Notice of Pre-AIA or AIA Status
The present application is being examined under the first-inventor-to-file provisions of AIA .
DETAILED ACTION
Claims Status
Claims 6-9, 13, 17-19, 22-24, 26, 31-32, 34-45, 48-50, 53 and 55 are cancelled.
Claims 1-5, 10-12, 14-16, 20-21, 25, 27-30, 33, 46-47, 51-52 and 54 are under examination on their merits.
Priority
Claims 1-5,10-12, 14-16, 20-21, 25, 27-30, 33, 46-47, 51-52 and 54 in this application claim the benefit of priority to U.S. Provisional Patent Application No. 63/482,560, filed January 31, 2023.
Information Disclosure Statement
Information disclosure statements (IDS) submitted on 06/21/2024 and 08/15/2025 are in compliance with the provisions of 37 C.F.R. 1.97. Accordingly, all references cited in these IDSs have been fully considered.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Objection to Abstract
The abstract describes RNA molecules and their compositions that are useful for inducing immune responses, but claims 29-30 and specifications (e.g., ¶¶[0013], [0046], [0047], [0071], [0083], [00120] and [00194]) also cite DNA molecules encoding viral antigens as alternative compositions. It is recommended that the abstract be updated to accurately describe the scope of claimed invention.
Objection to Specification
Influenza virus strains “H1N1, H3N2, Victoria-B, or Yamagata-B” and “Victoria B/Austria/1359417/2021, H3N2 A/Darwin/6/2021, H1N1 A/Wisconsin/588/2019, and Yamagata B/PHUKET/3073/2013” are cited in ¶¶[0010] and [0061], while “Victoria… Yamagata” are cited in ¶¶[0043] and [00193] as if there are different isolates of Victoria and Yamagata strains. “B Victoria B/Washington/02/2019” in FIG. 7H has the same ambiguity issue. Meanwhile, “ATX-0126” (an ionizable lipid) is cited on page 76, while claim 47 cites “ATX-126” twice. Examiner recommends internal consistencies with virus and lipid nomenclatures.
In ¶[00337], narratives for the dosage of saRNA state that “FIG. 7C shows levels of binding IgG antibodies in serum (AU/mL) vs. percentage changes in body weight of immunized female BALB/c mice. Lipids tested in the saRNA experiments included ATX-126, ATX-221, ATX-239, and ATX-240. Vaccinations were given in 0.5 μg, 10 μg, 20 μg, and 40 μg doses… All vaccines showed similar immunogenicity and tolerability at the lowest dose of 0.5mg (FIG. 7C; circles, lower right of graph). If the citation of “0.5mg” as the lowest of four dosages were correct, the other three doses would be off by three magnitudes (1000-fold).
Art-free Subject Matter
The following is a statement of reasons for the indication of allowable subject
matter:
SEQ ID NOs: 1-4 as cited in claims 28 and 33 are free of prior art of record at the “at least 80%” identity level: the closest prior art retrieved in various searches showed sequence identities between 71% and 72%, although their composite elements, as defined by SEQ ID NOs: 5-13, match sequences from prior art, with sequence identities between 92% (for SEQ ID NO: 10) and 100% (for SEQ ID NOs: 14-15).
Claim Objections
Claims 14-15 and 47 are objected as having inconsistent nomenclatures. Specifically, Victoria-B and Yamagata-B as virus strains in claim 14 (line 2) are cited as “Victoria B/Austria/1359417/2021” and “Yamagata B/PHUKET/3073/2013”, respectively, in claim 15 (lines 2-3, without the dash in each strain name). In specification, “Victoria… Yamagata” are cited in ¶[0043] and ¶[00193] without designation for virus type (B) or isolate (Austria or PHUKET). All capital letters in “PHUKET”(claim 15, line 3) is further inconsistent with “B Yamagata B/Phuket/3073/2013” cited in ¶[00341] and FIG. 8D. For claim 47, “ATX-126” is cited twice (in section c), but the structure of “ATX-0126” on page 76 has a leading 0 before 126. Examiner recommends internal consistencies with nomenclatures for virus strains and lipids as claimed for the invention.
Claim 16 is objected to as having a typographical error – line 11 reads “(d) each of the one or more RNA molecules further comprise a 5' untranslated region (UTR)”, but “compromise” should read “comprises” instead.
Claim 28 is objected to for its dependence on two rejected claims (claim 1 and claim 27).
Claim Rejections under 35 U.S.C. §112
The following is a quotation of 35 U.S.C. §112(b) which forms the basis for indefiniteness rejections set forth in this Office action:
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 47, 51 and 54 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 47 discloses that “the ionizable cationic lipid is selected from Table 6.” Table 6 renders the claim indefinite as it is not clear from which in Table 6 the lipids are taken: it could be any lipids referenced in Table 6. The claims should be complete in themselves, and the lipids desired should be added to the claim rather than reference to a table with multiple choices.
The term “about” in claims 51 and 54 is a relative term which render the claimed invention indefinite. The term “about” is not defined within the claims, while the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention regarding the extent of sequence similarity between virus strains for immunization.
Specifically, claims 51 and 54 recite “about” for amounts of composition matter. In the “definitions” section of specification, the term "about" as used “when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of +20%, or ±10%, or ±5%, or even ±1 % from the specified value” (¶[0053]), which is vague: the definition says “about” encompasses the listed variations. This is the same as comprises these variations. It is not clear if only these variations are encompassed or if others are also encompassed, and if so, their amplitudes.
The following is a quotation of the first paragraph of 35 U.S.C. §112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. §112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 10, 28 and 33 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. §112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
These claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Regarding claim 10, it discloses RNA sequence variants as “having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 13.” Claim 28 adds that “a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by any of SEQ ID NOs:1-4,” while claim 33 requires “(I) (i)… a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 5; or (ii) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 9; or (iii) both (i) and (ii); or (II) (i) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 6; or (ii) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 10; or (iii) both (i) and (ii); or (III) (i) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 7; or (ii) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 11; or (iii) both (i) and (ii); or (IV) (i) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 8; or (ii) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO:12; or (iii) both (i) and (ii); or (V) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by any of SEQ ID NOs: 1-4.” The corresponding specification has SEQ ID NOs: 1-15 as “artificial constructs” of DNA sequences ranging from 44 nucleotides (SEQ ID NO. 14) to 11183 nucleotides (SEQ ID NO. 4).
The first four SEQ ID NOs in specification (pages 123-136) have “Italicized text denotes nsP1-4 replicase sequences; bold text denotes NA sequences; bold and underlined text denotes HA sequences” (page 123), but they have no tracking for the potential site of variation to allow a PHOSITA to assess the range of sequence identity. The other claimed SEQ ID NOs (pages 136-143) have “codon optimized NA from H1N1 influenza strain (SEQ ID NO: 5), “codon optimized NA from H3N2 influenza strain (SEQ ID NO: 6), “codon optimized NA from B Victoria influenza strain (SEQ ID NO: 7), “codon optimized NA from B Yamagata influenza strain (SEQ ID NO: 8), “codon optimized HA from H1N1 influenza strain (SEQ ID NO: 9), “codon optimized NA from H3N2 influenza strain (SEQ ID NO: 10), “codon optimized HA from B Victoria influenza strain (SEQ ID NO: 11), “codon optimized HA from B Yamagata influenza strain (SEQ ID NO: 12), “nsP1-nsP4 of SEQ ID NOs: 1-4 (SEQ ID NO: 13), “5’ UTR of SEQ ID NOs: 1-4 (SEQ ID NO: 14) and “3’ UTR of SEQ ID NOs: 1-4 (SEQ ID NO: 15); none of these have annotations to guide the mapping of potential or preferred positions for mutation/variation. Even if they did, the claims as written are not drawn to specific mutations but permit mutation at any position.
According to MPEP §2163.04, “[t]he purpose of the written description requirement is to ‘ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor’s contribution to the field of art as described in the patent specification.’” Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1353-54 (Fed. Cir. 2010) (en banc) (quoting Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 920 (Fed. Cir. 2004)). To satisfy the written description requirement, the specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1562-63, 19 USPQ2d 1111 (Fed. Cir. 1991).
