScript) for 5 hours at 37° C. in the presence of 1:500 protein transport inhibitor (ThermoFisher) and anti-mouse CD107a-FITC(ThermoFisher). The cells were then incubated with live/dead for 10 minutes at room temperature, surface stains (anti-mouse CD4 BV510, anti-mouse CD8 APC-Cy7, anti-mouse CD62L BV711 and anti-mouse CD44 AF700) (BD-Biosciences) at room temperature for 30 minutes. The cells were then fixed and permeabilized according to manufacturer's instructions for BD Cytoperm Cytofix kit and stained with intracellular stains anti-mouse IL-2 PE-Cy7, anti-mouse IFN-γ APC, anti-mouse CD3c PE-Cy5 and anti-mouse TNFα BV605 (BioLegend) at 4° C. for 1 hour. The cells were subsequently analyzed with LSR II 18-color flow cytometer.
Tibialis anterior muscles of immunized animals were harvested and homogenized in T-PER extraction buffer (ThermoFisher) and protease inhibitor (Roche). Muscle homogenates were subsequently concentrated 20× with Amicon Ultra 0.5 mL Centrifugation kits with 3 kDA cutoffs (Milipore Sigma) and protein concentrations were quantified with BCA assays (ThermoFisher). For electrophoresis, 8 μL supernatants of Expi293F cells transfected with pVAX, DLmono_GT8, eOD-GT8-60mer or 50 μg muscle homogenates from mice immunized with the 80 μg aforementioned constructs co-formulated with 12U hyaluronidase were loaded onto 4-12% SDS Bis-Tris Gel (SDS-PAGE) or 3-8% Tris-Acetate Gel (pseudo-Native PAGE) for electrophoresis. For SDS-PAGE, all samples were reduced with heating of the samples in the presence of a reducing agent and LDS sample buffer (ThermoFisher) at 70° C. for 10 minutes. For Pseudo-Native PAGE, samples were only incubated with the LDS buffer at room temperature and loaded directly onto the 3-8% TA gel without boiling. Proteins were subsequently transferred to PVDF membrane from the gels, and stained with 3 μg/mL of VRC01 and 1 μg/mL anti-human GAPDH (for SDS-PAGE only, Clone D4C6R, Cell Signaling) in Odyssey Blocking Buffer/PBS/0.1% Tween (LI-COR Biosciences) overnight at 4° C., and 1:10,000 IRDye 800CW goat anti-human IgG (LI-COR Biosciences) in Odyssey Blocking Buffer/0.1% Tween/0.1% SDS at room temperature for 1 hour, and then scanned with LI-COR Odyssey CLx.
Recombinant 3BVE-GT8 was labelled with FITC with the lightning link kits according to manufacturer's instructions (Expedon). Spleens were harvested five weeks post the second immunization of 25 μg of DLnaono_LS_GT8, DLmono_GT8 or from Naïve mice. Single cells were then labelled with Live/Dead dye ultraviolet reactive (ThermoFisher) at room temperature for 10 minutes and incubated with mouse Fc-Block (Clone 93, ThermoFisher) at 1:200 dilution. Avi-Tagged GT8 was biotinylated and tetramerized with an excess of APC-streptavidin (ThermoFisher) as previously described [27]. The cells were washed with PBS and incubated with 1:200 A488-3BVE-GT8 and 1:200 APC-GT8-tetramer at 4° C. for 30 minutes. Without being washed, the cells were incubated with 1:200 anti-mIgD-APC/Cy7 (BioLegend), anti-mIgM-BV711 (Fisher Scientific), anti-mCD19-PECy7 (Biolegend), anti-mIgG-BV510 (Biolegend) in 1% FBS/PBS solution. The cells were then resuspended in 1× BDFix buffer and analysed with LSR II 18-color flow cytometer.
6-8 week old female BALB/c mice (Jackon Laboratory) were immunized with 1 μg of pVAX vector, DLmono_HA_CA09 or DLnano_3 BVE_HA_CA09 twice three weeks apart. The mice were subsequently transferred to BioQual Inc for challenge experiment. 35 days post the second immunization, the mice were intranasally inoculated with 10LD50 H1/A/California/07/09 in PBS. Weights of the mice were pre-recorded prior to the challenge and daily after the challenge until 7 days post inoculation, at which lungs from the mice were harvested and snap-frozen for viral load assay by RT-qPCR and histo-pathology by H&E staining. At any point, mice exhibiting more than 20% of weight loss as compared to baseline were euthanized (humane endpoint).
The amounts of RNA copies per gram lung tissue was determined using a real-time quantitative PCR (qPCR) assay. This assay utilized primers and a probe specifically designed to amplify and bind to a conserved region of the NP gene of influenza virus. The signal was compared to a known standard curve and calculated to give copies per gram tissue. Viral RNA was extracted from lung homogenates using MiniElute Virus Spin Kit (Qiagen). TAQMAN RT-PCR kit (Applied Biosystems, Inc., Carlsbad, CA) was used for amplification of viral RNA in the presence of 600 nM primers (CAL-1-U: ATGGCGTCTCAAGGCACCAA and CAL-1-D: GCACATTTGGATGTAGAATCTC) and 140 nM probe (CAL-1-P: 6FAM-CAGAGCATCTGTCGGAAGAATGATTG-TAMRA) with the following Thermocycler setting: 48° C. for 30 minutes, 95° C. for 10 minutes followed by 40 cycles of 95° C. for 15 seconds, and 1 minute at 60° C.
We have performed power analysis with R based on our preliminary data to determine the smallest sample size that would allow us to achieve a power of 0.9 with a pre-set a-value of 0.05. All statistical analyses were performed with PRISM V8.0 and R V3.5.1. Each individual data point was sampled independently. Two-tailed Mann Whitney Rank Tests were used to compare differences between groups. Bonferroni corrections were used when multiple comparisons were made.
