WO2023154821A2

WO2023154821A2 - Compositions comprising influenza hemagglutinin stem and method for enhancing cross-protective immunity

Info

Publication number: WO2023154821A2
Application number: PCT/US2023/062320
Authority: WO
Inventors: Jesse Erasmus
Original assignee: University Of Washington
Priority date: 2022-02-11
Filing date: 2023-02-09
Publication date: 2023-08-17
Also published as: WO2023154821A3

Abstract

Improved influenza hemagglutinin (HA) antigens that include a stem (HA2) domain and a transmembrane domain to tether the antigen to a cell membrane for improved immunogenicity with vaccination. In embodiments, the tethered, miniature HA antigens include amino acid residue substitutions, additions, and/or deletions for stabler trimerization at the cell membrane and do not include all or part of the HA2 head subdomain. In embodiments, the improved antigens facilitate production of cross-reactive antibodies against the stem domain. In embodiments, the antigens are encoded by RNA of an RNA vaccine and administered to individuals for broad immunogenicity against influenza viruses.

Description

COMPOSITIONS COMPRISING INFLUENZA HEMAGGLUTININ STEM AND METHOD FOR ENHANCING CROSS-PROTECTIVE IMMUNITY

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Patent Application No. 63/309,282, filed February 11, 2022, the contents of which are hereby incorporated by reference in their entirety for all purposes.

STATEMENT REGARDING SEQUENCE LISTING

The sequence listing associated with this application is provided in .xml format in lieu of a paper copy and is hereby incorporated by reference into the specification. The name of the .xml file containing the sequence listing is 3915-P1238WO-UW_Sequence- Listing_ST-26.xml. The file is 45 KB; was created on February 08, 2023; and is being submitted via Patent Center with the filing of the specification.

STATEMENT OF GOVERNMENT LICENSE RIGHTS

This invention was made with Government support under Grant No. 27220140006C, awarded by National Institute of Allergy and Infectious Diseases. The Government has certain rights in the invention.

BACKGROUND

Influenza viruses are pervasive and contribute to a significant healthcare burden globally, and broad-spectrum immunity against influenza viruses is a desirable goal for limiting spread and severity of disease. In addition, influenza viruses mutate frequently, and they have the potential to cause a global pandemic. Despite the risk these viruses pose to public health, progress with the development of vaccines that provide long-lasting broad-spectrum immunity has been limited.

Influenza viruses are enveloped animal viruses that are comprised of an internal ribonucleoprotein core containing a single-stranded RNA genome, and an outer lipoprotein envelope lined inside by a matrix protein. The segmented genome of influenza A and B viruses is comprised of eight molecules (seven for influenza C virus) of linear, negative polarity, single-stranded RNAs. These encode several polypeptides, including: the RNA-directed RNA polymerase proteins (PB2, PB1, and PA) and nucleoprotein (NP), which form the nucleocapsid; the matrix proteins (Ml, M2); two surface glycoproteins: hemagglutinin (HA) and neuraminidase (NA); and nonstructural proteins (NS1 and NS2). Transcription and replication of the genome occurs in the nucleus and assembly occurs at the plasma membrane.

Hemagglutinin is the major envelope glycoprotein of influenza A and B viruses. Influenza A and B virus HA proteins have an almost identical structure but have divergent sequences. The stem (HA2) domain of HA is one of the most conserved regions in HA, and HA stem-specific antibodies can confer broadly specific protection, mainly through Fc-mediated activities (e.g., complement fixation, macrophage activation, ADCC, etc.). In addition, neutralizing antibodies (nAbs) that target the stem require Fc activities for neutralization.

Ribonucleic acid (RNA) vaccines utilize RNA, e.g., messenger RNA (mRNA) to safely direct the body’s cellular machinery to produce a protein of interest, such as native proteins, antibodies, and other proteins that can have therapeutic activity inside and outside of cells. An RNA (e.g., mRNA) vaccine can be used to induce a balanced immune response against an antigen of interest, e.g., an antigen of a virus.

Despite previous progress with development of vaccines for influenza, the virus mutates and frequently undergoes antigenic drift. Existing vaccines, including seasonal influenza vaccines, have limited efficacy due to the high variability of the virus. This is due in large part to variation in the head subdomain of the HA2 domain of HA. As a result, administration of an existing vaccine provides only limited immunogenicity against multiple virus types and multiple phylogenetic groups, and very limited longitudinal immunogenicity against influenza viruses in general due to antigenic drift. While an RNA vaccine platform may be thought to have potential for improved influenza vaccination, success with such an approach would require improved antigens configured for generating broad-spectrum immunogenicity against multiple virus types and multiple phylogenetic groups that persists longitudinally despite continued antigenic drift.

Accordingly, there is a significant need for improved influenza antigens for use with RNA (e.g., mRNA) vaccine platforms for broadly protective immunogenicity against influenza viruses. The present disclosure addresses this and other unmet needs. SUMMARY

This summary is provided to introduce a selection of concepts in a simplified form that are further described below in the Detailed Description. This summary is not intended to identify key features of the claimed subject matter, nor is it intended to be used as an aid in determining the scope of the claimed subject matter.

In one aspect, the disclosure provides a hemagglutinin (HA) polypeptide, comprising a stem (HA2) domain and a transmembrane domain, and an amino acid substitution, an amino acid addition, and/or an amino acid deletion, relative to a natural HA polypeptide (e.g., a wild-type (WT) HA polypeptide) for improved trimerization and/or immunogenicity of the synthetic HA polypeptide. The transmembrane domain enables the synthetic HA polypeptide to be anchored to the cell membrane for improved immunogenicity against the stem domain, and the amino acid substitution, the amino acid addition, and/or the amino acid deletion enable the synthetic HA polypeptide to more stably trimerize at the cell membrane.

In embodiments, the synthetic HA polypeptide does not include a full-length HA1 head subdomain or does not include a portion of an HA1 head subdomain. Since the HA1 head subdomain undergoes frequent mutation and antigenic drift, omitting the HA1 head subdomain, or a portion thereof, reduces or eliminate immunogenicity generated against this subdomain during vaccination. This helps increase immunogenicity generated against the stem (HA2) domain of HA, which due to its relative conservation, allows for broadspectrum immunity against multiple influenza virus types and multiple influenza phylogenetic groups.

In various aspects, a hemagglutinin (HA) polypeptide is encoded by a nucleic acid of a nucleic acid vaccine. In embodiments, a synthetic HA polypeptide is encoded by an RNA (e.g., mRNA) of an RNA vaccine (e.g., mRNA vaccine). RNA vaccine compositions comprising RNA encoding HA antigens of the disclosure are disclosed, as well as methods of vaccinating against influenza that comprise administering an RNA vaccine composition of the disclosure to an individual.