MPEP §2163 also states that the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. A “representative number of species” means that the species which are adequately described are representative of the entire genus. See, e.g., AbbVie Deutschland GMBH v. Janssen Biotech, 759 F.3d 1285, 111 USPQ2d 1780 (Fed. Cir. 2014). Thus, when there is substantial variation within the genus, as here in which the DNA sequence variants can have any sequence in the range of “at least 80% identity”, one must describe a sufficient variety of species to reflect the variation within the genus. However, one of ordinary skill in this art cannot envision the structure of any DNA sequence or its corresponding protein/polypeptide with the required or preferred function other than SEQ IDs 1-15 provided by the Applicant or other relevant ones from prior art. Therefore, without any other representative sequence variants in the form of Tables/Figures or GenBank accession numbers, each of the DNA species of SEQ ID NOs: 1-15 is not sufficient enough to represent their respective genus for the “at least 80% identity” or other identity levels, so the claims encompassing SEQ ID NOs: 1-15 clearly fail the written description requirement.
Functionally defined genus claims can be inherently vulnerable to invalidity challenge for lack of written description support, especially in technology fields that are highly unpredictable, where it is difficult to establish a correlation between structure and function for the whole genus or to predict what would be covered by the functionally claimed genus. See ABBVIE DEUTSCHLAND GMBH & 2 CO. v. JANSSEN BIOTECH, INC., Appeals from the United States District Court for the District of Massachusetts in Nos. 09-CV-11340-FDS, 10-CV-40003-FDS, and 10-CV-40004-FDS, Judge F. Dennis Saylor, IV. See also Ariad, 598 F.3d at 1351 (“[T]he level of detail required to satisfy the written description requirement varies depending on the nature and scope of the claims and on the complexity and predictability of the relevant technology.”).
Even when several species are disclosed (e.g., SEQ ID NOs: 5-8 for codon optimized NA sequences from four influenza virus strains under subtypes A and B), these are not necessarily representative of the entire genus. AbbVie Deutschland GMBH v. Janssen Biotech, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (“The ’128 and ’485 patents, however, only describe species of structurally similar antibodies that were derived from Joe-9. Although the number of the described species appears high quantitatively, the described species are all of the similar type and do not qualitatively represent other types of antibodies encompassed by the genus”). Thus, when there is substantial variation within the virus strains and/or codon optimization, as SEQ ID NOs: 1-12 entail, one must describe a sufficient variety of each anticipated variant species to reflect the spectrum of variation within the genus to provide a "representative number” of species with comparable structure and/or function for a practical application (e.g., vaccination against different strains of influenza). Since the DNA genus recited in the instant claims is large, it would be very challenging to describe sufficient species to cover the structures/functions of the entire genus. A single DNA sequence for each influenza virus strain or several sequences for each virus lineage/subtype (A or B) is certainly inadequate.
Overall, at the time the invention was filed, the level of skill for preparing variant forms of DNA sequences for in vitro transcription and then packaging them into LNP toward a vaccine formulation with desired properties as immunogens was high. And even if a selection procedure was, at the time of the invention, sufficient to enable the skilled artisan to identify such variants with the recited functional properties, the written description provision of 35 U.S.C § 112 is severable from its enablement provision. Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336 (Fed. Cir. 2010). Thus, without detailed mapping of DNA sequence variations to specific positions, a skilled artisan generally would not be able to visualize or otherwise predict, a priori, what nucleotide position(s) with a particular set of functional properties (coding or noncoding) would look like structurally.
Thus, claims 10, 28 and 33 are rejected here for lacking sufficient written description.
Claims 10, 28 and 33 are also rejected under 35 U.S.C. §112(a) or 35 U.S.C. §112 (pre-AIA ), first paragraph, because the specification, while enabling for generating self-replicating mRNA encoding HA and NA antigens representing four influenza virus strains/isolates (SEQ ID NOs 1-13), neither the range of claimed sequence variations beyond SEQ ID NOs 1-13 nor their practical implication for clinical benefits (prophylactic or therapeutic) is enabled by any evidence of record.
Specifically, coding and non-coding sequence variations are cited as “having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 13” (claim 10), “a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by any of SEQ ID NOs:1-4” (claim 28) and “(I) (i)… a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 5; or (ii) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 9; or (iii) both (i) and (ii); or (II) (i) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 6; or (ii) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 10; or (iii) both (i) and (ii); or (III) (i) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 7; or (ii) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 11; or (iii) both (i) and (ii); or (IV) (i) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO: 8; or (ii) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by SEQ ID NO:12; or (iii) both (i) and (ii); or (V) an RNA molecule comprising a sequence with at least 80% sequence identity to the RNA sequence encoded by any of SEQ ID NOs: 1-4” (claim 33). The individual sequence variations and their combinations (e.g., SEQ ID NOs: 5, 9 and 13 are elements of SEQ ID NO: 1) are indefinite as the ranges encompass millions of possibilities, some of which are not expected to work at all, and the specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims. If the viability of virus strains could be established, the specific immune responses induced by these variants would be similar to the ones defined by SEQ ID NOs: 1-4.
Nature of the invention/Breadth of the claims. The claims are drawn to a composition of self-amplifying mRNA sequences encapsulated by lipid nanoparticles (LNPs), in a formulation suitable for monovalent and quadrivalent influenza vaccines. The target immunogens correspond to HA and NA polypeptides defined by SEQ ID NOs 5-12, although each chimeric mRNA also has other accessory sequences (5’ UTR, 3’ UTR and VEEV-derived sequence encoding four non-structural proteins) to facilitate mRNA transcription and amplification. In terms of broadest reasonable interpretation, the invention serves one main purpose: to combat seasonal influenza based on known viral sequences, especially four specific strains cited in claims 14-15 and grouped as “two from influenza A subtypes, H1N1 and H3N2, and two from influenza B subtypes, Victoria and Yamagata” (¶[00193]). Variant forms derived from these four strains are also claimed, but no specific sequences or functional correlates are provided.
State of the prior art/Predictability of the art. A peer-reviewed, non-patent literature published in October 2023 (Kackos et al. npj Vaccines volume 8, Article number 157) provided an example for the development of “seasonal quadrivalent mRNA vaccine” that “prevents and mitigates influenza infection” (title). “mRNA’s rapid, in vitro production makes it an appealing platform for influenza vaccination, and the success of SARS-CoV-2 mRNA vaccines in the clinic has encouraged the development of mRNA vaccines for other pathogens” (abstract). However, only “three types of influenza vaccine are currently available within the United States: inactivated influenza vaccines (IIV), live attenuated influenza vaccines (LAIV), and recombinant hemagglutinin (HA) protein subunit vaccines” (page 1, second paragraph below Introduction), although “preclinical studies of influenza mRNA vaccines targeting HA have been ongoing since as early as 2001” (page 6, first paragraph below DISCUSSION). Their teaching dealt with “immunogenicity and protective efficacy of a quadrivalent mRNA vaccine encoding HA from four seasonal influenza viruses, A/California/07/2009 (H1N1), A/Hong Kong/4801/2014 (H3N2), B/Brisbane/60/2008 (B-Victoria lineage), and B/Phuket/3073/2013 (B-Yamagata lineage)”, and “120 μg total dose of this quadrivalent mRNA vaccine induced robust antibody titers against each subtype that were commensurate with titers when each antigen was administered alone. Following A/California/04/2009 challenge, mice were fully protected from morbidity and mortality, even at doses as low as 1 μg of each antigen. Additionally, a single administration of 10 μg of quadrivalent mRNA was sufficient to prevent weight loss caused by A/California/04/2009” (abstract and Fig. 2 on page 3). Despite such promising data, cross protection against additional viral isolates in the same strain or lineage was not available, and “further investigation is needed to fully elucidate the effect of influenza mRNA vaccination on T cell response, and future studies of… quadrivalent mRNA vaccines should include this analysis” (page 8, first paragraph below Fig. 5). “Another marker of vaccine potency and efficacy that should be evaluated in subsequent quadrivalent influenza mRNA vaccine studies is longevity of the antibody response. Decline of…efficacy over time has been well-documented, even over the course of a single influenza season and is thought to correspond to waning antibody titers” (page 8, second paragraph on the left, below Fig. 5). None of these immunological and clinical parameters have been established for virus strains cited in claims 10, 28 and 33 of the instant application. Said another way, it is not predictable that the immunogens encompassed by the variants of these claims would provide protective or therapeutic effect clinically. Since the claims encompass variants that would lead to numerous peptide/immunogen mutations, it is not even predictable that the full scope of the claimed sequences would encode correct epitopes to induce protective or lasting immune responses.