To determine whether DNA/EP could be used to launch structurally designed, self-assembling protein nanoparticles in vivo, we encoded the transgene eOD-GT8-60mer in the pVAX1 vector and optimized the DNA cassette for in vivo nanoparticle expression (
Next, we examined the in vivo expression of both DNA-encoded GT8 monomer and nanoparticle constructs. Immunofluorescent staining of mouse muscles transfected with DNA/EP four days post injection (d.p.i) with VRC01 (a human broadly neutralizing antibody with high-affinity for GT8) showed that both DNA-encoded GT8 constructs expressed in vivo (
Next, we used a mannose binding lectin (MBL) labelling experiment to assess for in vivo antigen multimerization and nanoparticle assembly. MBL is a protein that can form hexamer and preferentially bind to highly repeated glycan structures on a pathogen/antigen surface [44]. A recent study by Tokatilian et al. demonstrated that only highly multimerized glycan structures (eOD-GT8-60mer but not eOD-GT8-monomer) could bind to MBL [26]. In our study, we similarly showed using ELISA that while VRC01 could bind to both protein GT8-60mer and GT8-monomer, murine MBL could only bind to protein GT8-60mer but not protein GT8-monomer (
As an additional way to assess in vivo nanoparticle formation, we employed a transmission electron microscopy-based technique, where thin sections of transfected muscles were stained with VRC01 and gold-conjugated anti-human IgG. Clusters of gold-labelled macromolecules suggestive of in vivo launched nanoparticles decorated with multiple copies of GT8 were only observed in mice injected with DLnano_LS_GT8 but not with DLmono_GT8 (
Using immunofluorescence staining with VRC01 (green), we determined that DLnano_LS_GT8 trafficked more efficiently to the draining lymph node and co-localized with the CD35+ follicular dendritic cells (in blue) in contrast with the DLmono_GT8 seven d.p.i. (
The ability of DLnano_LS_GT8 to improve humoral responses was observed in other animal models. Strikingly, two immunizations in C57BL/6 mice of DLmono_GT8 failed to induce seroconversion, while DLnano_LS_GT8 induced strong humoral responses (
We next compared the antibody responses induced by protein eOD-GT8-60mer and DLnano_LS_GT8. Protein eOD-GT8-60mer was subcutaneously administered in mice to be consistent with prior studies involving administration of this immunogen to mice [27, 28]; further, a relative high protein dose of 10 μg was used in this study as compared to prior study for protein versus DNA comparison [26]. We observed that two sequential immunizations of protein eOD-GT8-60mer co-formulated with Sigma Adjuvant System or DLnano_LS_GT8 in C57BL/6 mice induced similar humoral responses (
We next examined the induction of antigen-specific cellular responses by DNA nano-vaccines. DLnano_LS_GT8 elicited significantly stronger antigen (GT8)-specific cellular responses than DLmono_GT8 in BALB/c mice as determined by IFNγ-ELIspot assays (
In C57BL/6 mice, we also found that DLnano_LS_GT8 elicited strong T-cell responses to the full immunogen. Both CD4+ and CD8+ responses were predominantly to the LS domain, possibly due to the lack of CD8+ T-cell epitope in the GT8 domain for this inbred strain (
In comparison to protein eOD-GT8-60mer, we observed two immunizations of DLnano_LS_GT8 induced 2.2-fold higher T-cell responses by IFNγ-ELIspot assay (
To ensure that the observed phenomena were not limited to lumazine synthase scaffolded nanoparticles, we computationally designed additional GT8 nanoparticles. Using the crystal structures of ferritin from Helicobacter pylori (3BVE, a 24-mer), and PfV viral cage from Pyrococcus furiosus(2e0z, a 180-mer), we modeled GT8 at various geometries relative to the particle surface and designed appropriate flexible linkers. 3BVE-GT8 homogenously assembled into spherical nanoparticles by nsEM (
Valency of nanoparticles was found to be relevant to the dose-sparing phenomenon observed (
To determine if these findings could be applied to an immunogen relevant to a different infectious disease, we computationally designed a LS nanoparticle to display the receptor binding domain of the head of influenza hemagglutinin (LS_HA_NC99) based on the H1N1 strain A/New Caledonia/20/1999 and confirmed its assembly into homogenous 60-mer by both SEC, SEC-MAL and nsEM (
Additionally, in terms of elicited cellular responses, two immunizations of DLnano_LS_HA_NC99 induced 8.4-fold higher effector memory CD8+ T-cell responses than DLmono_HA_NC99 at 10 μg dose in terms of CD107a and IFNγ expression, similar to our prior findings (
Finally, we examined if homogenous in vitro assembly of the designed DLnano-vaccine was a pre-requisite to its enhanced potency. To this end, we studied the in vivo properties of a poorly folded nanoparticle. We used an alternative lumazine synthase scaffolded influenza construct, DNA-encoded LS_HA_CA09, based on the A/California/07/2009 strain which did not pass our biophysical filters, as in vitro expression of the construct showed 3+ peaks with the two largest peaks consisting of aggregates or smaller unassembled protein by SEC (
To further evaluate the induction of functional immune responses by DLnano-vaccines, we utilized a lethal influenza challenge model in mice. We constructed a ferritin-scaffolded receptor binding domain of hemagglutinin from H1/California/07/09 strain, DLnano_3 BVE_HA_CA09, that was leader sequence, codon and mRNA-optimized as compared to a previously reported construct [48]. We first confirmed its in vitro assembly into nanoparticles by SEC and nsEM (
In a separate set of experiments, we followed these three groups of immunized mice seven days post H1/CA09 challenge to determine lung viral load and pathology. It was observed, in this challenge study, that within the first seven days, 80% (4/5) of mice immunized with control pVAX vector succumbed to infection, but mice immunized with either DLmono_HA_CA09 and DLnano_3 BVE_HA_CA09 survived the first seven days (
Development of vaccines can be a challenging endeavor due to poor immunogenicity of certain vaccine antigens, which results in the need to increase the number of required vaccinations, dose per vaccination, and the required interval for patients to complete the vaccine regime. Particulate vaccine formulations can help boost immunogenicity but can be slow to develop on a large scale due to manufacturing complexities. Synthetic nucleic-acid based methods for the delivery of vaccine antigens have shown great promises, as they are often produced at significantly lower costs than their protein counterparts, can be manufactured to scale and bypass complex processes of assembly [49], offer superior safety profile and demonstrate remarkable thermo-stability to allow for extended shelf-lives [51].
