DETAILED ACTION
Disposition of Claims
Claims 1-9 are pending.
Examiner’s Note
All paragraph numbers (¶) throughout this office action, unless otherwise noted, are from the US PGPub of this application US20240342265A1, Published 10/17/2024.
Applicant is encouraged to utilize the new web-based Automated Interview Request (AIR) tool for submitting interview requests; more information can be found at https://www.uspto.gov/patent/laws-and-regulations/interview-practice.
Optional Authorization to Initiate Electronic Communications
The Applicant’s representative may wish to consider supplying a written authorization in response to this Office action to correspond with the Examiner via electronic mail (e-mail). This authorization is optional on the part of the Applicant’s representative, but it should be noted that the Examiner may not initiate nor respond to communications via electronic mail unless and until Applicant’s representative authorizes such communications in writing within the official record of the patent application. A sample authorization is available at MPEP § 502.03, part II. If Applicant’s representative chooses to provide this authorization, please ensure to include a valid e-mail address along with said authorization.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Should applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d) prior to declaration of an interference, a certified English translation of the foreign application must be submitted in reply to this action. 37 CFR 41.154(b) and 41.202(e).
Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Specification
A substitute specification in proper idiomatic English and in compliance with 37 CFR 1.52(a) and (b) is required. The substitute specification filed must be accompanied by a statement that it contains no new matter.
Claim Objections
Claim 1 is objected to because of the following informalities: to place the claim in proper form “SEQ ID No:” should be replaced with “SEQ ID NO:”. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b); Second Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-9 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.
The claims are generally narrative and indefinite, failing to conform with current U.S. practice. They appear to be a literal translation into English from a foreign document and are replete with grammatical and idiomatic errors. While it will be provided how the claims are being interpreted herein, the claim language must be amended to clarify the metes and bounds of what is being claimed.
For at least these reasons, claims 1-9 are rejected on the grounds of being indefinite.
Claim 1 and dependent claims 2-9 thereof 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 1 is drawn to an “attenuated recombinant West Nile virus, comprising: amino acid sequence of envelope E protein of the attenuated recombinant West Nile virus has at least 98% identical to SEQ ID No: 1; and compared with the SEQ ID No: 1, the amino acid sequence of the envelope E protein has amino acid substitutions at least at positions corresponding to position 138, position 172, position 173, position 276, and position 312.” The wording of the claim makes it unclear if the recited percentage is over a particular region of the envelope (E) protein, the full-length protein, or another sequence span. The claim does not provide an objective basis for determining positional correspondence where a candidate envelope protein includes an insertion or deletion relative to SEQ ID NO: 1.
For example, it is unclear whether the claimed substitutions are required at residues numbered 138, 172, 173, 276, and 312 in the candidate envelope protein itself, or at residues which align with positions 138, 172, 173, 276, and 312 after a sequence alignment. This distinction affects whether a given recombinant West Nile virus falls within the scope of claim 1. The specification states that the corresponding sequence numbers may differ among West Nile virus subtypes, but does not define the sequence span, alignment method, or other objective convention for determining the required positional correspondence. Therefore, one of ordinary skill in the art cannot determine with reasonable certainty whether a particular E protein meets both the recited sequence identity limitation and the five substitution limitations.
Applicant may amend the claim to identify the relevant sequence span for calculating percent identity and clarify whether the required substitutions are at the listed positions of SEQ ID NO: 1 or at residues aligned to those positions under an objectively-defined sequence-comparison convention. For example, one suggestion would be to amend the claim along the lines of:
“1. An attenuated recombinant West Nile virus (WNV) comprising an envelope (E) protein, wherein:
(a) the amino acid sequence of the E protein has at least 98% amino acid sequence identity to SEQ ID NO: 1; and
(b) when the amino acid sequence of said E protein is aligned with SEQ ID NO: 1, said amino acid sequence of said E protein comprises an amino acid substitution at each residue aligned with positions 138, 172, 173, 276, and 312 of SEQ ID NO: 1.”
Since a skilled artisan would not be reasonably apprised as to the metes and bounds of the claimed invention, instant claim 1 is rejected on the grounds of being indefinite. Claims 2-9 are also rejected since they depend from claim 1, but do not remedy these deficiencies of claim 1.
Claim 3 is 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.
Regarding claim 3, the language “mutated/substituted amino acids include, but are not limited to, the presence of mutations with similar structure and properties as follows” is unclear, as the language fails to provide a clean, limiting boundary as to what is, and what is not, encompassed by the claim.
Additionally, the amino acid “glutamine” at line 4 is noted as being “(Glu/E)”, when the art-accepted abbreviations for glutamine are “(Gln/Q)” and the “(Glu/E)” abbreviations are for glutamic acid. Therefore, it is unclear which amino acid is being claimed at line 4.