In another prior art, Vogel et al. 2018 (Molecular Therapy 26(2): 446-455) evaluated the efficacy of “a trivalent RNA vaccine” against influenza infection in Balb/c mice. Following a prime-boost regime with a 3-week interval, mice immunized intramuscularly with 1.5 or 0.5 µg of three sa-RNA vaccines showed immune protection against seasonal H1N1 and B influenza, as gauged by body weight and viral load in the lung (Figure 4 on page 451). Further experiments with mice immunized with “1.5 µg Cal’09 H1N1 HA... formulated sa-RNA alone or a trivalent… sa-RNA vaccine containing 1.5 µg each of RNA encoding HA from A/California/07/2009 (H1N1), A/Hong Kong/1/68 (X31, H3N2) and B/Massachusetts/2/2012, those receiving the Cal’09 sa-RNA vaccine were protected against homologous challenge with “Cal’09 H1N1” viruses (Figure 5E) and “partially protected” against heterologous challenge with “X31 H3N2” viruses (Figure 5E), suggesting that cross-protection induced by sa-RNA is limited, as seen in natural infection: a mismatch between vaccine components and circulating H3N2 viruses in the 2015–2016 Northern Hemisphere flu season rendered the vaccination ineffective (Kackos et al., page 1, right column below Abstract). Indeed, when Bertholet Girardin et al. 2021 (PGPub 2021/0252133 A1, published 08/19/2021) tested “an immunogenic composition” of “self-replicating RNA molecules” that are “encapsulated in a lipid nanoparticle (LNP)” (¶[0131]), vaccination in mice did not lead to cross-reactive antibody responses” (¶¶[0410]-[0411]). This third reference further supports the conclusion above that vaccine immunogen variants would not necessarily yield functional or immunogenic variants to offer any utility in the clinic against heterologous virus strains. Overall, evidence from three references cited above consistently indicated that strain-specific immunity predominates after vaccination with mRNA vaccines encoding influenza HA and/or NA immunogens. Thus, a top priority in vaccination against seasonal influenza is a close match in sequence/antigen homology between virus strains chosen for vaccine formulation and circulating viruses that are prone to “genetic drift” and “immune escape” mutations (Kackos et al., page 1, second paragraph under INTRODUCTION).
Working examples. The disclosed working examples (e.g., FIG. 3, FIG. 4 and FIG. 5) first demonstrated the overall antibody (IgG) titers and binding affinities. Weight loss after vaccination (FIG. 6), immunogenicity versus tolerability (FIG. 7) and antigen- and strain-specific IgG titers (FIG. 7 to FIG. 9) were also assessed. Again, these experiments fell short of in vitro neutralization assays or in vivo viral challenges after vaccination, let alone the evaluation of clinically relevant outcome measures like T-cell immunity, virus load, transmission rate, survival and other parameters taught and recommended by Kackos et al.
Guidance in the specification. The invention focused on the design of mRNA compositions (FIG. 1, FIG. 2 and ¶¶[0057]-[00191]), the choice of ionizable lipids (¶¶[00194]-[00196]), lipid formulations/LNPs and related procedures ((¶¶[00197]-[00284]), antibody (IgG) titers and binding affinities (FIG. 3, FIG. 4 and FIG. 5), as well as methods for inducing immune responses ((¶¶[00293]-[00315]). The final product/formulation “is frozen during storage and thawed prior to administration. In some embodiments, the suspension is frozen at a temperature below about 70°C. In some embodiments, the suspension is diluted with sterile water during intravenous administration. In some embodiments, intravenous administration comprises diluting the suspension with about 2 volumes to about 6 volumes of sterile water. In some embodiments, the suspension comprises about 0.1 mg to about 3.0 mg RNA/mL, about 15 mg/mL to about 25 mg/mL of an ionizable cationic lipid, about 0.5 mg/mL to about 2.5 mg/mL of a PEG-lipid, about 1.8 mg/mL to about 3.5 mg/mL of a helper lipid, about 4.5 mg/mL to about 7.5 mg/mL of a cholesterol, about 7 mg/mL to about 15 mg/mL of a buffer, about 2. 0 mg/mL to about 4. 0 mg/mL of NaCl, about 70 mg/mL to about 110 mg/mL of sucrose, and about 50 mg/mL to about 70 mg/mL of glycerol. In some embodiments, a lyophilized RNA-lipid nanoparticle formulation can be resuspended in a buffer” (¶[00302]). “In some embodiments, the compositions… are administered to a subject such that a RNA concentration of at least about 0.05 mg/kg, at least about 0.1 mg/kg, at least about 0.5 mg/kg, at least about 1.0 mg/kg, at least about 2.0 mg/kg, at least about 3.0 mg/kg, at least about 4.0 mg/kg, at least about 5.0 mg/kg of body weight is administered in a single dose or as part of single treatment cycle. In some embodiments, the compositions of the disclosure are administered to a subject such that a total amount of at least about 0.1 mg, at least about 0.5 mg, at least about 1.0 mg, at least about 2.0 mg, at least about 3.0 mg, at least about 4.0 mg, at least about 5.0 mg, at least about 6.0 mg, at least about 7.0 mg, at least about 8.0 mg, at least about 9.0 mg, at least about 10 mg, at least about 15 mg, at least about 20 mg, at least about 25 mg, at least about 30 mg, at least about 35 mg, at least about 40 mg, at least about 45 mg, at least about 50 mg, at least about 55 mg, at least about 60 mg, at least about 65 mg, at least about 70 mg, at least about 75 mg, at least about 80 mg, at least about 85 mg, at least about 90 mg, at least about 95 mg, at least about 100 mg, at least about 105 mg, at least about 110 mg, at least about 115 mg, at least about 120 mg, or at least about 125 mg RNA is administered in one or more doses up to a maximum dose of about 300 mg, about 350 mg, about 400 mg, about 450 mg, or about 500 mg RNA” (¶[00303]). The specification goes on to recommend administration for “one time” or “may be administered two times” (¶¶[00312]-[00313]) or “can be administered one, two, three, four, five, six, seven, eight, nine, ten, or more times. Timing between two or more administrations can be one week, two weeks, three weeks, four weeks, five weeks, six weeks, seven weeks, eight weeks, nine weeks, weeks, ten weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, 45 weeks, 46 weeks, 47 weeks, 48 weeks, 49 weeks, 50 weeks, 51 weeks, 52 weeks, or more weeks, and any number or range in between” (¶[00309]). “In some aspects, timing between two or more administrations is one month, two months, three months, four months, five months, six months, seven months, eight months, nine months, ten months, 11 months, 12 months, 13 months, 14 months, 15 months, 16 months, 17 months, 18 months, 19 months, 20 months, 21 months, 22 months, 23 months, 24 months, or more months, and any number or range in between. In other aspects, timing between two or more administrations can be one year, two years, three years, four years, five years, six years, seven years, eight years, nine years, ten years, or more years, and any number or range in between” (¶[00309]). Such broad range of dosage and timing interval alone renders the invention practically unconvincing.
Amount of experimentation necessary. As taught by Kackos et al. 2023, effort toward a quadrivalent vaccine against seasonal influenza must fully demonstrate strain-specific immunological correlates and clinical efficacy in terms of prophylactic and therapeutic outcomes, which are lacking in or absent from the instant application. Kackos et al. further noted that “mice were vaccinated with HA for multiple influenza subtypes”, but “only CA09 was chosen for challenge as other mouse-adapted virus stocks were not available” (page 8, first paragraph on the right, below Fig. 5), suggesting that preclinical murine models are not readily available for assessing strain-specific outcome measures. Thus, experimentation with virus challenge not only incurs technical hurdles but also depends on the availability of preclinical models, so the amount of work for testing efficacy against each virus strain is quite burdensome even for skilled artisans in the field.