In this study, through the use of computational modeling and biophysical characterization, we engineered multimeric forms of HIV and influenza antigens which folded properly in vitro and displayed the desired antigenic profiles. We showed that these designer nano-vaccines can assemble in vivo when delivered using synthetic DNA and adaptive electroporation, through direct evidence from pseudo-Native PAGE analysis (
This work interrogated factors which might contribute to the enhanced adaptive immune responses of DLnano-vaccines. Homogeneous in vitro assembly of these computationally designed DLnano-vaccines is important for their downstream success, as poorly assembled DNA-encoded LS_HA_CA09 did not elicit similarly potent immune responses (
When DNA-launched nano-vaccines were compared to recombinant protein nano-vaccines, widely considered as an extremely potent vaccine formulation in terms of induction of antibody responses [52], we observed DLnano-vaccines induced comparable humoral responses to recombinant protein nanovaccines, but uniquely induced potent CD8+ T-cell responses in an MBL-complement independent manner. The observation that DLnano-vaccines function independently of MBL-complement pathway is likely of interest for clinical translation of such vaccines, as approximately 5-20% of human populations have MBL deficiency (plasma MBL <100 ng/mL) [53, 54]. The role of T cells in immune surveillance to mediate protection provides a strong rationale for exploring this unique property of DLnano-vaccine [55], especially for such diseases as liver-stage malaria [56], influenza for the elderlies [57, 58], and cancer [59]. The unique ability for DLnano vaccination to induce CD8+ T-cell responses may be related to its distinct mechanism of antigen uptake and presentation. Antigen presenting cells, such as macrophages, are known to migrate into the site of electroporation to scavenge antigens expressed through DNA cassettes associated with apoptotic cells [49]. Prior studies observed that co-delivery of DNA vaccines with pro-apoptotic mutated Caspase 2 or Fas significantly increased both CD4+ and CD8+ T-cell responses to the vaccine antigens [60, 61]. Such distinct mechanism of antigen processing might lead to more efficient cross-presentation to the MHC Class I pathway. Additionally, APCs including DCs and macrophages may also be directly transfected with the inoculated DNA cassettes in vivo [62, 63], and the two mechanisms may be synergistic in the induction of CD8+ T-cell immunity. Our findings also demonstrated that DLnano-vaccine could improve induced CD8+ T-cell responses by eight to ten-fold relative to their monomeric counterparts. Given that DNA-vaccines can already induce CD8+ T-cell responses in patients to cause histopathological regression of HPV-driven cervical dysplasia [4], the finding is relevant and whether DLnano-vaccines can further improve the clinical response rates should be explored.
Importantly, significant dose sparing can be realized with DLnano-vaccines. A dose of 1 μg of plasmid DNA, a dose at which we historically would not expect to observe robust sero-conversion [64], was able to induce clear functional HAI titers in mice. Fewer immunizations of DLnano-vaccine could induce the same, if not higher, titers of antibodies. Given recent advances in the electroporation technology has improved the potency and consistency of immune responses induced by DNA vaccines in patients [4, 37-39, 63, 65], it will be important to determine whether DLnano-vaccines can also help to reduce doses used in the clinic and lower the number of clinical visits required for vaccination. These advances may have important implications for outbreak control, and for global deployment including of vaccinations in more resource limited settings.
It will be important to build on these initial studies to improve DLnano-vaccines. For example, while it is known that cross-linking of B-cell receptors through multivalent antigen display can improve B-cell responses [15], studies to examine the mechanisms for the improved CD8+ T-cell responses for DLnano-vaccines relative to their monomeric counterparts are also important. Due to the unique ability of DLnano-vaccine to elicit strong CD8+ T-cell immunity, new DLnano-vaccines should be designed and evaluated to target diseases like cancer and T-cell dependent infectious diseases. The combined advantages of a simplified cost-effective temperature-stable platform, with the ability to retain in vivo structural integrity may be of value for the development of additional vaccines for HIV, influenza as well as other infectious diseases.
This work demonstrates that that advances in synthetic DNA and adaptive electroporation technologies have allowed for in vivo assembly of complex computationally designed particulate nano-vaccines to induce improved humoral and cellular responses, and to confer functional protective benefits in a survival study. As DNA can be rapidly manufactured to scale with low costs, it can be envisioned that computationally designed nano-vaccines can be rapidly evaluated to expedite clinical translational and global deployment of various promising vaccine candidates.
Compositions comprising self-assembling vaccines and methods of using the same have been previously described in International Application No. PCT/US2019/068444 filed on Dec. 23, 2018, and U.S. provisional application No. 62/982,038 filed on Feb. 26, 2020, each of which is incorporated by reference in its entirety herewith. In those disclosures, it was demonstrated that nanoparticles can be engineered by rational methods and assemble in vitro and in vivo. Using two different antigens, HIV antigen and influenza antigen, it was shown that DNA-Launched nanoparticles (DL-nano) can make superior vaccines.
Cytolytic T cells (CTL) is an extremely important branch of adaptive immune system, which can selectively kill target cells through release of cytokines, granzyme and perforin, as well as mediating target cell apoptosis through Fas and Fas-Ligand interaction [70]. T cells engineered with artificial receptors for anti-tumor activity is an exciting area of research but may come with limitations in throughput and costs. Therefore, induction of broad endogenous antigen-specific CTL through vaccination may, therefore, be an important approach to treat cancer [71].
However, induction of CTL through vaccination can be challenging as it requires antigen presenting cells (APCs) to present HLA-restricted epitopes to the MHC I pathway and provide costimulatory signal to prime CD8+ T cells [72]. Using viral vectors modified to encode target antigens is an approach to drive CTL responses, potentially through direct transduction of target cells [73]. Additionally, special adjuvants can be used to facilitate cross-presentation of target antigens, which to varying degrees promote phago-lysosomal escape and retro-translocation of target antigens into the cytosol [74]. Alternatively, dendritic cells (DCs) can be loaded ex vivo with saturating concentrations of peptides and adoptively transferred back into the host to prime CD8+ T cells [75]. Each approach has certain drawback: relatively few adjuvants have been demonstrated to help prime CD8+ T-cell responses in clinic [76], viral-vectored vaccine can be limited by pre-existing immunity against the viral vector [77], and manufacturing issues with large-scale production of DC vaccines.
DNA vaccination has also been observed to elicit CD8+ T-cell responses both in preclinical animal models and in clinical trials [78], plausibly through a combination of direct transfection of target cells along with cross presentation of DNA-encoded antigens [80]. We previously reported a new strategy to use DNA to launched in vivo produced nanoparticle vaccines, which resulted in significant improvements in the rate of seroconversion, magnitude of humoral response, dose sparing, and protection from viral challenge [81]. Additionally, we have also observed DNA vaccination of antigens scaffolded by in vivo assembled nanoparticles induced significantly improved CD8+ T-cell responses compared to DNA-encoding non-scaffolded antigens [81]. In this work, we compared the ability of DNA and protein vaccinations of identical nanoparticle antigens to induce CTL responses in mice. We discovered that intramuscular DNA vaccination, but not RIBI, CpG, or poly (I:C) adjuvanted protein vaccination, was capable of inducing robust CTL responses against influenza and HIV antigens. Mechanistic studies revealed that in comparison to protein vaccination, DNA launched nanoparticle vaccines uniquely induced apoptosis of transfected muscle tissues, which was followed by infiltration of antigen presenting cells (APCs), including pro-inflammatory M1 macrophages, to scavenge antigens. CTL responses were significantly attenuated when phagocytic macrophages were depleted or in cDC deficient BATFK3 KO mice. Finally, DNA launched nanoparticle vaccines induced more potent and consistent CTL responses against immunodominant epitopes on tumor-associated antigens Trp2 and Gp100 than conventional monomeric DNA vaccines or CpG adjuvanted peptide vaccines and facilitated tumor rejection in 80% of mice in the prophylactic B16-F10 melanoma model. This work therefore provides a demonstration that induction of transient physical stress through DNA-launched nanoparticle vaccination may be a safe, easy and robust way to facilitate antigen cross presentation and CTL priming to target cancer.