Other aspects of the disclosure include a nucleic acid encoding the synthetic HA polypeptide, a nucleic acid expression vector that comprises the nucleic acid, and a recombinant host cell that comprises the nucleic acid expression vector. Pharmaceutical compositions that comprise the synthetic HA polypeptide, the nucleic acid, the nucleic acid expression vector, and/or the recombinant host cell, and a pharmaceutically acceptable carrier, are also provided.

DESCRIPTION OF THE DRAWINGS

The foregoing aspects and many of the attendant advantages of the disclosed subject matter will become more readily appreciated as the same become better understood by reference to the following detailed description, when taken in conjunction with the accompanying drawings.

FIG. 1 shows an illustration of example influenza structures (nucleoprotein; NP, influenza virus) and influenza HA antigens as a full length hemagglutinin (FL HA or FL HA_teth), a secreted miniature HA (miniHAsec), and a tethered miniature HA (miniHAteth) of the present disclosure (top). The influenza synthetic HA polypeptide antigens is encoded by Venezuelan equine encephalitis virus (VEEV)-strain TC83 replicating RNA (repRNA) vaccines (bottom).

FIG. 2A shows binding antibody responses against homologous (Hl Brisbane) hemagglutinin (HA) protein in mice primed on day 0 and boosted on day 28 (dotted line) with full length HA (FL HA_teth), secreted HA stem (miniHAsec), or tethered HA stem (miniHAteth) encoded in repRNA.

FIG. 2B shows binding antibody responses against heterologous (Hl California) hemagglutinin (HA) protein in mice primed on day 0 and boosted on day 28 (dotted line) with full length HA (FL HA_teth), secreted HA stem (miniHAsec), or tethered HA stem (miniHAteth) encoded in repRNA.

FIG. 3A shows results from ELISA showing antibody responses against Hl HA (left) and H5 HA (right) at four weeks after a boost immunization with repRNA encoding full-length HA (FL), miniHAsec, or miniHAteth, while rHA-primed animals were boosted with another dose of adjuvanted rHA. Prior to the boost immunization, mice were immunized with a homologous FL HA derived from H1N1 A/Brisbane/59/2007.

FIG. 3B shows results from Hl HA ELISPOT showing immune cell responses against Hl HA at four weeks after a boost immunization with repRNA encoding full- length HA (FL), miniHAsec, or miniHAteth, while rHA-primed animals were boosted with another dose of adjuvanted rHA. Prior to the boost immunization, mice were immunized with a homologous FL HA derived from H1N1 A/Brisbane/59/2007. FIG. 4A shows results evaluating cross-protective efficacy against a stringent H5N1 A/Vietnam/1204/2004-PR8 recombinant virus challenge in mice via the intranasal route. Percent weight loss results demonstrate immunogenicity and efficacy against H5N1 challenge of booster repRNAs encoding FL in mice pre-immune to homologous full-length HA. Individual data lines correspond to results obtained from individual mice.

FIG. 4B shows percent weight loss results demonstrating immunogenicity and efficacy against H5N1 challenge of booster repRNAs encoding miniHAteth in mice pre- immune to homologous full-length HA. Individual data lines correspond to results obtained from individual mice.

FIG. 4C shows percent weight loss results demonstrating immunogenicity and efficacy against H5N1 challenge of booster repRNAs encoding miniHAsec in mice pre- immune to homologous full-length HA. Individual data lines correspond to results obtained from individual mice.

FIG. 4D shows percent weight loss results demonstrating immunogenicity and efficacy against H5N1 challenge of booster repRNAs encoding a strain-matched rehydrogel-adjuvanted recombinant HA (rHA) in mice pre-immune to homologous full- length HA. Individual data lines correspond to results obtained from individual mice.

FIG. 4E shows percent weight loss results for a mock group after a stringent H5N1 A/Vietnam/1204/2004-PR8 recombinant virus challenge in mice via the intranasal route.

FIG. 5 shows probability of survival results for FL / FL (mice pre-immune to homologous FL HA and boosted with FL HA), FL / miniHAteth (mice pre-immune to homologous FL HA and boosted with miniHAteth), FL / miniHAsec (mice pre-immune to homologous FL HA and boosted with miniHAsec), rHA / rHA (rHA-primed animals boosted with another dose of adjuvanted rHA), and mock groups after a stringent H5N1 A/Vietnam/1204/2004-PR8 recombinant virus challenge in mice via the intranasal route.

FIG. 6A shows a wild-type HA2 domain from Group Al, A/Brisbane/59/2007 (H1N1) (SEQ ID NO:3). Underlined residues can be substituted or mutated to improve trimerization and/or immunogenicity. The targeted mutations or substitutions can include HOT, F73Y, V76I, K78C, F80Y, L83S, R86C, E88K, N89Q, L90I, N91E, V94E, D95I, D96E, G97E, F98I, I99E, D100K, and/or T103C, as shown at FIG. 6B (SEQ ID NO: 11).

FIG. 6B shows an example miniature HA tethered from Group Al, Al miniHAteth (SEQ ID NO: 11). Underlined residues correspond to changes in the amino acid sequence relative to wild-type HA2 of FIG. 6A, i.e., differences contained in SEQ ID NO: 11 with respect to SEQ ID NO:3. The changes can include one or more targeted mutations or substitutions at specific amino acids of the HA2 domain (e.g., HOT, F73Y, V76I, K78C, F80Y, L83S, R86C, E88K, N89Q, L90I, N91E, V94E, D95I, D96E, G97E, F98I, I99E, D100K, and/or T103C), addition of an N-terminal sequence that includes a signal peptide and at least part of an HA1 domain (i.e., MKVKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL ENGGGGKYVC SAKLRMVTGL RNKPSKQSQ), and addition of a C-terminal sequence that includes a transmembrane domain i.e., LAIYSTVASS LVLLVSLGAI SFW) and a cytoplasmic domain (i.e., MC SNGSLQCRIC I).

FIG. 7 A shows a wild-type HA2 domain from Group A2, A/AICHI/2/1968 (H3N2) (SEQ ID NO:4). Underlined residues can be substituted or mutated to improve trimerization and/or immunogenicity. The targeted mutations or substitutions can include L2I, I18V, T32I, D46N, K51M, L52V, substitution of the segment spanning K58 to N95 with LMEQGGPDCYL (i.e., the segment spanning L139 to L149 of SEQ ID NO: 12 of FIG. 7B), E103L, N116R, K121R, R123K, R124K, E132D, and/or E150G.