Although actual clinical data are not necessarily required to establish enablement (see MPEP §2164.02), the specification must nonetheless provide sufficient guidance and representative examples to enable a person of ordinary skill in the art to practice the full scope of the claims. Under MPEP §2164.01(a), the specification must enable the full scope of the claimed invention. However, for the reasons discussed above, it would require undue experimentation for a skilled artisan to use the claimed compositions and methods, especially in terms of virus variants/isolates, proper formulation, dosage, delivery mode and quantifiable readouts for in vitro and in vivo tests. In view of the breadth of the claims for the spectrum of virus strains/variations, the limited guidance in the specification, and the unpredictability of the art, a person of ordinary skill would be required to undertake extensive experimentation to determine prophylactic and therapeutic efficacy in preclinical and clinical systems. Such experimentation would require a research program rather than routine optimization (see MPEP §2164.03). Thus, claims 10, 28 and 33 in the instant application are clearly not enabled for their full scope of invention under 35 U.S.C. §112(a).
Claim Rejections under 35 U.S.C. §101
35 U.S.C. §101 reads as the following:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4, 12 and 14-15 are rejected under 35 U.S.C. §101 because they are directed to naturally-occurring elements that are not patent-eligible pursuant to the Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc., -- U.S.-- (June 13, 2013) (hereafter “Myriad”).
For an analysis of claims 1-4, 12 and 14-15 as a whole, the invention is drawn to a composition of matter (Step 1), and its elements are directed to judicial exceptions: in this case (Step 2A-Prong One), the subject matter is RNA molecules from four natural strains/isolates of influenza virus (claim 3) named as H1N1, H3N2, Victoria-B, and Yamagata-B (claim 14 and ¶[00129]), and they represent two known virus subtypes (A and B), with four specific variant forms cited in claim 15. According to Carascal et al. 2022. (Front. Immunol. 13: 878943), the A and B subtypes contain eight RNA gene segments, including HA and NA that are labeled as gene 4 and gene 6, respectively, as shown in their FIGURE 1 (cited on page 3, second paragraph on the left; also pasted below). These genes correspond to HA and NA cited in claims 1-2 and 12 of the instant application.
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FIGURE 1 from Carascal et al. 2022 (page 3).
Combining any of the viral RNA from four different virus strains (as in claim 1b) at “an equimolar ratio” (claim 4) does not do anything to change the structure or function for any of the RNA molecules individually. Furthermore, there is no function given to the composition as a whole that is different from the individual components in claim 1 as broadly as currently recited. As for claim 12, the protein/polypeptide encoded by HA and NA genes are known as “major surface antigens” that serve as immune targets (immunogens) for host immune responses (Carascal et al., page 13, last paragraph on the left), with HA being “the current standard target in influenza vaccine development” (page 12, second paragraph on the right). By definition, influenza viruses and their variants all inherently possess RNA genomes and associated protein products in order to retain functionality as infective virus particles, and such natural elements are the basis of natural immunity after infection, as taught by Carascal et al. (page 2, first paragraph on the left). Overall, as RNA compositions, none of the limitations cited in claims 1-4, 12 and 14-15 alter the structure or function of the naturally existing viral RNA molecules or their corresponding proteins/peptides possessed by natural influenza virus subtypes and strains. Thus, Step 2A-Prong One here establishes that the subject matter of claims 1-4, 12 and 14-15 is directed to one of four natural influenza virus strains and their inherent RNA sequences or protein products present on virus particles, with frequent variations that result from antigenic drift. Since the claims are product claims, they are not incorporated into a practical application as there are no application steps at all. Also, since there is no claim element that is beyond the judicial exception(s), no claim element prevents monopoly of the said exception(s).
Further, in view of Step 2B above, claims 1-4, 12 and 14-15 do not recite additional elements that amount to significantly more than the judicial exception, because even the variant forms and protein subunits (as immunogens) are also part of nature, and each of them serves the same coherent function as seen in natural infection or when applied to any practical application, including vaccine formulations (the basis of inactivated or attenuated vaccines). Consideration of all elements as a combination also fails to add other meaningful limitations to the exception not already present when the elements are considered separately. Indeed, Carascal et al. 2022 also taught that virus strains are abundant in natural forms, as influenza immunogens like HA possess inherent plasticity due to antigenic drift (page 9, first paragraph on the left). Thus, claims 1-4, 12 and 14-15 do not invoke any of the considerations that courts have identified as providing significantly more than the exceptions of natural products: even when viewed as a combination of natural matter with one or more components or variants thereof, the invention does not provide any structural or functional features to qualify as a patentably eligible application. Accordingly, the invention of claims 1-4, 12 and 14-15 as a whole does not amount to significantly more than an exception of natural matter, and these claims are directed to a non-statutory subject matter under 35 U.S.C. §101 in view of the Subject Matter Eligibility Test for Compositions of Matter.
Claim Rejection under 35 USC §102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. §102 that form the basis for the rejection under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim 33 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jasny et al. 2021 (PGPub 20210162037 A1, published 06/03/2021).
Jasny et al. 2021 taught the use “mRNA sequences” as “vaccines against infections with influenza viruses”, along with “the preparation of a pharmaceutical composition” for “prophylaxis or treatment of influenza virus infections” (abstract). Their SEQ ID NOs 182971, 178798, 178794, 182894, 181058, 165705, 164425, and 180649, which have 94.3%, 93.6%, 95.5%, 95.8%, 94.2%, 92.3%, 94.5% and 96.0% identity with SEQ ID NOs 5, 6, 7, 8, 9, 10, 11, and 12, respectively, in claim 33 of the instant application, are NA and HA gene variants (FIG. 1-4 and ¶[0138]), with corresponding ranges of sequence identifiers that include all SEQ ID NOs above and labelled as “a preferred embodiment” for their invention (¶[0138]). Claim 77 in Jasny et al (on page 66) further disclosed “a pharmaceutical composition comprising at least one mRNA encoding an influenza virus hemagglutinin (HA) protein, or an antigenic fragment thereof, and at least one mRNA encoding an influenza neuraminidase (NA) protein, or an antigenic fragment thereof.” In other words, the compositions of SEQ ID NOs 5, 6, 7, 8, 9, 10, 11, and 12 in the instant application are fully anticipated by Jasny et al. at the sequence identity level between 92.3% and 96.0%, all exceeding the 80% identity cited in claim 33. Thus, the invention of claim 33 was anticipated by a single prior art before the time of invention.
Claim 54 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bertholet Girardin et al. 2021 (PGPub 2021/0252133 A1, published 08/19/2021)).
Bertholet Girardin et al. 2021 taught the use of “immunogenic or pharmaceutical compositions comprising self-replicating RNA molecules that encode influenza virus antigens for treating and/or preventing influenza infections” (abstract), and their “pharmaceutical composition (such as a vaccine composition)… comprises or consists of (i) from 3 to 10 self-replicating RNA molecules wherein each self-replicating RNA molecule encodes a polypeptide comprising an antigen from influenza virus, wherein each antigen is from a different strain of influenza virus to the other antigens and wherein the self-replicating RNA molecules are formulated in lipid nanoparticles (LNP), (iii) a pharmaceutical carrier, diluent and/or buffer”(¶[0325]). “A liposome encapsulating an RNA comprises the following steps: (a) mixing (i) a first solution comprising a solvent, an ionizable cationic lipid, a zwitterionic lipid, a sterol, and a PEGylated lipid selected; and (ii) a second solution comprising water and the RNA; and (b) removing the solvent.” Alternatively, “an ethanol dilution process was used to produce the LNP formulation with the following molar ratios of lipid components: DSPC: cholesterol: PEGDMG 2000: DLinDMA 10:48:2:40 molar percent. An 8:1 N:P molar ratio (nitrogen on DlinDMA to phosphate on RNA) and 100 mM citrate buffer (pH 6) were used for the formulations” (¶[0401]). Apart from the use of an ionizable cationic lipid, N:P ratio at 8:1 in the final composition matches the upper end “of about 5:1 to about 7:1” cited in claim 54 of the instant application.