i. Design of DNA-Launched Nanoparticles
The self-assembling nanoparticles scaffolding Trp2 and Gp100 peptides were engineered using structure-guided design, as described in the results section. DNnano_LS_GT8 and DLnano_LS_HA(NC99) were developed in prior work and disclosed in International Application No. PCT/US2019/068444 filed on Dec. 23, 2018, and U.S. provisional application No. 62/982,038 filed on Feb. 26, 2020, each of which is incorporated by reference in its entirety herewith.
ii. DNA Design and Plasmid Synthesis
Protein sequences for IgE Leader Sequence and eOD-GT8-60mer were as previously reported [82, 83]. Protein sequence for HAI_NC99 was obtained from GenBank (accession number AY289929.1). DNA encoding protein sequences were codon and RNA optimized as previously described [82]. The optimized transgenes were synthesized de novo (GenScript) and cloned into a modified pVAX-1 backbone under the control of the human CMV promoter and bovine growth hormone poly-adenylation signal.
iii. Animals
All animal experiments were carried out in accordance with animal protocols 201214, 201115, and 201221 approved by the Wistar Institute Institutional Animal Care and Use Committee (IACUC). For DNA-based immunization, 6 to 8 week old female C57BL/6, BALB/c or B6.129S(C)-Batf3tm1Kmm/J mice (Jackson Laboratory) were immunized with DNA vaccines via intramuscular injections into the tibialis anterior muscles, coupled with or without intramuscular EP with the CELLECTRA 3P device (Inovio Pharmaceuticals). For DNA immunizations using DLnano_LS_GT8 and DLnano_LS_HA(NC99) as antigens (except in dose comparison study,
For vaccinations in mechanistic study (
For tumor challenge, B16-F10 (ATCC) were maintained in 10% FBS/DMEM under low passage (less than 10) and B16-F10-Luc2 cells (ATCC) were maintained in 10% FBS/DMEM enriched with 10 μg/mL blasticidin (Gibco) with routine testing for mycoplasma contaminations and other mouse pathogens. Cells were trypsinized and strained through 70 μm strainer to generate single cell suspensions. They were then administered sub-cutaneously to mice (105 cells to each mouse in 100 μL PBS). The tumor size was measured every two days with a digital caliper, and tumor volume was determined with the formula V=0.5W2L (V=tumor volume, W=tumor width, L=tumor length). Mice with tumor volume greater than 2000 mm3 or with any dimension exceeding 2 cm were euthanized for humane purposes. For recombinant anti-PD1 (RMP1-14, Bio X Cell) administration in melanoma therapeutic treatment model, 200 μg of antibody was injected intraperitoneally in 100 u L PBS to each mouse weekly. For mechanistic study to determine the role of CD8+ T-cells in mediating in vivo control of tumor growth (
i. Production of Recombinant Protein eOD-GT8-60Mer, HA(NC99)-60Mer, LS_Trp2188-60Mer and LS_Gp10025-60Mer
Expi293F cells (Invitrogen) were transfected with pVAX plasmid vector encoding the eOD-GT8-60mer, HA(NC99)-60mer, LS_Trp2188-60mer or LS_Gp10025-60mer with PEI (Sigma Aldrich)/OPTI-MEM (Invitrogen) and harvested 6 days post-transfection. Transfection supernatant was first purified with affinity chromatography using the AKTA pure 25 system and gravity flow columns filled with GNL Lectin beads (GE Healthcare). The eluate fractions from the affinity purification were pooled, concentrated and dialyzed into 1×PBS buffer before being loaded onto the SEC column and then purified with size exclusion chromatography using the Superose 6 Increase 10/300 GL column. (GE healthcare) Identified eluate fractions were then collected and concentrated to 1 mg/mL in PBS as previously described (81).
ii. ELISA—GT8-Binding ELISA
96-well half area plates (Corning) were coated at room temperature for 8 hours with 1 μg/mL MonoRab anti-His antibody (GenScript), followed by overnight blocking with blocking buffer containing 1×PBS, 5% skim milk, 10% goat serum, 1% BSA, 1% FBS, and 0.2% Tween-20. The plates were then incubated with 2 μg/mL of his-tagged GT8-monomer at room temperature for 2 hours, followed by addition of mice sera serially diluted with PBS with 1% FBS and 0.1% Tween and incubation at 37° C. for 2 hours. The plates were incubated at room temperature for 1 hour with anti-mouse IgG H+L HRP (Bethyl) at 1:20,000 dilution, followed by addition of TMB substrates (ThermoFisher) and then quenched with 1M H2SO4. Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader. Endpoint titer is defined as the highest dilution at which the OD of the post-immune sera exceeds the cut-off (mean OD of naïve animals plus standard deviations of the OD in the naïve sera multiplied with standard deviation multiplier f at the 99% confidence level).
iii. ELISA—HA-Binding ELISA
96-well half area plates were coated at 4° C. overnight with 2 μg/mL of recombinant HA(ΔTM)(H1N1/A/New Caledonia/20/1999) (Immune Technology), and blocked at room temperature for 2 hour with the buffer as described above. The plates were subsequently incubated with serially diluted mouse sera at 37° C. for 2 hours, followed by 1-hour incubation with anti-mouse IgG H+L HRP (Bethyl) at 1:20,000 dilution at room temperature and developed with TMB substrate. Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader.
iv. Antigenic Profile Characterization of Designed GT8, Tpr2 and Gp100-Nano-Vaccines
Corning half-area 96-well plates were coated with 2 μg/mL of GT8-monomer, COD-GT8-60mer, Trp2-60mer and Gp100-60mer at 4° ° C. overnight. The plates were then blocked with the buffer as described in the GT8-binding ELISA section for 2 hours at room temperature, followed by incubation with serially diluted VRC01 at room temperature for 2 hours. The plates were then incubated with anti-human Fc (cross-adsorbed against rabbits and mice) (Jackson Immunoresearch) at 1:10,000 dilution for 1 hour, followed by addition of TMB substrate for detection. Absorbance at 450 nm and 570 nm were recorded with BioTEK plate reader.