FIG. 7B shows an example miniature HA tethered from Group A2, A2 miniHAteth (SEQ ID NO: 12). Underlined residues correspond to changes in the amino acid sequence relative to wild-type HA2 of FIG. 7A, i.e., differences contained in SEQ ID NO: 12 with respect to SEQ ID NO:4. The changes can include one or more targeted mutations or substitutions at specific amino acids of the HA2 domain (e.g., L2I, 118 V, T32I, D46N, K51M, L52V, substitution of the segment spanning K58 to N95 with LMEQGGPDCYL (i.e., the segment spanning L139 to L149 of SEQ ID NO: 12 of FIG. 7B), E103L, N116R, K121R, R123K, R124K, E132D, and/or E150G), addition of an N-terminal sequence that includes a signal peptide and at least part of an HA1 domain (i.e., MKTIIALSYI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTITNDQI EVTNATELVF PGCGVLKLAT GMRNVPEKQT R), and addition of a C-terminal sequence that includes a transmembrane domain and a cytoplasmic domain (i.e., SGYKDWI LWISFAISCF LLCVVLLGFI MWACQRGNIR CNICI).

DETAILED DESCRIPTION

The present disclosure is based on the development of influenza viral antigens that provide superior cross reactivity and protective effect for multiple strains of influenza virus. As described in more detail below, the modified extant HA2 polypeptides are modified to include transmembrane domains, forcing expression of the polypeptides on the cell surface. The polypeptides are improved, through mutations, substitutions, deletions, and/or modifications that enable the polypeptides to stably trimerize at the cell surface. Unexpectedly, presentation of these trimeric polypeptide antigens at the cell surface also provided a significantly enhanced immune response, especially upon restimulation (/.< ., boost) after prior infection or vaccination.

Unless specifically defined herein, all terms used herein have the same meaning as they would to one skilled in the art of the present invention. Practitioners are particularly directed to Sambrook J., et al. (eds.), Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Press, Plainsview, New York (2001); Ausubel, F.M., et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, New York (2010); Coligan, J.E., et al. (eds.), Current Protocols in Immunology, John Wiley & Sons, New York (2010) Mirzaei, H. and Carrasco, M. (eds.), Modern Proteomics - Sample Preparation, Analysis and Practical Applications in Advances in Experimental Medicine and Biology, Springer International Publishing, 2016; and Comai, L, et al., (eds.), Proteomic: Methods and Protocols in Methods in Molecular Biology, Springer International Publishing, 2017, for definitions and terms of art.

For convenience, certain terms employed in this description and/or the claims are provided here. The definitions are provided to aid in describing particular embodiments and are not intended to limit the claimed subject matter, because the scope of the invention is limited only by the claims.

The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.”

The words “a” and “an,” when used in conjunction with the word “comprising” in the claims or specification, denotes one or more, unless specifically noted.

Unless the context clearly requires otherwise, throughout the description and the claims, the words “comprise,” “comprising,” and the like, are to be construed in an inclusive sense as opposed to an exclusive or exhaustive sense, which is to indicate, in the sense of “including, but not limited to.” Words using the singular or plural number also include the plural and singular number, respectively. The word “about” indicates a number within range of minor variation above or below the stated reference number. For example, “about” can refer to a number within a range of 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% above or below the indicated reference number.

As used herein, the term “nucleic acid” refers to a polymer of nucleotide monomer units or “residues”. The nucleotide monomer subunits, or residues, of the nucleic acids each contain a nitrogenous base (i.e., nucleobase) a five-carbon sugar, and a phosphate group. The identity of each residue is typically indicated herein with reference to the identity of the nucleobase (or nitrogenous base) structure of each residue. Canonical nucleobases include adenine (A), guanine (G), thymine (T), uracil (U) (in RNA instead of thymine (T) residues) and cytosine (C). However, the nucleic acids of the present disclosure can include any modified nucleobase, nucleobase analogs, and/or non- canonical nucleobases, as are well-known in the art. Nucleic acid modifications to the nucleic acid monomers, or residues, encompass any chemical change in the structure of the nucleic acid monomer, or residue, which results in a noncanonical subunit structure. Such chemical changes can result from, for example, epigenetic modifications (such as to genomic DNA or RNA), or damage resulting from radiation, chemical, or other means. Illustrative and nonlimiting examples of noncanonical subunits, which can result from a nucleic acid modification, include uracil (for DNA), 5 -methylcytosine, 5-hydroxymethylcytosine, 5-formethylcytosine, 5 -carboxy cytosine b-glucosyl-5- hydroxy-methylcytosine, 8-oxoguanine, 2-amino-adenosine, 2-amino-deoxyadenosine, 2 -thiothymidine, pyrrolo-pyrimidine, 2-thiocytidine, or an abasic lesion. An abasic lesion is a location along the deoxyribose backbone but lacking a base. Known analogs of natural nucleotides hybridize to nucleic acids in a manner similar to naturally occurring nucleotides, such as peptide nucleic acids (PNAs) and phosphorothioate DNA.

As used herein, the terms “polypeptide” and “protein” are interchangeable and refer to a polymer in which the monomers are amino acid residues that are joined together through amide bonds. When the amino acids are alpha-amino acids, either the L-optical isomer or the D-optical isomer can be used, the L-isomers being preferred. The term polypeptide or protein as used herein encompasses any amino acid sequence and includes modified sequences such as glycoproteins. The terms polypeptide and protein are specifically intended to cover naturally occurring proteins, as well as those that are recombinantly or synthetically produced.

One of skill will recognize that individual substitutions, deletions, or additions to a peptide, polypeptide, or protein sequence which alters, adds, or deletes a single amino acid or a percentage of amino acids in the sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that are considered to be conservative substitutions for one another:

(1) Alanine (A), Serine (S), Threonine (T),

(2) Aspartic acid (D), Glutamic acid (E),

(3) Asparagine (N), Glutamine (Q),

(4) Arginine (R), Lysine (K),

(5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V), and

(6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

Reference to sequence identity addresses the degree of similarity of two polymeric sequences, such as protein sequences. Determination of sequence identity can be readily accomplished by persons of ordinary skill in the art using accepted algorithms and/or techniques. Sequence identity is typically determined by comparing two optimally aligned sequences over a comparison window, where the portion of the peptide or polynucleotide sequence in the comparison window can comprise additions or deletions (e.g., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical amino-acid residue or nucleic acid base 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 window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Various software driven algorithms are readily available, such as BLAST N or BLAST P to perform such comparisons.

Disclosed are materials, compositions, and components that can be used for, can be used in conjunction with, can be used in preparation for, or are products of the disclosed methods and compositions. It is understood that, when combinations, subsets, interactions, groups, etc., of these materials are disclosed, each of various individual and collective combinations is specifically contemplated, even though specific reference to each and every single combination and permutation of these compounds may not be explicitly disclosed. This concept applies to all aspects of this disclosure including, but not limited to, steps in the described methods. Thus, specific elements of any foregoing embodiments can be combined or substituted for elements in other embodiments. For example, if there are a variety of additional steps that can be performed, it is understood that each of these additional steps can be performed with any specific method steps or combination of method steps of the disclosed methods, and that each such combination or subset of combinations is specifically contemplated and should be considered disclosed. Additionally, it is understood that the embodiments described herein can be implemented using any suitable material such as those described elsewhere herein or as known in the art.