Regarding lengths of polynucleotides, Bertholet Girardin’s “self-amplifying mRNA molecule” had “a chimeric replicon without insert” consisting of 9993 nucleotides (SEQ ID NO: 2 in ¶[0041] and on pages 37-38); their H1N1-derived HA insert (SEQ ID NO: 3 on page 39) had another 1704 nucleotides. Together, their mRNA replicon with a single HA insert added up to 11697 nucleotides total, which is within “a length of about 5,000 to about 20,000 nucleotides” cited in claim 54. Moreover, the HA antigen in Bertholet Girardin’s design (Figure 1a) had HA nucleotides from two virus strains “selected from seasonal strains of type H1 or H3, or pandemic strains… such as H5 or H7” (¶[0071]). Their “H3N2 (A/Bilthoven)” sequence has 1784 nucleotides (SEQ ID NO: 7 on page 40), which is slightly (80-nucleotides) longer than their H1N1-derived HA insert (SEQ ID NO: 3 on page 39). Thus, size variations in the mRNA transcripts before LNP encapsulation are dictated by the origin of each HA insert itself and by the number of inserts in each immunogenic composition, as taught by Bertholet Girardin et al., so the limitations of claim 54 in the instant application are met by a single reference – as an anticipation of Bertholet Girardin et al., before the invention of claim 54 was filed.
Claim Rejections under 35 USC §103
The following is a quotation of 35 U.S.C. §103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. §103 are summarized as the following:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-5, 11-12, 14-16, 21, 27, 29-30, 46, 51-52 and 54 are rejected under USC §103 as being unpatentable over Bertholet Girardin et al. 2021 (PGPub 2021/0252133 A1, published 08/19/2021) in view of Jasny et al. 2021 (PGPub 20210162037 A1, published 06/03/2021).
Bertholet Girardin et al. 2021 taught “pharmaceutical compositions comprising self-replicating RNA molecules that encode influenza virus antigens for treating and/or preventing influenza infections” (abstract), and their “vaccine composition… comprises or consists of (i) from 3 to 10 self-replicating RNA molecules wherein each self-replicating RNA molecule encodes a polypeptide comprising an antigen from influenza virus, wherein each antigen is from a different strain of influenza virus to the other antigens and wherein the self-replicating RNA molecules are formulated in lipid nanoparticles(LNP), (iii) a pharmaceutical carrier, diluent and/or buffer”(¶[0325]). Using “monocistronic… and bicistronic replicons” based on “TC83 alphavirus vector” comprising of “VEE/SINV (Venezuelan equine encephalitis-Sindbis virus) chimeric replicon containing T7 DNA polymerase promoter” (¶[0406]), each of their self-replicating mRNA had a chimeric sequence consisting of an “nsPs” replicase region, a subgenomic promoter (SGP) placed before a fusion sequence encoding two units of haemagglutinin (HA) antigens from H5 and H1 virus strains, followed by a 3’ untranslated region (3’UTR) (Figure 1a and Figure 6, pasted below). A self-cleavage sequence (2A) was placed between HA genes from two virus strains (H5 and H1) to facilitate peptide cleavage (Figure 1a and ¶[0015]). Bertholet Girardin also named other alternatives of the “alphavirus-based replicon” as “a replicase from a Sindbis virus, a Semliki forest virus, an eastern equine encephalitis virus, a Venezuelan equine encephalitis virus, etc.” (¶[0025], and “each self-replicating RNA molecule… encodes (i) a RNA-dependent RNA polymerase which can transcribe RNA from the self-replicating RNA molecule and (ii) a polypeptide comprising an antigen from influenza virus. The polymerase can be an alphavirus replicase, e.g. comprising one or more of alphavirus proteins nsP1, nsP2, nsP3 and nsP4” (¶[0026]) (also shown in Figure 6). “The self-replicating RNA can conveniently be prepared by in vitro transcription (IVT). IVT can use a (cDNA) template created and propagated in plasmid form in bacteria, or created synthetically… For instance, a DNA-dependent RNA polymerase (such as the bacteriophage T7, T3 or SP6 RNA polymerases)” (¶[0033]) (also cited in ¶[0387] and Figure 6).
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Figure 6 from Bertholet Girardin et al. 2021. Arrows point to key elements of a cloning vector (TC83) for IVT.
Self-amplifying mRNA (SAM replicon) molecules in Bertholet Girardin et al. included “bi-cistronic SAM (H5-H1)” and “monomeric HA” controlled by a subgenomic promoter (SGP) (Figure 1 and ¶[0015]). “An ethanol dilution process was used to produce the LNP formulation with the following molar ratios of lipid components: DSPC: cholesterol: PEGDMG 2000: DLinDMA 10:48:2:40 molar percent. An 8:1 N:P molar ratio (nitrogen on DlinDMA to phosphate on RNA) and 100 mM citrate buffer (pH 6) were used for the formulations” (¶[0401]). For multivalent compositions, “equal amount of RNAs were mixed prior to encapsulation in LNPs (¶[0401]), and self-amplification efficiency of RNA was first measured by quantitative detection of the intracellular dsRNA in BHK cells and then verified by flow cytometric analysis of protein analytes (¶[0406]). When “Balb/c mice were vaccinated i.m. twice, 3 weeks apart,” “SAM(H1)+SAM(H5)/LNP candidate vaccines” induced immune responses “comparable to monocistronic SAM(H1-Cal) or SAM(H5-turkey)” (FIG. 2a & 2b and ¶[0410]). However, “cross-reactive antibodies against antigenically distant heterologous strains A/PR/8/1934 (H1N1) and A/Perth/16/2009 (H3N2) were not detected after two doses of bicistronic SAM(H5-H1) or monocistronic SAM(H1-Cal), SAM(H5-turkey) or combinations of SAM(H1)-SAM(H5) vaccines” (¶¶[0410]-[0411]), suggesting that strain-specific immunity predominates. These teachings established the DNA template for IVT (¶[0387 and Figure 6]) and methods for preparing mRNA-LNP compositions (products), including the use of ionizable cationic lipids in LNP (¶[0318]), as well as N:P ratio at 8:1 in the final composition (¶[0401]); they also taught a clear incentive for multivalent (combination) vaccines against different influenza virus strains (e.g., H5 and H1 in Figure 1a), because “available flu vaccines are strain-specific and provide protection against only vaccine strain viruses” (¶[0003]), and “new approaches need to be developed to… provide vaccines that show protection against multiple strains and/or subtypes of influenza virus” (¶[004]). They indeed taught “vaccination with a cocktail of SAM vectors expressing HA of H3, H1, H5 and H7 influenza subtypes (Example 5, ¶¶[0413]-[0417]), noting further that H1N1 and H3N2 strains are subtype A, while Victoria and Yamagata lineages belong to subtype B (¶[0051]).
Bertholet Girardin et al. also taught that their “self-replicating RNA molecules… may encode an influenza antigen from any type (A-type, B-type, C-type) and any subtype (H1 to H18 and N1 to N11) of influenza viruses, or immunogenic fragments or variants thereof” (¶[0050]), including virus strains like A/Fujian/411/2002, A/Brisbane/10/2007, A/Texas/50/2012 (H3N2), A/turkey/Turkey/1/2005 (H5N1) and A/California/07/2009, A/PR/8/1934 (H1N1) ([0417]).
However, Bertholet Girardin et al. fell short of teaching self-replicating mRNA molecules that encode HA and NA variants in a 5’-3’ orientation (chimeric/fusion sequence), with additional accessory components like 5’ UTR. These deficiencies are overcome by Jasny et al. 2021, as they taught “mRNA sequences” as “vaccines against infections with influenza viruses”, along with “the preparation of a pharmaceutical composition” for “prophylaxis or treatment of influenza virus infections” (abstract), noting that “mRNA-based vaccines comprising mRNA sequences encoding different antigens of an influenza virus (particularly hemagglutinin (HA) and neuraminidase (NA)) were extremely effective in inducing an antigen-specific immune response against influenza virus” (¶[0103]) and that “mRNA sequences encoding different antigens of different influenza viruses can be effectively combined in one mRNA-based vaccine” (¶[0104]). Their “preferred embodiments” for “a coding region” encoded “at least one full-length protein of hemagglutinin (HA), and/or at least one full-length protein of neuraminidase (NA) of an influenza virus or a variant” (¶[0109]), resulting in “a pharmaceutical composition comprising at least one mRNA encoding an influenza virus hemagglutinin (HA) protein, or an antigenic fragment thereof, and at least one mRNA encoding an influenza neuraminidase (NA) protein, or an antigenic fragment thereof” (claim 77 on page 66). Following successful preclinical evaluations in mice (¶¶[0664]-[0680]) and non-human primates (¶[0681]), a clinical trial included “an mRNA composition comprising four HA and three NA influenza antigens (septivalent HA+NA) or with an mRNA composition comprising multiple HA and multiple NA influenza antigens (multivalent HA + NA) (¶[0686]), along with other monovalent and multivalent designs with LNP formulations (TABLE 18 through TABLE 20 on pages 65-66), because such polyvalent vaccines “comprising multiple RNA sequences encoding multiple different antigens of multiple different influenza viruses” are “particularly advantageous for a universal, broadly protecting influenza/flu vaccine” (¶[0104]).