v. HAI Assay
Mice sera were treated with receptor-destroying enzyme (RDE, 1:3 ratio; SEIKEN) at 37° ° C. overnight for 18-20 hours followed by complement and enzyme inactivation at 56° C. for 45 minutes. RDE-treated sera were subsequently cross-adsorbed with 10% rooster red blood cells (Lampire Biologicals) in PBS at 4° C. for 1 hour. The cross-adsorbed sera were then serially diluted with PBS in a 96-well V-bottom microtiter plates (Corning). Four hemagglutinating doses (HAD) of A/New Caledonia/20/99 (BEI) were added to each well and the serum-virus mixture was incubated at room temperature for 1 hour. The mixture was then incubated with 50 μl 0.5% v/v rooster red blood cells in 0.9% saline for 30 minutes at room temperature. The HAI antibody titer was scored with the dot method, and the reciprocal of the highest dilution that did not cause agglutination of the rooster red blood cells was recorded.
vi. ELISpot Assay
Spleens from immunized mice were collected and homogenized into single cell suspension with a tissue stomacher in 10% FBS/1% Penicillin-streptomycin in RPMI 1640. Red blood cells were subsequently lysed with ACK lysing buffer (ThermoFisher) and percentage of viable cells were determined with Trypan Blue exclusion using Vi-CELL XR (Beckman Coulter). 200,000 cells were then plated in each well in the mouse IFNγ ELISpot plates (MabTech), followed by addition of peptide pools that span both the lumazine synthase, GT8 or HA domains, or individual Trp2 (SVYDFFVWL) and Gp10025 peptide (EGPRNQDWL) at 5 μg/mL of final concentration for each peptide (GenScript). The cells were then stimulated at 37° C. for 16-18 hours, followed by development according to the manufacturer's instructions. Spots for each well were then imaged and counted with ImmunoSpot Macro Analyzer.
vii. Intracellular Cytokine Staining
Single cell suspension from spleens of immunized animals were prepared as described before and stimulated with 5 μg/mL of peptides (GenScript) for 5 hours at 37° C. in the presence of 1:500 protein transport inhibitor (ThermoFisher) and anti-mouse CD107a-FITC(ThermoFisher). The cells were then incubated with live/dead for 10 minutes at room temperature, surface stains (anti-mouse CD4 BV510, anti-mouse CD8 APC-Cy7) (BD-Biosciences) at room temperature for 30 minutes. The cells were then fixed and permeabilized according to manufacturer's instructions for BD Cytoperm Cytofix kit and stained with intracellular stains anti-mouse IL-2 PE-Cy7, anti-mouse IFN-γ APC, anti-mouse CD3c PE-Cy5 and anti-mouse TNFα BV605 (BioLegend) at 4° C. for 1 hour. The cells were subsequently analyzed with LSR II 18-color flow cytometer.
viii. Immunofluorescence
To detect presence of cleaved caspase-3 using immunofluorescence, four days after C57BL/6 mice were intramuscularly immunized with DLnano_LS_GT8 or protein COD-GT8-60mer, tibialis anterior muscles of the mice were harvested and preserved in 4% PFA/PBS for 4 hours at room temperature and then stored overnight in 70% EtOH/H2O at 4° C. The tissues were then serially dehydrated for paraffin embedding, and blocked in 3% BSA/PBS for 1 hour at room temperature, permeabilized with 0.5% Triton X-100/PBS, followed by overnight staining with rabbit anti-cleaved caspase 3 (1:200, Cell Signaling). The sections were then washed and stained with anti-Rabbit Alexa Fluor 594 antibody (1:200, Invitrogen) for 1 hour at room temperature, then counterstained with 0.5 μg/mL DAPI and imaged with Leica SP5 confocal microscopes.
ix. Serum CK and LDH Assay
Mouse serum CK and LDH enzymatic activity was measured 0, 1, 4, 7 and 10 days following intramuscular administrations of 25 μg DLnano_LS_GT8 or 10 μg RIBI-adjuvanted protein eOD-GT8-60mer or from untreated control mice using colorimetric assays according to manufacturer's protocol (Abcam Ab 155901 and Ab 65393). Changes in absorbance at 450 nm was measured at 37° C. under kinetics mode over time using the BioTEK plate reader.
x. TUNEL Assay
TUNEL assay was performed on fixed muscle specimen according to manufacturer's protocol (Abcam). Briefly, four days post treatments with DNA or protein vaccine, tibialis anterior muscles were harvested and fixed in 4% paraformaldehyde/PBS for 3 hours at 4° C. The tissues were then dehydrated and paraffin-embedded, the sample sections were then rehydrated by serial transfer of the tissues from 100% Ethanol to 70% Ethanol/water. The specimen was then permeabilized by treatment with Proteinase K at room temperature for 20 minutes. Endogenous peroxidase was then quenched by treatment of tissue sections with 3% H2O2 in methanol. The sections were then incubated with TdT enzyme in the equilibration buffer at room temperature for 1.5 hours in a humidified chamber, and the reactions were stopped with the stop solution provided in the kit. The sections were then blocked with provided blocking buffer at room temperature for 10 minutes and labelled with provided detection conjugate diluted 1:25 in blocking buffer at room temperature for 30 minutes. The sections were then developed with DAB substrate at room temperature for 15 minutes and then counter stained with methyl green before they were imaged with Nikon Eclipse 80i under 20× and 60× magnification.
xi. Flow Analyses of Muscle Tissues Post DNA or Protein Vaccination
Following intramuscular protein or DNA vaccinations in C57BL/6 mice, at each specified timepoint, transfected muscles were harvested. Cells were extracted from muscles through 30 minutes incubation digestion buffer-Hanks' Balanced Salt Solution [Gibco], supplemented with 0.5% collagenase (Life Technologies), 0.2% BSA, and 0.025% trypsin at 37° C. The cells were then stained with Ultra-Violet reactive (Live/Dead dye, 1:333 in PBS), and then with 1:200 dilution of anti-CD11b-PerCPCy5.5, anti-CD11c-PE, anti-MHC_Class II APC_Cy7, anti-F4/80_PE Cy 7 and anti-CD206-APC (Biolegend) in 2% FBS/PBS at room temperature for 1 hour before they were permeabilized with BD CytoPerm/CytoFix for 20 minutes at 4° C. and subsequently labelled with FITC-lightning link labelled VRC01 (Expedon) at 4° C. for 1 hour. The cells were then resuspended in 1× BD Permeabilization Wash buffer for analyses on LSR II 18-color flow cytometer.