Publications cited herein and the subject matter for which they are cited are hereby specifically incorporated by reference in their entireties.

INFLUENZA HA ANTIGENS

In a general aspect, the disclosure provides improved influenza hemagglutinin (HA) polypeptide antigens. In embodiments, the HA polypeptides are synthetic. In embodiments, the HA polypeptides comprise a stem (HA2) domain and a transmembrane domain, and also comprise an amino acid substitution, addition, and/or deletion, relative to a reference HA polypeptide, such as a natural (e.g., wild-type; WT) HA polypeptide. These changes to the HA polypeptide sequence result in synthetic HA polypeptides with improved trimerization and/or immunogenicity relative to natural HA polypeptides and previous engineered antigenic HA polypeptides. In particular, in embodiments, changes to the HA polypeptide sequence include adding a transmembrane domain to a secreted, miniature HA (miniHA) antigen (see, e.g., Freyn el al. Molecular Therapy Vol. 28 No 7 July 2020.) Addition of the transmembrane domain to miniHA (/.< ., miniHAsec) results in a tethered form of miniHA, miniHAteth (e. , Al miniHAteth, A2 miniHAteth, Bl miniHA^, and/or B2 miniHA^). Example miniHA_tetj1 polypeptides include but are not necessarily limited to: GROUP Al - A/BRISBANE/59/2007(HlNl) miniHA_teth, GROUP A2 - A/AICHI/2/1968(H3N2) miniHA_teth, GROUP Bl - B/VICTORIA/02/1987 miniHA^, and Group B2 - B/Yamagata/16/1988 miniHA^. The tethered miniHA localizes to the cell membrane and unexpectedly increases the immunogenicity of the antigens and the protective effect of vaccination with the antigens. While any transmembrane domain is encompassed by this disclosure, in embodiments, the transmembrane domain is an influenza HA transmembrane domain. The transmembrane domain can be derived from the same or a different influenza strain as the HA antigen.

In embodiments, the synthetic HA polypeptide does not include a full-length HA1 head subdomain or does not include a portion of an HA1 head subdomain. In embodiments, the full-length HA1 head subdomain or the portion thereof is deleted or, in embodiments, is substituted for a linker, such as an improved linker. Without wishing to be bound by any particular theory, it is believed that omitting the HA1 head subdomain exposes the stem (HA2) domain at the cell membrane which acts as an antigen for an immune response. Since the stem (HA2) domain is relatively conserved and has a lower rate of mutation in the virus, it is believed that immunogenicity against the stem (HA2) domain improves cross-reactivity of the immune system against multiple virus types and multiple phylogenetic groups that persists longitudinally despite continued antigenic drift of the HA1 head subdomain in the virus.

In certain embodiments, the synthetic HA polypeptide consists essentially of, or consists of, a stem (HA2) domain and a transmembrane domain, including an amino acid substitution, addition, and/or deletion, relative to a reference HA polypeptide, as disclosed herein. In such embodiments, a full-length HA1 head subdomain, or a portion of an HA1 head subdomain, is/are excluded from the scope of the embodiment and any corresponding claims. In this manner, omission of the HA1 head subdomain or the portion thereof from the synthetic HA polypeptide enables generation of a robust and cross-protective immune response against the stem (HA2) domain.

In embodiments, the amino acid substitution, the amino acid addition, and/or the amino acid deletion comprises one or more targeted mutations or substitutions to the HA2 domain to promote trimerization. Example targeted mutations or substitutions of a wildtype HA2 domain from Group Al, A/Brisbane/59/2007 (H1N1) (SEQ ID NO:3) include one or more of HOT, F73Y, V76I, K78C, F80Y, L83S, R86C, E88K, N89Q, L90I, N91E, V94E, D95I, D96E, G97E, F98I, I99E, D100K, and/or T103C (SEQ ID NO: 11); see also FIGs 6A and 6B. Example targeted mutations or substitutions of a wild-type HA2 domain from Group A2, A/AICHV2/1968 (H3N2) (SEQ ID NO:4) include one or more of L2I, I18V, T32I, D46N, K51M, L52V, substitution of the segment spanning K58 to N95 with LMEQGGPDCYL (i.e., the segment spanning LI 39 to L 149 of SEQ ID NO: 12 of FIG. 7B), E103L, N116R, K121R, R123K, R124K, E132D, and/or E150G (SEQ ID NO: 12); see also FIGs 7A and 7B. In embodiments, the transmembrane domain comprises, consists essentially of, or consists of an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to SEQ ID NO: 10. In embodiments, the transmembrane domain has an amino acid sequence with at least 80% identity to SEQ ID NO: 10.

In embodiments, the synthetic HA polypeptide comprises, consists essentially of, or consists of an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to one of SEQ ID NOs:3- 6. In embodiments, the synthetic HA polypeptide has an amino acid sequence with at least 60% identity or at least 70% identity to one of SEQ ID NOs:3-6.

In embodiments, the synthetic HA polypeptide comprises, consists essentially of, or consists of an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to one of SEQ ID NOs: 11- 12. In embodiments, the synthetic HA polypeptide has an amino acid sequence with at least 80% identity or at least 90% identity to one of SEQ ID NOs: 11-12.

In embodiments, the amino acid substitution, the amino acid addition, and/or the amino acid deletion is/are selected from differences contained in SEQ ID NO: 11 with respect to SEQ ID NO:3. Example differences contained in SEQ ID NO: 11 with respect to SEQ ID NO:3 can include one or more targeted mutations or substitutions at specific amino acids of the HA2 domain (e.g., HOT, F73Y, V76I, K78C, F80Y, L83S, R86C, E88K, N89Q, L90I, N91E, V94E, D95I, D96E, G97E, F98I, I99E, D100K, and/or T103C), addition of an N-terminal sequence that includes a signal peptide and at least part of an HA1 domain (i.e., MKVKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL ENGGGGKYVC SAKLRMVTGL RNKPSKQSQ), and addition of a C-terminal sequence that includes a transmembrane domain (z.e., LAIYSTVASS LVLLVSLGAI SFW) and a cytoplasmic domain (z.e., MC SNGSLQCRIC I) (FIGs 6A and 6B).

In embodiments, the amino acid substitution, the amino acid addition, and/or the amino acid deletion is/are selected from differences contained in SEQ ID NO: 12 with respect to SEQ ID NO:4. Example differences contained in SEQ ID NO: 12 with respect to SEQ ID NO:4 can include one or more targeted mutations or substitutions at specific amino acids of the HA2 domain (e.g., L2I, I18V, T32I, D46N, K51M, L52V, substitution of the segment spanning K58 to N95 with LMEQGGPDCYL (z.e., the segment spanning L139 to L149 of SEQ ID NO: 12 of FIG 7B), E103L, N116R, K121R, R123K, R124K, E132D, and/or E150G), addition of an N-terminal sequence that includes a signal peptide and at least part of an HA1 domain (z.e., MKTIIALSYI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTITNDQI EVTNATELVF PGCGVLKLAT GMRNVPEKQT R), and addition of a C-terminal sequence that includes a transmembrane domain and a cytoplasmic domain (z.e., SGYKDWI LWISFAISCF LLCVVLLGFI MWACQRGNIR CNICI) (FIGs 7A and 7B).