Jasny et al. also taught the use of various accessory components in an RNA molecule (claim 85 on page 66), including “5’-CAP structure”, “a 5'-UTR element”, “a 3'-UTR element” and “a poly(A) sequence of about 25 to about 400 adenosines…” “A 5'-UTR is typically understood to be a particular section of messenger RNA (mRNA). It is located 5' of the open reading frame of the mRNA. Typically, the 5'-UTR starts with the transcriptional start site and ends one nucleotide before the start codon of the open reading frame.” (¶[0072]). “Preferably, the 5'-UTR corresponds to the sequence which extends from a nucleotide located 3' to the 5'-cap” (¶[0072]). “A 3'-UTR is typically the part of an mRNA which is located between the protein coding region (i.e. the open reading frame, coding sequence)… and the poly(A) sequence of the mRNA” (¶[0071]).
To develop an influenza vaccine with one or more mRNA molecules that encode NA and HA antigens in a 5’-3’ orientation and capable of inducing immune responses to NA and HA immunogens derived from different influenza virus strains, a skilled artisan could adopt the RNA structure of H5 + H1 in Bertholet Girardin et al. 2021 (Figure 1b) and then use the HA + NA format/concept taught by Jasny et al. 2021 (TABLE 20 on page 66) to readily arrive at one or more mRNA composition capable of inducing NA- and HA-specific immune responses, as taught by both references. The target virus strains can come from both references, and Bertholet Girardin’s composition alone already had “3 to 10 self-replicating RNA molecules wherein each self-replicating RNA molecule encodes a polypeptide comprising an antigen from influenza virus, wherein each antigen is from a different strain of influenza virus to the other antigens (¶[0325]). According to Bertholet Girardin, the choice of influenza virus strains can be any combinations of types and subtypes (¶[0050]), so targeting four virus strains using RNA molecules encoding NA and HA was an obvious option. There would be reasonable success in making the RNA composition, as having two viral antigens in one RNA was a known art (Bertholet Girardin, Figure 1a), while the 5’-3’ orientation of instant claim 1 is just one of two choices when NA and HA are chosen as the target immunogens. The virus strains taught by both references are more than four. Taken together, it would have been obvious for each RNA in the obvious composition to encode an NA and HA from one influenza virus and to combine multiple such RNAs that encode the same antigens of 2, 3, 4, or more virus strains into one composition for the advantages stated in the prior art above. Thus, the limitations of claims 1-3 are rendered obvious by two references, as an application of rationale B of MPEP 2143: Simple substitution of one known element (an HA of the primary reference for an NA of the secondar reference, both form the same virus) for another to obtain predictable results with reasonable expectation of success. The motivation for including NA and HA antigens from multiple (e.g., four or more) virus strains is also obvious: to induce immune responses broad enough to cover single or multiple viruses circulating in a host population, thereby improving the chance of immune protection. Indeed, traditional influenza vaccines have taught the same motivation for broadening immune responses: “for 2015-16, U.S.-licensed trivalent influenza vaccines contain hemagglutinin (HA) derived from an A/California/July/2009 (H1N1)-like virus, an A/Switzerland/9715293/2013 (H3N2)-like virus, and a B/Phuket/3073/2013-like (Yamagata lineage) virus. Quadrivalent influenza vaccines contain these vaccine viruses, and a B/Brisbane/60/2008-like (Victoria lineage) virus” (Jasny et al., [¶0004]).
Once the RNA molecules encoding NA and HA antigens from different virus strains are made using the collective teachings of two references discussed supra, following the teaching of Jansy et al. (e.g., TABLE 16) would allow the formulation of polyvalent RNA vaccines targeting different virus strains, as they taught the use of “Septavalent HA + NA” vaccine for intramuscular (i.m.) injection in human subjects (70 µg total mRNA in a 500 µl dose), and their mRNA species are mixed at an equimolar ratio (“each mRNA represented equally in the composition”) (Table 16). Thus, the limitations of claim 4 are also met by Jasny and Bertholet Girardin. Also, doses are result effective variables as they affect amplitude of immune response in this case and so each dose and ratio between any and all immunogens will be arrived at by routine experimentation.
Coming to claims 5, 11-12, 14-15 and 27, Bertholet Girardin taught the use of alphavirus-derived non-structural proteins (nsPs) as a replicase that drives RNA amplification (Figure 1a and Figure 6), and they also placed the sequence encoding nsPs before a subgenomic promoter (Figure 1a) to ensure the amplification of downstream RNA encoding NA and HA antigens (5’-3’ orientation) for different influenza virus strains. Moreover, their “self-replicating RNA molecules… may encode an influenza antigen from any type (A-type, B-type, C-type) and any subtype (H1 to H18 and N1 to N11) of influenza viruses, or immunogenic fragments or variants thereof” (¶[0050]). Thus, it would have been obvious that all the mRNAs obvious above could have had one or more nsPs required for mRNA replication fused to the encoding sequences for HA and NA. This would make them self-replicating and, on the protein level, cleavage sites as discussed above could be used to separate replicase (for example), NA and HA. This would have been obvious before the filing of the instant application as a mere use of known prior art elements to arrive at predictable results. The subgenomic promoter could be used rather than second cleavage cite between the replicase encoder and the HA and NA encoding sequences. Jasny et al. further taught the use of myriad nucleotide sequences encoding full-length or partial NA and HA immunogens derived from various influenza virus strains, including type A and type B (e.g., TABLE 16). Validation of virus-specific antibody and T-cells in vaccine recipients, as taught by both references (Figure 2 through Figure 4 in Bertholet Girardin et al. and FIG. 5 through FIG. 22 in Jasny et al.), confirmed the presence of antigenic fragments derived from NA and HA immunogens. Thus, sequences encoding such HA and NA peptides as in instant claim 12 were known in the prior art and would have been obvious to use in the obvious constructs above to arrive at predictable results, an immunogenic response against influenza strains. Such sequences such as full length sequences of NA and HA from each virus strain targeted would have been obvious here. Moreover, “B/Phuket/3073/2013” in Jasny et al. 2021 (TABLE 8 and TABLE 16) was the “Yamagata B/PHUKET/3073/2013” virus cited in claims 14-15 of the instant application. The choice of other influenza virus strains could readily come from the teachings of both references. These would be obvious choices from which to derive the full-length HA and NA encoding sequences above for use in the obvious mRNA composition for the advantage of creating a composition that stimulated immunity against said strains.
Regarding claims 16 and 21, Jasny et al. taught the use of “a 5'-UTR element”, “a 3'-UTR element” and other accessory components in RNA molecules encoding NA and HA immunogens from influenza viruses (claims 79-85 on page 66); their 5'-UTR “is located 5' of the open reading frame of the mRNA”, which “starts with the transcriptional start site and ends one nucleotide before the start codon of the open reading frame” (¶[0072]) and “extends from a nucleotide located 3' to the 5'-cap” (¶[0072]). Their “3'-UTR is typically the part of an mRNA which is located between the protein coding region (i.e. the open reading frame, coding sequence)… and the poly(A) sequence of the mRNA” (¶[0071]).
As for claims 29-30, mRNA production through IVT requires a DNA composition with 5’ UTR and T7 promoter, which are taught by Bertholet Girardin et al (Figure 6). “The process of manufacturing a self-replicating RNA comprises a step of IVT to produce a RNA”(¶[0387]), which is facilitated by “a DNA-dependent RNA polymerase (such as the bacteriophage T7, T3 or SP6 RNA polymerases)” (¶[0033] and Figure 6).