xii. Negative Stain EM of Purified Nanoparticles
The nanoparticles were produced in Expi293 cells, purified using Agarose bound lectin beads (Agarose Galanthus Nivalis Lectin, Vector Laboratories) followed by size exclusion chromatography (GE Healthcare) using the Superose 6 Increase 10/300 GL column. The proteins were further dialyzed into Tris-buffered saline (TBS). A total of 3 μL of purified proteins was adsorbed onto glow discharged carbon-coated Cu400 EM grids. The grids were then stained with 3 μL of 2% uranyl acetate, blotted, and stained again with 3 μL of the stain followed by a final blot. Image collection and data processing was performed on a FEI Tecnai T12 microscope equipped with a Oneview Gatan camera at 90,450× magnification at the camera and a pixel size of 1.66 Å.
xiii. In Vivo Imaging
For B16-F10-Luc2 challenge study, tumor challenged mice received 150 mg/kg administration of VivoGlo™ Luciferin (Promega) at each timepoint formulated in sterile PBS, and then imaged with IVIS Spectrum CT for Bioluminescence with the auto-exposure settings (or for 60s, whichever is shorter) 10 minutes post injection.
xiv. Statistics
Power analysis was performed with R based on our preliminary data to determine the smallest sample size that would allow us to achieve a power of 0.9 with a pre-set a-value of 0.05. All statistical analyses were performed with PRISM V8.2.1 and R V3.5.1. Each individual data point was sampled independently. Two-tailed Mann Whitney Rank Tests were used to compare differences between groups. Log Rank test was used to compare survival between two groups in challenge survival studies. Bonferroni corrections were used to adjust for multiple comparisons.
i. DNA-Launched but not Recombinant Protein Nanoparticle Vaccines Induced CD8+ T-Cell Responses to HIV and Influenza Antigens
First, we compared adaptive immune responses induced by DNA vaccination and protein vaccination adjuvanted by Sigma Adjuvant System (or RIBI). We utilized two model antigens: a priming HIV antigen eOD-GT8-60mer and an influenza hemagglutinin (H1 A/NewCaledonia/20/1999) 60mer antigen scaffolded by lumazine synthase [86, 87]. DNA-Launched nanoparticle Lumazine Synthase decorated with an anti-HIV-1 immunogen eOD-GT8 (DLnano_LS_GT8,
We determined if the observation could be replicated when an alternative nanoparticle-scaffolded influenza antigen was evaluated. Indeed, two vaccinations of DLnano_LS_HA(NC99) and RIBI-adjuvanted protein HA(NC99)_60 mer induced similar binding antibody titers to recombinant NC99 hemagglutinin (
ii. Induction of Tissue Apoptosis and APC Infiltration by DNA-Launched Nanoparticle Vaccines were Important for CD8+ T-Cell Priming
We hypothesized distinct modality of antigen uptake and presentation for DNA-launched nanoparticle vaccine as compared to protein nanoparticle vaccine may attribute to unique induction of CTL responses by DLnano-vaccines. Previous studies observed that co-administration of DNA-vaccines with DNA-cassettes encoding pro-apoptotic genes led to significantly improved induced CTL responses [90]. We, therefore, hypothesized that DNA/EP vaccinations could create a pro-inflammatory environment at the site of transfection through the induction of tissue apoptosis, thereby promoting infiltration of APCs and antigen uptake from apoptotic myocytes expressing DNA-cassette encoded antigens.
We first assessed the extent of muscle tissue damage upon vaccine administration with an immunofluorescence assay to stain for cleaved caspase 3, which would be present in cellular cytosol following apoptotic signaling events [91]. In C57BL/6 mice, four days post injection (d.p.i), hypercellularity and expression of cleaved caspase 3 were only observed in the muscles of mice immunized with DLnano_LS_GT8 combined with EP but not in those vaccinated with protein eOD-GT8-60mer co-formulated in RIBI without EP or in naïve mice (
We performed a time course experiment and observed that DLnano_LS_GT8 induced tissue apoptosis was transient, peaking at 6 d.p.i and was fully resolved by 14 d.p.i (
We next examined the consequences of induced tissue apoptosis in terms of tissue APC infiltration. Indeed, seven d.p.i, we observed increased influx of CD11b+F4/80+ macrophages into muscles of mice treated with DLnano_LS_GT8 and EP compared to protein eOD-GT8-60mer formulated in RIBI without EP (
To determine the functional roles played by macrophages in priming of CD8+ T-cell responses by DNA-launched nanoparticle vaccines, we systemically depleted the macrophage populations in C57BL/6 mice prior to DNA vaccinations. Depletion was carried out through intravenous (IV) injection of clodrosome, which specifically depleted phagocytic macrophages [93]. Single IV infusion of clodrosome specifically depleted CD11b+F4/80+ macrophages but not CD11c+MHC Class II+ DCs in the spleens of animals one d.p.i (
iii. DNA-Launched Nanoparticle Vaccines Scaffolding Trp2188 and Gp10025 Peptides Mediated Protection Against Melanoma Challenge in Mice
To demonstrate the functional relevance of CD8+ T-cell priming by DNA-launched nanoparticle vaccines in the treatment of cancer, we designed novel nanoparticle vaccines displaying immunodominant CD8+ T-cell epitopes. The self-assembling nanoparticles were engineered using a structure-guided process. In our preliminary experiments, Lumazine Synthase on its own does not express well in mammalian cell lines and we hypothesized that it could not be used on its own to scaffold anti-tumor peptide antigens. We engineered a new version of DLnano_LS_GT8 capable of displaying peptide antigens. In this construction, the heavily glycosylated GT8 domain facilitates solubilization and secretion of designed nanoparticles and could potentially be replaced by other heavily glycosylated domains. To ensure epitope accessibility and homogenous nanoparticle assembly, N-linked glycans in proximity to the C-terminus of GT8 were removed by mutations in the PNGS sequence; additionally, a 15 amino acid linker was also incorporated to the C-terminus of GT8 upstream of the scaffolded anti-tumor peptide(s). We designed nanoparticles presenting 60 copies of Trp2188 peptide (DLnano_LS_Trp2188) and Gp10025 peptide (DLnano_LS_Gp10025). Homogenous in vitro assemblies of DLnano_LS_Trp2188 and DLnano_LS_Gp10025 were observed by Size Exclusion Chromatography, SEC, (
We next compared CTL responses induced by DLnano-vaccines to CpG adjuvanted peptide vaccines head-to-head. We observed that both DLnano_LS_Trp2188 and CpG adjuvanted Trp2188 peptide vaccination induced peptide-specific CD8+ T-cell responses, though responses induced by DLnano_LS_Trp2188 vaccination were significantly higher (
We next compared induction of CD8+ T-cell responses to Trp2 (SVYDFFVWL) and Gp100 (EGPRNQDWL) epitopes in B16-F10 melanoma bearing mice, which received cither control PBS treatment or protein versus DNA vaccinations of nanoparticles scaffolding 60 copies of Trp2 and Gp100 peptides. Anti-PD1 treatments were administered to three groups of mice (Groups 2-4) in the study three days post tumor inoculation and weekly thereafter (