In embodiments, the HA2 domain is or is derived from an influenza Al HA2 domain, an influenza A2 HA2 domain, an influenza B 1 HA2 domain, or an influenza B2 HA2 domain. Example HA2 domains are shown at SEQ ID NOs:3-6. Accordingly, in embodiments, the influenza HA2 domain which is or is the basis for derivation of the HA2 domain of the synthetic HA polypeptide comprises an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to one of SEQ ID NOs:3-6.

In embodiments, the synthetic HA polypeptide further comprises a cytoplasmic domain positioned adjacent to the transmembrane in the sequence of the polypeptide. The cytoplasmic domain, when present, extends into the cytoplasm of the cell when the polypeptide is tethered to the cell membrane. NUCLEIC ACIDS ENCODING INFLUENZA HA ANTIGENS

In another aspect, the present disclosure provides a nucleic acid encoding a synthetic HA polypeptide according to any embodiment disclosed herein. In embodiments, the nucleic acid includes DNA, RNA, modified DNA, modified RNA, messenger RNA (mRNA), or replicating RNA (repRNA) which includes self-replicating RNA (srRNA). In at least some instances, the nucleic acid is configured or used for in vitro production of the synthetic HA polypeptide using techniques known in the art. In other instances, the nucleic acid is configured or used for in vivo production of the synthetic HA polypeptide, for example, in instances where it is an antigen produced as a result of administration of an mRNA vaccine to a subject.

In embodiments, DNA or RNA includes a DNA or RNA sequence, respectively, that encodes for a transmembrane domain of the synthetic HA polypeptide. In embodiments, the DNA or RNA sequence encodes a transmembrane domain that comprises an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to SEQ ID NO: 10. In embodiments, the DNA or RNA sequence encodes a transmembrane domain that comprises an amino acid sequence with at least 80% identity to SEQ ID NO: 10.

In embodiments, DNA or RNA includes a DNA or RNA sequence, respectively, that encodes for a synthetic HA polypeptide that comprises an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to one of SEQ ID NOs:3-6. In embodiments, the DNA or RNA sequence encodes a synthetic HA polypeptide that comprises an amino acid sequence with at least 60% identity or at least 70% identity to one of SEQ ID NOs:3-6.

In embodiments, DNA or RNA includes a DNA or RNA sequence, respectively, that encodes for a synthetic HA polypeptide that comprises an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to one of SEQ ID NOs: 11-12. In embodiments, the DNA or RNA sequence encodes a synthetic HA polypeptide that comprises an amino acid sequence with at least 80% identity or at least 90% identity to one of SEQ ID NOs: 11-12.

In embodiments, a repRNA includes an RNA sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to one of SEQ ID NOs: 13-14. In embodiments, the RNA sequence has at least 80% identity or at least 90% identity to one of SEQ ID NOs: 13-14.

In another aspect, the disclosure provides a nucleic acid expression vector comprising a polynucleotide sequence, e.g., DNA or RNA, encoding a synthetic HA polypeptide according to any embodiment described herein. The vector includes any construct that facilitates delivery of the polynucleotide sequence encoding the synthetic HA polypeptide to a target cell and/or expression of the polynucleotide sequence within the cell. In embodiments, the vectors are viral vectors, circular nucleic acid constructs (e.g., plasmids), or nanoparticles.

Various viral vectors are known in the art and are encompassed by the present disclosure. See, e.g., Machida, C. A. (ed.), Viral Vectors for Gene Therapy: Methods and Protocols, Humana Press, Totowa, New Jersey (2003); Muzyczka, N., (ed.), Current Topics in Microbiology and Immunology. Viral Expression Vectors, Springer-Verlag, Berlin, Germany (2012), each incorporated herein by reference in its entirety. In embodiments, the viral vector is an adeno associated virus (AAV) vector, an adenovirus vector, a retrovirus vector, or a lentivirus vector. A specific embodiment of an AAV vector includes the AAV2.5 serotype. In embodiments, the expression vector includes a promoter operatively linked to the polynucleotide sequence encoding the synthetic HA polypeptide using genetic engineering techniques known in the art.

In another aspect, the disclosure provides a recombinant host cell comprising a nucleic acid expression vector comprising a polynucleotide sequence encoding a synthetic HA polypeptide as disclosed herein. In embodiments, the cell is used for production of the HA antigen and/or replication of the vector or a portion thereof. In another aspect, the disclosure provides a method of making a host cell as described herein. In embodiments, the method comprises transforming a cell with a nucleic acid or a vector as described herein and permitting transcription in the cell. In embodiments, the cell is a mammalian cell, optionally a human cell. In embodiments, the cell is engineered in vitro, and in other embodiments, the cell is engineered in vivo, e.g., by administering to a subject a nucleic acid expression vector comprising a polynucleotide sequence encoding a synthetic hemagglutinin (HA) polypeptide antigen as disclosed herein. In such embodiments, the body harboring the cell is administered an effective amount of the nucleic acid, vector, and/or a composition comprising the nucleic acid and/or the vector.

PHARMACEUTICAL COMPOSITIONS

In another aspect, the disclosure provides a pharmaceutical composition for administration to a subject for a prophylactic or therapeutic purpose. In embodiments, the pharmaceutical composition comprises a synthetic HA polypeptide as disclosed herein, a nucleic acid (e.g., a repRNA nucleic acid, such as SEQ ID NO: 13, SEQ ID NO: 14, and/or another repRNA) having a polynucleotide sequence encoding a synthetic HA polypeptide as disclosed herein, a nucleic acid expression vector having a polynucleotide sequence encoding a synthetic HA polypeptide as disclosed herein, and/or a recombinant host cell having a nucleic acid or a nucleic acid expression vector with a polynucleotide sequence encoding a synthetic HA polypeptide as disclosed herein, and a pharmaceutically acceptable carrier.

In particular embodiments, the disclosure provides RNA vaccines formulated as pharmaceutical compositions, including but not limited to mRNA vaccines. An RNA vaccine of the disclosure comprises one or more ribonucleic acids (RNAs) comprising one or more polynucleotide sequences encoding one or more synthetic HA polypeptides of the disclosure.