Regarding claims 46 and 51, the use of ionizable cationic lipid and choice of N:P ratio are also taught by Bertholet Girardin. Their “methods of manufacturing a non-viral delivery system comprising a liposome encapsulating an RNA comprise the following steps: (a) mixing (i) a first solution comprising a solvent, an ionizable cationic lipid, a zwitterionic lipid, a sterol, and a PEGylated lipid selected; and (ii) a second solution comprising water and the RNA; and (b) removing the solvent” (¶[0318]). For “LNP/RNA formulation”, “equal amount of RNAs were mixed prior to encapsulation in LNPs” (¶[0401]). “An ethanol dilution process was used to produce the LNP formulation with the following molar ratios of lipid components: DSPC: cholesterol: PEGDMG 2000: DLinDMA 10:48:2:40 molar percent. An 8:1 N:P molar ratio (nitrogen on DlinDMA to phosphate on RNA) and 100 mM citrate buffer (pH 6) were used for the formulations” (¶[0401]). Accordingly to Jasny et al., “the nitrogen/phosphate (N/P) ratio of mRNA or nucleic acid to cationic or polycationic compound” may vary “in the range of about 0.1-10, preferably in a range of about 0.3-4 or 0.3-1, and most preferably in a range of about 0.5-1 or 0.7-1” (¶[0472]). Thus, both references taught the use of ionizable cationic lipid in the RNA-LNP composition, and the N:P (N/P) ratio taught by these references ranges from 0.1-10, meeting the limitations of claims 46 and 51.
For claim 52, “immunogenic or pharmaceutical compositions comprising self-replicating RNA molecules” taught by Bertholet Girardin et al. “encode influenza virus antigens for treating and/or preventing influenza” (abstract), while “mRNA sequences” taught by Jasny et al. are “usable as mRNA-based vaccines against infections with influenza viruses” (abstract). Bertholet Girardin’s method was for “prevention and/or treatment against influenza disease, comprising the administration of the immunogenic composition or pharmaceutical composition… to a person in need thereof" (¶[0010]. Jasny taught “methods of treating or preventing influenza virus infections or disorders related thereto… by administering to a subject in need thereof a pharmaceutically effective amount of the mRNA sequence, the (pharmaceutical) composition or the vaccine according to the invention. Such a method typically comprises an optional first step of preparing the mRNA sequence, the composition or the vaccine of the present invention, and a second step, comprising administering (a pharmaceutically effective amount of) said composition or vaccine to a patient/subject in need thereof” (¶[0531]). Thus, vaccinating a subject against influenza virus using the composition from claim 1 of the instant application is an intended use that is rendered obvious by methods from the two references.
For a skilled artisan, arriving at the main invention of claims 1-5 and 27 for a self-replicating RNA vaccine capable of inducing NA- and HA-specific immune responses would involve the following steps. First, starting with Figure 1a and Figure 6 of Bertholet Girardin et al. 2021 would yield a framework for self-replicating mRNA, including a replicase portion (nsP1-nsP4), a subgenomic promoter (SGP, the equivalent of sgP cited in claim 11) at the 5’ end. Second, to expand the antigenic coverage for each targeted virus strain, the first sequence after SGP is replaced by an NA gene fragment taught by Jasny et al. (depending on the virus strains of interest). Third, the HA sequence (labeled as H1 for the H1N1 virus in Figure 1a) and a 3’ UTR sequence stay put at the 3’ end. Fourth, the joint mRNA design from the first three steps still needs a DNA template (a vector) for IVT production of self-replicating mRNA, so regulatory sequences for 5’ UTR and a T7 promoter are added at the 5’ end of a DNA template (Figure 6 in Bertholet Girardin et al.) to ensure the IVT orientation and efficiency of mRNA transcription, as taught by Bertholet Girardin et al. Fifth, in vitro transcribed self-replicating mRNA encoding NA and HA immunogens is encapsulated in LNP separately or jointly, with the latter leading to a multivalent formulation that covers four virus strains (two each for subtype A and subtype B viruses), as taught by Bertholet Girardin et al. and Jasny et al.. After administration to a subject (mouse, non-human primate or human in Jasny et al. 2021), immune responses to NA and HA antigens (translated in vivo from self-replicating mRNA) generate HA- and NA-specific immunity that can be quantified by immunoassays, as taught by Jasny et al. 2021 ( ¶¶[628]-[0631]). Thus, the structural and functional elements as cited above effectively meet the limitations of claims 1-5 and 27.
As discussed supra, other limitations cited in claims 11-12, 14-16, 21, 29-30, 46 and 51-52 are also met by the collective teachings of Bertholet Girardin and Jasny. A skilled artisan would have a reasonable success in the design, manufacture and practical use of self-replicating mRNA encoding NA and HA immunogens derived from four influenza virus strains, because DNA vectors for genetic engineering and in vitro transcription kits are readily available and taught in sufficient detail by Bertholet Girardin et al. 2021. The RNA-LNP composition and formulation in a mixture (multivalent vaccine) could also follow the collective teachings of Bertholet Girardin et al. and Jasny et al. to ensure adequate coverage of virus types/subtypes (A and B) or their specific lineages/strains. The methods of use (immunization) and detection of antigen-specific immune responses are taught by the two references as well. Thus, the invention of claims 1-5, 11-12, 14-16, 21, 27, 29-30, 46 and 51-52 as a whole was rendered prima facie obvious by two complementary references that predated the filing of the invention, as an example of Rationale B of MPEP §2143: Simple substitution of one known element for another to obtain predictable results with reasonable success.
With respect to claim 54, the indefiniteness of about is discussed supra and so the obvious self-replicating mRNA-encoding plasmids/DNAs above meet limitation i). The other limitations of this claim are obvious options as discussed supra in the obvious composition and so claim 54 is obvious here also for the reasons supra.
Claims 10 and 25 are rejected under USC §103 as being unpatentable over Bertholet Girardin et al. 2021 (supra) and Jasny et al. 2021 (supra) as applied to claims 1-5, 11-12, 14-15, 27, 29-30, 46 and 51-52, further in view of Sullivan et al. 2021 (PGPub 20210290756 A1, published 09/23/2021).
For limitations and reasons discussed supra, Bertholet Girardin et al. and Jasny et al. rendered the invention of claims 1-5, 11-12, 14-16, 21, 27, 29-30, 46 and 51-52 obvious in terms of making and using RNA-LNP compositions capable of inducing immune responses against NA- and HA-specific immunogens derived from one or more influenza virus strains, including “Yamagata B/PHUKET/3073/2013” and others known in prior art. Bertholet Girardin et al. also taught the use of “a replicase from a Sindbis virus, a Semliki forest virus, an eastern equine encephalitis virus, a Venezuelan equine encephalitis virus, etc.” (¶[0025], which comprises “one or more of alphavirus proteins nsP1, nsP2, nsP3 and nsP4” (¶[0026]) (also shown in Figure 6), but neither Bertholet Girardin nor Jasny provided a nucleotide sequence matching SEQ ID NO: 13 that encodes nsP1-4 (cited in claim 10) or SEQ ID NO: 15 for a 3’ UTR (cited in claim 25). These deficiencies are overcome by Sullivan et al. 2021, as their SEQ ID NO: 50 and SEQ ID NO: 53 had 94.7% and 100% match with SEQ ID NO: 13 and SEQ ID NO: 15, respectively, from the instant application. nsP1 through nsP4 in Sullivan et al. were labeled as “VEEV replicase genes” (FIG. 1A) derived from Venezuelan equine encephalitis virus, which is consistent with the teaching of Bertholet Girardin (¶[0025]. The compositions in Sullivan et al. 2021 “include nucleic acid molecules encoding viral replication and antigenic proteins, and lipids” (abstract) that “are useful for inducing immune responses” (abstract), sharing a common goal (nucleic acid-based vaccine composition) with claims 10 and 25 in the instant application.
A skilled artisan could readily substitute the nsP1-4 and 3’ UTR sequence in Bertholet Girardin et al. with the corresponding sequences from Sullivan et al. 2021 for an influenza vaccine based on RNA-LNP composition, because nsP1-4 and 3’ UTR are essential elements in self-replicating RNA, as taught by Bertholet Girardin et al. (labeled as nsPs and 3’UTR in Figure 1a; as nsP1-nsP4 and 3’UTR in Figure 6). The choice of VEEV sequence and its variants was also made obvious by Bertholet Girardin: “mutant or wild-type virus sequences can be used, e.g. the attenuated TC83 mutant of VEEV has been used in replicons” (¶[0025]). Thus, the invention of claims 10 and 25 as a whole is rendered obvious by three references before the time of invention: as another example of Rationale B of MPEP 2143.