CD8+ T-cells can play an extremely important role in surveillance against intracellular pathogens and tumors. In the cancer space, presence of tumor infiltrating CD8+ T-cell is correlated with improved prognosis in cancer patients [100, 101]. Induction of CD8+ T-cell responses also corresponds to improved tumor control and survival in various preclinical animal studies [102]. Such observations have led to the use of T-cell based therapies, such as DC vaccines or in vitro expansion and adoptive transfer of tumor infiltrating lymphocytes (TIL), in cancer patients, achieving varying degrees of success [103, 104]. Alternatively, several reports also describe the anti-tumor activity of antigen-specific CD4 T-cells. TH1 cells, for instance, are responsible for immune responses against tumors by either enhancing CD8 T-cell response or activating macrophages to phagocytose cancerous cells [105]. CD4 CTL is another sub-set of CD4 T cells that have acquired cytolytic activity and demonstrated clear anti-tumor activity. Transfer of these tumor-reactive CD4 CTL cells into lymphopenic hosts, followed by tumor irradiation and anti-CTLA-4 antibody treatment, results in T-cell expansion and the expression of IFN-g and granzyme-B, as well as regression of established tumors [106]. Our work in this paper mainly focuses on designing DNA-launched nanoparticle vaccines scaffolding CD8+ T-cell epitopes, but nano-vaccines scaffolding CD4+ T-cell epitopes should also be closely examined in future work.
Induction of CTL responses by vaccination can be challenging and not readily achieved by vaccination with protein or inactivated virus. For example, the most advanced malaria vaccines under development, RTS,S, which contains repeat and T-cell epitopes of CircumSporozoite Protein fused to hepatitis B surface antigen to form protein particles, could induce antibody but not CD8+ T-cell response to the vaccine antigens [107].
DNA vaccines have been shown to elicit CD8+ T-cell responses both in preclinical animal models and in clinical trials [78, 84]. Prior mechanistic studies highlighted plausible contributions by direct transfection of DCs and macrophages with DNA cassettes [79]. Additionally, cross presentation of DNA-cassettes encoded antigens was also believed to be important for priming CTL through more indirect evidence [80]. In this work, we observed DNA/EP mediated tissue apoptosis to trigger macrophage infiltration and uptake of antigen expressed by and associated with the host cells, which may subsequently transfer sequestered peptides to cDCs for priming of CD8+ T cells. It should be emphasized that while macrophages were found to be essential to the induction of CD8+ T-cell responses induced by DLnano-vaccines, the clodrosome treatments described in this manuscript systemically depleted macrophages, including—but were not limited to—the electroporation-induced muscle-infiltrating macrophages. Future study to further characterize the biology of these muscle-infiltrating macrophages, such as through the use of single-cell transcriptomics, is likely important, as the insights may be harnessed to promote the induction of more robust anti-tumor CD8+ T-cell immunity by DLnano- and other types of cancer vaccines. Induced tissue apoptosis was observed to be transient and local, as we would expect given strong safety profile of DNA vaccines in clinic [78].
We also demonstrated the importance of CD8+ T-cell priming by DNA-launched nanoparticle vaccines in a melanoma challenge model. We designed a novel and generalizable nanoparticle platform for displaying CD8+ T cell epitopes to various tumor antigens. Several mutations were introduced near the C-terminus of the eOD-GT8-60mer scaffolding domain to knock out the glycosylation sites to reduce steric hinderance, allowing for more efficient display of CTL epitopes at the C-terminus and homogeneous assembly of the designed nano-vaccines into 60-mer. As a proof-of-principle, we engineered two nanoparticle vaccines scaffolding 60 copies of CD8+ epitopes from Trp2 and Gp100. DNA-cassettes encoding anti-melanoma LS-nanoparticles scaffolding Trp2 and Gp100 epitopes could elicit significantly improved CTL responses to both targets as compared to conventional monomeric DNA vaccines or CpG adjuvanted peptide vaccines. DNA but not protein vaccinations of Trp2188 and Gp10025 60mer elicited CTL responses in mice, suppressed tumor growth and prolonged overall survival in the therapeutic tumor challenge model, and conferred 80% protection when the vaccines were prophylactically administered. The work provided a demonstration that robust CTL responses can be generated with great simplicity by harnessing physical injury to create a pro-inflammatory environment that favored APC infiltration, antigen uptake and cross-presentation. Induced CTL responses can be directed to whole antigens, such as to GT8 or to influenza (
The sequences used in this Example or the ones that can be used in the method described herein are provided in Table X below.
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
EGPRNQDWL
(SEQ ID NO: 112)
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
SVYDFFVWL
(SEQ ID NO: 114)
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
RAHYNMQDIFIEDF
(SEQ ID NO: 116)
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
TGRAMLGTHTMEVTVYH
GGIMD
Q
VPFSVGG
EGPRNQDWL
(SEQ ID NO: 118)
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
KYICNSSCM
(SEQ ID NO: 120)
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
TGRAMLGTHTMEVTVYH
(SEQ ID NO: 122)
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
IMDQVPFSV
(SEQ ID NO: 124)
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
SLLMWITQC
(SEQ ID NO: 126)
MDWTWILFLVAAATRVHS
MQIYEGKLTAEGLRFGIVASRANHALVDRLVEGAIDAIVRH
GGREEDITLVRVCGSWEIPVAAGELARKEDIDAVIAIGVLCRGATPSFDYIASEVSKGLADLS
LELRKPITFGVITADTLEQAIEAAGTCHGNKGWEAALCAIEMANLFKSLRGGSGGSGGSG
GSGGGDTITLPCRPAPPPHCSSNITGLILTRQGGYSNDNTVIFRPSGGDWRDIARCQIAGTV
VSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLNTSVEINCTGAGHCNISRAKWDNTLKQI
ASKLREQYGNKTIIFKPSSGGDPEFVNHSFNCGGEFFYCDSTQLFDSTWFDST
GGSGSGG
GS
LEFYLAMPFATPMEAEL
(SEQ ID NO: 128)
Optimal CTL activity may require the antigen be robustly presented on APCs, one molecular adjuvant employed in cancer vaccine models involved in DC activation is CD40 ligand (CD40L). It is possible that molecular adjuvant, such as CD40L, could also be synergistic with anti-PD1 antibodies. We thus examined whether CD40L can be formulated as a nanoparticle since simple genetic fusions do not work. The next generation designs were used to form nanoparticles. We then examined whether CD40L nanoparticles can express in vivo and if so, whether CD40L nanoparticles can function as an adjuvant in vivo.