The term “pharmaceutical composition” refers to the combination of an active agent with a carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo or ex vivo. A “pharmaceutically acceptable carrier,” after administered to or upon a subject, does not cause undesirable physiological effects. The carrier in the pharmaceutical composition must be “acceptable” also in the sense that it is compatible with the active ingredient and can be capable of stabilizing it. One or more solubilizing agents can be utilized as pharmaceutical carriers for delivery of an active agent. Examples of a pharmaceutically acceptable carrier include, but are not limited to, biocompatible vehicles, adjuvants, additives, and diluents to achieve a composition usable as a dosage form. Examples of other carriers include colloidal silicon oxide, magnesium stearate, cellulose, and sodium lauryl sulfate. Additional suitable pharmaceutical carriers and diluents, as well as pharmaceutical necessities for their use, are described in Remington’s Pharmaceutical Sciences.

In embodiments, the RNA vaccine is provided as an alphavirus-derived replicon RNA vaccine, and in embodiments, the RNA vaccine is formulated as a cationic nano emulsion. An example of a cationic nano emulsion includes a lipid inorganic nanoparticle (LION) emulsion designed to enhance vaccine stability and intracellular delivery of the vaccine. LION is a highly stable cationic squalene emulsion with 15-nm superparamagnetic iron oxide (Fe₃O4) nanoparticles (SPIO) embedded in the hydrophobic oil phase. Squalene is a known vaccine adjuvant, and a key component of LION is the cationic lipid l,2-dioleoyl-3 -trimethylammonium propane (DOTAP), which enables electrostatic association with RNA molecules when combined by a simple 1 : 1 (v/v) mixing step. When mixed, electrostatic association between anionic repRNA and cationic DOTAP molecules on the surface of LION promotes immediate complex formation and an increase in particle size to an intensity -weighted average diameter of 90 nm (see, for example, Erasmus JH et al. An Alphavirus-derived replicon RNA vaccine induces SARS-CoV-2 neutralizing antibody and T cell responses in mice and nonhuman primates. SCIENCE TRANSLATIONAL MEDICINE. 5 Aug 2020. Vol 12, Issue 555).

In embodiments, RNA vaccines (including polynucleotides and their encoded polypeptides) in accordance with the present disclosure are used for treatment or prevention of infection with influenza. In embodiments, influenza RNA vaccines are administered prophylactically or therapeutically as part of an active immunization scheme to healthy individuals or early in infection during the incubation phase or during active infection after onset of symptoms. In embodiments, the amount of RNA vaccines of the present disclosure provided to a cell, a tissue, or a subject is an amount effective for immune prophylaxis.

In embodiments, influenza RNA (e.g., mRNA, repRNA) vaccines are administered with other prophylactic or therapeutic compounds. As a non-limiting example, a prophylactic or therapeutic compound is an adjuvant or a booster. As used herein, when referring to a prophylactic composition, such as a vaccine, the term “booster” refers to an extra or additional administration of the prophylactic (vaccine) composition (e.g., boost) compared to an initial administration (e.g., prime). In embodiments, a booster (or booster vaccine) is given after an earlier administration of the prophylactic composition. The time of administration between the initial administration of the prophylactic composition and the booster can be, but is not limited to, 1 minute, 2 minutes, 3 minutes, 4 minutes, 5 minutes, 6 minutes, 7 minutes, 8 minutes, 9 minutes, 10 minutes, 15 minutes, 20 minutes 35 minutes, 40 minutes, 45 minutes, 50 minutes, 55 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 1 day, 36 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 10 days, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year, 18 months, 2 years, 3 years, 4 years, 5 years, 6 years, 7 years, 8 years, 9 years, 10 years, 11 years, 12 years, 13 years, 14 years, 15 years, 16 years, 17 years, 18 years, 19 years, 20 years, 25 years, 30 years, 35 years, 40 years, 45 years, 50 years, 55 years, 60 years, 65 years, 70 years, 75 years, 80 years, 85 years, 90 years, 95 years or more than 99 years. In example embodiments, the time of administration between the initial administration of the prophylactic composition and the booster can be, but is not limited to, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 6 months or 1 year.

As another example, influenza RNA (e.g., mRNA, repRNA) vaccines are administered to individuals who have not previously received a prophylactic composition of an influenza vaccine. In such instances, the influenza RNA (e.g., mRNA, repRNA) vaccine is administered to the individual as a single boost, i.e., one (1) boost, as at least part of a vaccine treatment or regimen.

In embodiments, influenza RNA vaccines are administered intramuscularly, intranasally, or intradermally, similar to the administration of inactivated vaccines known in the art.

The influenza RNA vaccines are able to be utilized in various settings depending on the prevalence of the infection or the degree or level of unmet medical need. As a nonlimiting example, the RNA vaccines are utilized to treat and/or prevent influenza infection. RNA vaccines have superior properties in that they produce much larger antibody titers, better neutralizing immunity, produce more durable immune responses, and/or produce responses earlier than other commercially available vaccines. Accordingly, the disclosure provides pharmaceutical compositions including influenza RNA vaccines and RNA vaccine compositions and/or complexes optionally in combination with one or more pharmaceutically acceptable excipients. In embodiments influenza RNA (e.g., mRNA, repRNA) vaccines are formulated or administered alone or, alternatively, in conjunction with one or more other components. For instance, influenza RNA vaccines (vaccine compositions) can comprise other components including, but not limited to, adjuvants.

In embodiments, the influenza RNA (e.g., mRNA, repRNA) vaccine is provided as a tetra- or tri-valent RNA vaccine applied to at least Group 1 Influenza A, Group 2 Influenza A, and Group B influenza viruses. For example, an influenza RNA (e.g., mRNA) vaccine comprises one or more RNA sequences encoding one or more synthetic HA polypeptides with modified HA2 domains. Example natural HA2 domains that can provide the basis for such synthetic HA2 domains include, but are not necessarily limited to, GROUP Al - A/BRISBANE/59/2007(HlNl) (SEQ ID NO:3), GROUP A2 - A/AICHI/2/1968(H3N2) (SEQ ID NO:4), GROUP Bl - B/VICTORIA/02/1987 (SEQ ID NO:5) and GROUP B2 - B/Yamagata/16/1988 (SEQ ID NO:6). Any of these or other influenza HA HA2 domains can be used or modified as described herein to include, among other possible modifications, an amino acid substitution, addition, and/or deletion, relative to the corresponding natural HA polypeptide, for improved trimerization and/or immunogenicity of the synthetic HA polypeptide. For example, the amino acid substitution, the amino acid addition, and/or the amino acid deletion is/are selected from differences contained in SEQ ID NO: 11 with respect to SEQ ID NO:3 or is/are selected from differences contained in SEQ ID NO: 12 with respect to SEQ ID NO:4 (see FIGs 6A, 6B, 7A, and 7B).