Claim 20 is rejected under USC §103 as being unpatentable over Bertholet Girardin et al. 2021 (supra) and Jasny et al. 2021 (supra) as applied to the rejection of claims 1-5, 11-12, 14-16, 21, 27, 29-30, 46 and 51-52, further in view of Chahal & McPhartlan 2022 (PGPub 2022/0298210 A1, published 09/22/2022).
As discussed supra, Bertholet Girardin et al. and Jasny et al. rendered the invention of claim 1 obvious, but they fell short of teaching a 5’ UTR sequence that matches SEQ ID NO: 14 cited in claim 20 (a dependent of claim 1). This deficiency was overcome by Chahal & McPhartlan 2022, as their SEQ ID NO: 27 showed 100% identity with SEQ ID NO: 14 in the instant application. A skilled artisan could readily adopt this sequence for an mRNA-LNP composition toward an influenza vaccine because Chahal & McPhartlan also used “a DNA plasmid encoding the replicon sequence template” with a “T7 promoter” to “produce… replicon RNA”, using “the 5' UTR, nsP1-4 ORF, and SGP… set forth in SEQ ID NO: 27” as a structural unit (¶[0019]). The motivation was also obvious, as Chahal & McPhartlan aimed to produce “artificial alphavirus-derived RNA replicon expression systems” (title) that comprise “nucleic acid sequences encoding at least one modified nonstructural protein, and synthetic nucleic acid sequences encoding at least one heterologous protein” capable of “inducing an immune response in a subject” (abstract): the intended use was vaccination, as in claim 20 of the instant application. Thus, the invention of claims 1 and 20 as a whole is rendered obvious by three references before its effective filing date, as another example of Rationale B of MPEP §2143.
Claims 46-47 are rejected under USC §103 as being unpatentable over Bertholet Girardin et al. 2021 (supra) and Jasny et al. 2021 (supra) as applied to the rejection of claims 1-5, 11-12, 14-16, 21, 27, 29-30, 46 and 51-52, further in view of Lerner et al. 2022 (WO 2022150485 A1, published 07/14/2022).
While the invention of claims 1 and 46 is rendered obvious by Bertholet Girardin et al. and Jasny et al. as an example of Rationale B of MPEP §2143, all discussions in the first 103 being incorporated here, the two references still fell short of teaching the use of ATX-126 cited in claim 47 as the ionizable cationic lipid for RNA-LNP compositions that are capable of inducing immune responses against NA- and HA-specific immunogens derived from one or more influenza virus strains selected from prior art. This deficiency is overcome by Lerner et al., as they taught “the encapsulation of… recombinant RNA molecules and the use of… recombinant RNA molecules and/or particles for the treatment and prevention of cancer” (abstract). Their “synthetic RNA viral genomes… are encapsulated in a lipid nanoparticle (LNP)”, which “comprises one or more cationic lipids” (¶[00390]). CAT2 lipid in Lerner et al. (Table 21 and ¶[00380]) is the equivalent of ATX-126, which has an official CA index name of “butanoic acid, 4,4'-[[[[3-(dimethylamino)propyl]thio]carbonyl]imino]bis-,1,1'-bis(1-heptyloctyl) ester” (coded as 2230647-37-5). As implied by claim 47, the selection of ATX-126 is one optional step, as other choices are also expected work. The 35 lipids taught by Lerner (Table 21 on pages 111-115) can attest to the extent of lipids already considered suitable for RNA-LNP compositions. Indeed, each of the 35 lipids is also expected to work as “a pharmaceutically acceptable salt or solvate” (00380]). Thus, a skilled artisan could readily recognize ATX-126 (claim 47 of the instant application) as an optional ionizable cationic lipid (claim 46 of the instant application) for LNP, as one of the options taught by Lerner et al. Thus, the invention of claims 1 and 46-47 as a whole is rendered obvious by three references before its effective filing date, as an example of Rationale B of MPEP §2143.
Conclusion
No claims are allowed.
Additional Prior Art Cited but Not Applied
Nachbagauer et al. WO 2022/221335 A1, published 10/20/2022 and of record (Information Disclosure Statement, 08/15/2025).
This prior art taught the composition and use of mRNA-LNP as “respiratory virus combination vaccines” (title). “In some embodiments, the vaccine comprises 2-4 mRNA polynucleotides comprising an ORF encoding an influenza virus antigen” (page 5, lines 28-29), with “one or more non-coding sequences in an untranslated region (UTR), optionally a 5' UTR or 3' UTR” (page 13, lines 34-35), and “the LNP comprises a molar ratio of 20-60% ionizable amino lipid, 5-25% non-cationic lipid, 25-55% sterol, and 0.5-15% PEG-modified lipid” (page 14, lines 9-10). “The mRNA vaccines… comprise mRNAs encoding HA, and optionally, NA antigens of the influenza viruses circulating at the time of design of the vaccines” (page 21, lines 22-23). The four virus strains listed in FIG. 1 and FIG. 2 included “N1 Wisconsin, N2 HK, B Phuket and B Washington,” which are similar to the four strains cited in claims 14-15 of the instant application. When four formulations were tested at doses ranging from 0.8 µg to 8.0 µg/mouse (Table 1 on page 91), “similar neutralizing titers were observed between the combination vaccine and individual antigen vaccines at day 21” (page 90, lines 31-34 and page 91, line 1). In addition, “a single 1.5 µg DNA encoding the same gene formulated the same way as the sa-RNA” was included as a reference, and “both DNA vaccines and the sa-RNA reduced weight loss after influenza Cal’09 H1N1 infection” (Figure 6 and page 449, last paragraph on the right and page 450, first paragraph below Figure 3). Thus, both DNA- and mRNA-based multivalent influenza vaccines had been tested successfully against multiple virus strains in preclinical trials before the instant application was filed.
Yang et al. 2006 (WO 2006/098901 A2, published 09/21/2006).
This prior art taught “polypeptides, polynucleotides, methods, compositions, and vaccines comprising influenza hemagglutinin and neuraminidase variants” (abstract). In claims 81-82 (page 83), they taught “an RNA template” with “nucleic acid corresponding to one or more of SEQ ID NO: 1-48 or a fragment thereof, or… one or more nucleic acid sequence of a similar strain to strains comprising the sequences in SEQ ID NO: 1-48”, and “wherein the RNA template is replicable.” SEQ ID NOs: 1-48 correspond to 24 HA and 24 NA gene sequences for 15 type A and 9 type B influenza virus strains (Figure 2, pages 49/50 and 50/50), including H1N1 (e.g., A/Texas/36/91 – SEQ ID NO: 13 for HA; SEQ ID NO: 14 for NA), H3N2 (e.g., A/Sydney/05/97 – SEQ ID NO: 7 for HA; SEQ ID NO: 8 for NA), B-Victoria/504/2000 (SEQ ID NO: 27 for HA; SEQ ID NO: 28 for NA) and B/Yamanashi/166/98 (SEQ ID NO: 23 for HA; SEQ ID NO: 24 for NA). They also taught that “gene encoding regions (typically and preferably encoding HA and NA or fragments thereof) selected from SEQ ID NO:1 through SEQ ID NO:48 or from similar strains” can be used toward “immunogenic compositions” (¶[0010]). Aside from the B-Victoria strain that matched Victoria B in claims 14-15 of the instant application, two other strains (H3N2 A/Darwin/6/2021 and H1N1 A/Wisconsin/588/2019) in claims 14-15 fall into the category of similar strains under H1N1 (A/Texas/36/91) and H3N2 (A/Sydney/05/) taught by Yang et al., with further support from Jasny et al. who taught the use of “A/California/7/2009 (H1N1)… A/Netherlands/602/2009 (H1N1), A/Hong Kong/4801/2014 (H3N2)” (¶[0618] and TABLE 8). In other words, HA and NA or fragments thereof can be readily selected from various influenza virus strains to represent subtypes A and B toward a nucleic-acid-based vaccine composition.
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/JIANMING TANG/
Examiner, Art Unit 1671
/Michael Allen/ Supervisory Patent Examiner, Art Unit 1671
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