We first designed three constructs by formulating CD40L as a trimer or 60mers. These three constructs encode the following proteins.
CEEMRRQFEDLVKDITLNKEEKKENSFEMQRGDEDPQIAAHVVSEANSN
AASVLQWAKKGYYTMKSNLVMLENGKQLTVKREGLYYVYTQVTFCSNRE
PSSQRPFIVGLWLKPSSGSERILLKAANTHSSSQLCEQQSVHLGGVFEL
QAGASVFVNVTEASQVIHRVGESSFGLLKL
As shown in
We then examined whether modification to CD40L can facilitate the nanoparticle's expression and assembly. We found that a structural design of 3 new glycans to CD40L (
KSNLVMLENGSQLTVNRSGLYYVYTQVTFCSNREPSSQRPFIVGLWLKP
SSGSERILLKAANTHSSSQLCEQQSVHLGGVFELQAGASVFVNVTEASQ
VIHRVGFSSFGLLKLG**
Other constructs involved in the development of this work include constructs encoding the following polypeptides:
GGSGGSGGG
GELKAIAQELKAIAKECKAIAYELKAIAQGAG
GGSGGSGGSGGS
GGGDKVEEEVNLHEDFVFIKKLKRCNKGEGSLSLLNCEEMRRQFEDLVKDITLN
GGHHHHHH**
GSGGSGGSGGSGGG
MKVKqLADAVEELASANYHLANAVARLAKAVGER
GGS
GIAAHVVSEANSNAASVLQWAKKGYYTMKSNLVMLENGKQLTVKREGLYYVY
We next examined whether it is possible to formulate CD40L nanoparticle with anti-PD1 antibodies. To this end, we created a plasmid DNA that encodes the engineered CD40L and a PD1 scFv-CD40L fusion protein. The PD1 scFv used in this experiment contains the following sequences:
This fusion protein (CD40L-(Gly3Ser1)4linker-pembroPD1-VH-Linker(C4S1)3-PembroPD1-VL-Hig Tag) has the following sequence (CD40L: underlined; pembroPD1-VH: italic and underlined; linker: bold; PembroPD1-VL: bold and underlined; self-assembling polypeptide: italic):
KSNLVMLENGSQLTVNRSGLYYVYTQVTFCSNREPSSQRPFIVGLWLKP
SSGSERILLKAANTHSSSQLCEQQSVHLGGVFELQAGASVFVNVTEASQ
VIHRVGFSSFGLLKLG
GGGSGGGSGGGSGGGS
QVQLVQSGVEVKKPGAS
VKVSCKASGYTFTNYYMYWVRQAPGQGLEWMGGINPSNGGTNFNEKFKN
RVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTT
VTVSS
GGGGSGGGGSGGGGS
EIVLTQSPATLSLSPGERATLSCRASKGV
STSGYSYLHWYQQKPGQAPRLLIYLASYLESGVPARFSGSGSGTDFTLT
ISSLEPEDFAVYYCQHSRDLPLTFGGGTKVEIKR
.
A schematic of the resulted CD40L/anti-PD1 combo nanoparticle is shown in
Other constructs involved in the development of this work include CD40L-Tri cloning and CD40L-Tri cloning.
The CD40L-Tri coding sequence is composed of an optimized IL-2 signal (MRRMQLLLLIALSLALVTNS), an octahistidine, a trimeric leucine zipper GCN4pII heptad repeat derived from the wildtype dimeric GCN4 repeat found in Saccharomyces cerevisiae (GDRMKQIEDKIEEILSKIYHIENEIARIKKLIGER), a flexible 17 amino acid linker (TSGGSGGTGGSGGTGGS), and the extracellular domain of human CD40L (amino acids 51-261). The coding sequence was codon-optimized for CHO cell expression and synthesized by Genscript (Piscataway, NJ). The calculated molecular weight after signal cleavage is 30,093 daltons with a pI of 7.63. There is one predicted N-glycosylation site, which is expected to increase the molecular weight to the observed 35 kDa. The amino acid sequence of the resulted protein has the following sequence (IL-2 signal: bold and underlined; trimeric leucine zipper GCN4pII heptad repeat: italic; linker: bold; CD41L: underlined):
The mCD40L-Tri-PD-1ScFv cloning resulted in a construct encoding the following amino acid sequence (IL-2 signal: bold and underlined; trimeric leucine zipper GCN4pII heptad repeat: italic; linker: bold; CD41L: underlined; pembroPD1-VH: italic and underlined; linker: bold; PembroPD1-VL: bold and underlined; His tag: bold, italic and underlined):
MRRMQLLLLIALSLALVTNS
GDRMKQIEDKIEEILSKIYHIENEIARIK
KLIGER
TSGGSGGTGGSGGTGGSDKVEEEVNLHEDFVFIKKLKRCNKGE
GGGS
EVQLQESGPGLVKPSQSLSLTCSVTGYSITSSYRWNWIRKFPGNR
LEWMGYINSAGISNYNPSLKRRISITRDTSKNQFFLQVNSVTTEDAATY
YCARSDNMGTTPFTYWGQGTLVTVSS
GGGGSGGGGSGGGGSDIVMTQGT
LPNPVPSGESVSITCRSSKSLLYSDGKTYLNWYLQRPGQSPQLLIYWMS
TRASGVSDRFSGSGSGTDFTLKISGVEAEDVGIYYCQQGLEFPTFGGGT
KLELK
HHHHHH
This application claims priority to U.S. Provisional Application No. 62/982,038, filed Feb. 26, 2020, and U.S. Provisional Application No. 63/047,245, filed Jul. 1, 2020, the entire contents of each of the aforementioned applications are incorporated by reference herein in its entirety.
The present disclosure was made with government support under NIH IPCAVD Grant U19 A1109646-04, NIH CIVICS Grant 4270101374, NIH Grant R01GM103899 and NIH Grant R01GM129357 awarded by the National Institutes of Health. The government has certain rights in the disclosed inventions.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US21/20105 | 2/26/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 62982038 | Feb 2020 | US | |
| 63047245 | Jul 2020 | US |