In embodiments wherein the influenza RNA (e.g., mRNA, repRNA) vaccine is provided as a tetra-valent RNA vaccine, the vaccine includes RNA encoding for HA polypeptide antigens that correspond to Group Al, Group A2, Group Bl (e.g., Victoria), and Group B2 (e.g, Yamagata) viruses. In embodiments wherein the influenza RNA (e.g, mRNA) vaccine is provided as a tri-valent RNA vaccine, the vaccine includes HA polypeptide antigens that correspond to Group Al, Group A2, and Group Bl or Group B2 viruses. For a tetra-valent RNA vaccine, a synthetic Group Al HA polypeptide, a synthetic Group A2 HA polypeptide, a synthetic Group Bl HA polypeptide, and a synthetic Group B2 HA polypeptide are produced as a result of administration of the vaccine. For a tri-valent RNA vaccine, a synthetic Group Al HA polypeptide, a synthetic Group A2 HA polypeptide, and a synthetic Group Bl HA polypeptide or a synthetic Group B2 HA polypeptide are produced as a result of administration of the vaccine.

In embodiments, the synthetic HA polypeptide produced as a result of administration of the vaccine includes modifications, such as an amino acid substitution, addition, and/or deletion, relative to the corresponding natural HA polypeptide, for improved trimerization and/or immunogenicity of the synthetic HA polypeptide. With reference to Group Al and Group A2, the amino acid substitution, the amino acid addition, and/or the amino acid deletion is/are selected from differences contained in SEQ ID NO: 11 (synthetic Group Al miniHAteth) with respect to SEQ ID NO:3 or is/are selected from differences contained in SEQ ID NO: 12 (synthetic Group A2 miniHAteth) with respect to SEQ ID NO:4 (see FIGs 6A, 6B, 7A, and 7B). With reference to Group Bl (e.g., Victoria) and Group B2 (e.g., Yamagata), the synthetic HA2 domain can include the same or similar or corresponding modifications, such as an amino acid substitution, addition, and/or deletion, relative to the corresponding natural HA2 domain, for improved trimerization and/or immunogenicity of the synthetic HA polypeptide. For example, the amino acid substitution, the amino acid addition, and/or the amino acid deletion the same as or similar to or corresponding to differences contained in SEQ ID NO: 11 with respect to SEQ ID NO:3 or is/are selected from differences contained in SEQ ID NO: 12 with respect to SEQ ID NO:4 (see FIGs 6A, 6B, 7A, and 7B), such as the addition of a transmembrane domain (e.g., SEQ ID NO: 10), optionally including a cytoplasmic domain, for anchoring the synthetic HA polypeptide to the cell membrane.

In embodiments, the influenza RNA (e.g., mRNA, repRNA) vaccine comprises an RNA having an RNA sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identity to one or more of SEQ ID NOs: 13-14. In embodiments, the RNA sequence has at least 80% identity or at least 90% identity to one or more of SEQ ID NOs: 13-14. VACCINATION METHODS

In another aspect, the disclosure provides a method for immunizing an individual against influenza, the method comprising administering to an individual an effective amount of a pharmaceutical composition as disclosed herein. In certain embodiments, the individual does not need or otherwise will not have received an initial (prime) administration of the vaccine, for example, due to the individual having been previously exposed to influenza and not being naive to the virus. Accordingly, in embodiments of the method, the individual is not naive to influenza and the administering comprises administering to the individual the pharmaceutical composition as a single boost (i.e., one (1) boost administration) as at least part of a vaccine treatment. Given the prevalence of influenza and the frequency of non-naive individuals in the population, in these or other embodiments, the method does not include a prime or prophylactic administration.

In embodiments, an immune response is produced by an individual as a result of administration of a vaccine of the disclosure. In embodiments, the immune response is against an influenza virus of a strain that is different from the strain from which the influenza hemagglutinin (HA) antigen expressed on the cell is derived. This is possible due to the cross-reactivity observed from presentation of the stem antigen (/.< ., HA2) in the context of being anchored on a cell membrane. In embodiments, the immune response is an enhanced and/or protective immune response. This is possible, as established herein, where the HA2 antigen presented on a cell surface not only induces a strong immune response as determined by antibody titer, but also increases and prolongs survival and reduces weight loss after boost administration. In embodiments, the subject has been previously infected with an influenza virus, and in at least some embodiments, the subject has been previously vaccinated against an influenza virus.

EXAMPLE: IMPROVEMENTS TO HA STEM-BASED IMMUNOGENS

The following example is set forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and is not intended to limit the scope of what the inventors regard as their invention nor is it intended to represent that the experiments below are all or the only experiments performed.

Various repRNA-mediated expression strategies have been under evaluation for improving cross-protective immune responses to influenza immunogens. Of the immunogens evaluated, a stable trimeric hemagglutinin stem, termed miniHA, demonstrated efficient expression and immunogenicity when expressed from a platform. The original development of miniHA utilized a structure-based approach to replace the head domain of H1N1 A/Brisbane/59/2007 HA with an improved linker as well as targeted mutations to promote the trimerization of a soluble HA ectodomain that could be produced as a recombinant subunit protein (see, for example, Impagliazzo, A. et al. A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen. Science 349(6254): 1301-1306 (2015)). Impagliazzo et al. were able to demonstrate cross- protective efficacy in mice against heterologous H5N1 A/Hong Kong/156/97 challenge after 3 doses of this vaccine candidate in an influenza virus-naive animal.

Given the ability for nucleic acid-based vaccine approaches to drive antigen expression in vivo, and evidence that full-length membrane-tethered glycoprotein antigens can potentially enhance immune responses to the target antigen, it was queried in this example whether improvements to cross-protective immune responses to miniHA could be obtained by reintroducing the transmembrane and cytoplasmic domains of H1N1 A/Brisbane/59/2007 HA and expressing this tethered version of miniHA from a LION/repRNA platform.

To answer this question, the original secreted miniHA (miniHAsec), the membrane-tethered version (miniHAteth), or the full-length HA (FL) of H1N1 A/Brisbane/59/2007 was encoded in the repRNA platform (FIG. 1). Homologous as well as heterologous Hl HA antibody responses were evaluated by enzyme linked immunosorbent assay (ELISA) following a prime and boost immunization (FIGs 2A and 2B). While binding antibody responses were similar between groups after the prime immunization, the boost immunization demonstrated superior homologous and heterologous binding antibody responses in the miniHAteth group, suggesting that a membrane-tethered presentation of a conserved epitope antigen improves the targeted selection of affinity -matured antibodies in the vaccinated individual.

Given that vaccines against influenza will ultimately be administered in previously vaccinated or previously infected individuals, it was next addressed whether the secreted or tethered presentation of miniHA influenced cross-reactive and -protective immune responses in mice previously immunized with a homologous FL HA derived from H1N1 A/Brisbane/59/2007. In this example, C57BL/6 mice (n=5/group) received a 1 pg prime immunization with LION/repRNA encoding FL HA or a strain-matched rehydrogel-adjuvanted recombinant HA (rHA). Then 4 weeks later, the FL HA repRNA- primed animals were boosted with 1 pg repRNA encoding FL HA, miniHAsec, or miniHAteth, while the rHA-primed animals were boosted with another dose of adjuvanted rHA. At four weeks after the boost immunization, homologous antibody and T-cell responses (FIGs 3A and 3B), heterologous antibody responses against an H5 HA (FIG. 3 A), and cross-protective efficacy against a stringent H5N1 A/Vietnam/1204/2004-PR8 recombinant virus challenge in mice via the intranasal route were evaluated (FIGs 3C and 3D). By HA binding-antibody ELISA, the magnitude of post-boost responses between repRNA groups were similar, while the adjuvanted rHA group demonstrated superior IgG responses against both Hl and H5 HAs (FIG. 3A). By HA peptide enzyme linked immunosorbent spot (ELISPOT) assay of splenocytes, the membrane-tethered immunogens (FL HA and miniHAteth) demonstrated superior antigen-specific T cell responses (FIG. 3B). However, despite the elevated levels of homologous and heterologous IgG induced by the rHA prime/boost group or both the binding antibody and T cell responses induced by the FL HA repRNA prime/boost group, these two groups experienced rapid weight loss and subsequent euthanasia with 20% and 0% survival, respectively, following challenge with 100 TCID50 H5N1/PR8 virus (FIGs 3C and 3D). Like the rHA group, the miniHAsec booster group exhibited rapid weight loss with 20% survival. Interestingly, the miniHAteth booster group appeared to delay weight loss and resulted in 60% survival, suggesting that this presentation of the miniHA antigen could potentially improve boosted immune responses in those previously exposed to homologous H1N1 HA (FIGs 4A, 4B, 4C, 4D, 4E, 5). Additionally, it is possible that increasing the dose of the booster immunization or combining it with a secondary, highly conserved antigen, could improve the protective outcome in this example.

While illustrative embodiments have been illustrated and described, it will be appreciated that various changes can be made therein without departing from the spirit and scope of the disclosure.

Claims

CLAIMS The embodiments of the invention in which an exclusive property or privilege is claimed are defined as follows:

1. A synthetic hemagglutinin (HA) polypeptide, comprising a stem (HA2) domain and a transmembrane domain; wherein the synthetic HA polypeptide comprises an amino acid substitution, addition, and/or deletion, relative to a natural HA polypeptide, for improved trimerization and/or immunogenicity of the synthetic HA polypeptide.

2. The synthetic HA polypeptide of claim 1, wherein the synthetic HA polypeptide does not include a full-length HA1 head subdomain.

3. The synthetic HA polypeptide of any one of claims 1-2, wherein the full- length HA1 head subdomain or a portion thereof is substituted for a linker.

4. The synthetic HA polypeptide of any one of claims 1-3, wherein the amino acid substitution, the amino acid addition, and/or the amino acid deletion comprises one or more targeted mutations or substitutions to the HA2 domain to promote trimerization and/or to promote a cross-protective immune response.

5. The synthetic HA polypeptide of any one of claims 1-4, wherein the transmembrane domain comprises an amino acid sequence with at least 80% identity to SEQ ID NO: 10.

6. The synthetic HA polypeptide of any one of claims 1-5, wherein the synthetic HA polypeptide comprises an amino acid sequence with at least 60% identity to one of SEQ ID NOs:3-6.

7. The synthetic HA polypeptide of any one of claims 1-6, wherein the synthetic HA polypeptide comprises an amino acid sequence with at least 70% identity to one of SEQ ID NOs:3-6.

8. The synthetic HA polypeptide of any one of claims 1-5, wherein the synthetic HA polypeptide comprises an amino acid sequence with at least 80% identity to one of SEQ ID NOs: 11-12.

9. The synthetic HA polypeptide of any one of claims 1-6, wherein the synthetic HA polypeptide comprises an amino acid sequence with at least 90% identity to one of SEQ ID NOs: 11-12.

10. The synthetic HA polypeptide of any one of claims 1-5, wherein the amino acid substitution, the amino acid addition, and/or the amino acid deletion is/are selected from differences contained in SEQ ID NO: 11 with respect to SEQ ID NO:3 or is/are selected from differences contained in SEQ ID NO: 12 with respect to SEQ ID NO:4.

11. The synthetic HA polypeptide of any one of claims 1-5, wherein the HA2 domain is or is derived from an influenza Al HA2 domain, an influenza A2 HA2 domain, an influenza Bl HA2 domain, or an influenza B2 HA2 domain.

12. The synthetic HA polypeptide of any one of claims 1-11, wherein the synthetic HA polypeptide further comprises a cytoplasmic domain.

13. A synthetic hemagglutinin (HA) polypeptide, comprising: an HA2 domain comprising an amino acid substitution, an amino acid addition, and/or an amino acid deletion, relative to a natural HA2 domain, for improved trimerization and/or immunogenicity of the synthetic HA polypeptide, wherein the HA2 domain is or is derived from an influenza Al HA2 domain, an influenza A2 HA2 domain, an influenza B 1 HA2 domain, or an influenza B2 HA2 domain; and a transmembrane domain for attachment of the synthetic HA polypeptide to a membrane of a cell; wherein the synthetic HA polypeptide does not include a full-length HA1 head subdomain.

14. The synthetic HA polypeptide of claim 13, wherein the amino acid substitution, the amino acid addition, and/or the amino acid deletion is/are selected from differences contained in SEQ ID NO: 11 with respect to SEQ ID NO:3 or is/are selected from differences contained in SEQ ID NO: 12 with respect to SEQ ID NO:4.

15. The synthetic HA polypeptide of any one of claims 13-14, wherein the synthetic HA polypeptide comprises an amino acid sequence with about 100% identity to one of SEQ ID NOs: 11-12.

16. A nucleic acid comprising a polynucleotide sequence encoding the synthetic HA polypeptide of any one of claims 1-15, optionally wherein the polynucleotide sequence has at least 80% identity or at least 90% identity to one or more of SEQ ID NOs: 13-14.

17. A nucleic acid expression vector, comprising the polynucleotide sequence of claim 16.

18. A recombinant host cell, comprising the nucleic acid expression vector of claim 17.

19. A pharmaceutical composition, comprising the synthetic HA polypeptide of any one of claims 1-15, the nucleic acid of claim 16, the nucleic acid expression vector of claim 17, and/or the recombinant host cell of claim 18, and a pharmaceutically acceptable carrier.

20. A method for immunizing an individual against influenza, the method comprising administering to an individual an effective amount of the pharmaceutical composition of claim 19.

21. The method of claim 20, wherein the individual is not naive to influenza and the administering comprises administering to the individual the pharmaceutical composition of claim 18 as a single boost as at least part of a vaccine treatment.