Finally, at line 5, the limitation of “other basic amino acids” is present. It is unclear if applicant is attempting to claim another fundamental amino acid (e.g. there are 20 “basic” or “standard” amino acids, while there are over 140 non-basic or non-proteinogenic amino acids) or if applicant is attempting to claim an amino acid with a specific charge at a specific pH (e.g. proteinogenic amino acids with positively charged side chains at physiological pH around 7.4, namely arginine, lysine, and histidine). As a definition has not been provided for in the claim or the specification, and as the claim is already drawn to the three known proteinogenic amino acids with positively charged side chains at physiological pH, it is unclear what is meant by “other basic amino acids” at line 5.
For at least these reasons, claim 3 is rejected on the grounds of being indefinite.
Claims 4 and 6 and dependent claim 5 thereof 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.
The term “safe” or “safely” in the claims is a relative term which renders the claim indefinite. The term “safe/safely” is not defined by the claim, 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. While the specification notes that “knocking out the viral genes responsible for pathogenicity to ensure the safety of oncolytic virus therapy is one of the essential conditions for the success of this treatment” (¶[0009]) and mutations in the E protein that result in a WNV that “did not cause infection and disease in sensitive animals” (¶0032]) and that reduction in viral toxicity can increase its safety as an oncolytic virus (¶[0060]) or losing the ability to infect the CNS while having no toxicity to other tissues and organs from the peripheral administration (¶[0078]) vaguely eludes to the idea of what may be considered “safe”, it remains that no clear definition of a “safe” WNV is provided, it is unclear how one is to gauge “toxicity” of other tissues/organs in any host, or how one can clearly define if the resulting WNV is “safe” or “unsafe”.
As this is a relative term without a clear definition provided for in the art or specification, it is rejected on the grounds of being indefinite. Claim 5 is also rejected for depending upon claim 4, but not clarifying the metes and bounds of claim 4.
Claim 5 and dependent claim 6 thereof 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.
The terms “good live-attenuated WNV”, “retained viral antigenicity”, and “retained replication capacity” in claim 5 are relative terms which renders the claim indefinite. The terms “good live-attenuated WNV”, “retained viral antigenicity”, and “retained replication capacity” are not defined by the claim, 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. It is unclear if the retention of viral antigenicity is measured specifically by a T/B cell response, or is measured by the ability of the virus to be recognized by certain antibodies, or elicits a specific strength/type of response compared to the wild-type, unmutated version of the WNV. Similarly, it is unclear how to compare if the virus has retained “replication capacity”, as it is unclear what to compare it to (e.g. which “base” virus to compare it to), or if it is determined if the virus can still replicate in a specific cell type or system type. Finally, it is unclear how to determine if the resulting WNV is “good” or “bad” as a live-attenuated WNV vaccine, as the metrics for determining the above two limitations (e.g. replication capacity and viral antigenicity) have not been defined.
As the metes and bounds of the claim are unclear, claim 5 is rejected on the grounds of being indefinite. Claim 6 is included in this rejection for depending upon claim 5, but not clarifying the metes and bounds of claim 5.
Claim 7 is 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 7 is drawn to “[t]he attenuated recombinant West Nile virus according to claim 1, wherein: the WNA RNA vector/oncolytic WNV embeds foreign genes, including T-cell costimulator CD86, without affecting virus replication, which targets T-cell activation for oncolytic-immunotherapy of cancers.” However, the antecedent basis of “the WNA RNA vector/oncolytic WNV” is unclear, as “WNA” appears to be a typographical error (e.g. “WNV”) and neither a RNA vector nor an oncolytic WNV are recited in claim 1.
Furthermore, the limitation of “without affecting virus replication” is a relative term of degree without an appropriate frame of reference. It is unclear as to what “base” virus said WNV of claim 7 should be compared to determine if viral replication has, or has not, been affected.
For at least these reasons, the metes and bounds of claim 7 are unclear. Claim 9 is rejected for depending upon claim 7, but not clarifying the metes and bounds of claim 7.
Claim 9 is 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 9 is drawn to “[t]he attenuated West Nile virus according to claim 7, wherein: the oncolytic WNV with the CD86/CD80 is used for immunotherapy of solid cancers including small-cell lung cancer, liver cancer, neuroblastoma, neuroglioma, and leukemia.” However, the antecedent basis of “the CD86/CD80” is unclear, as claim 7 only recited CD86, so it is unclear if CD86/CD80 is meant to be a fusion protein, CD86, CD80, both CD86 and CD80, or some other alternative interpretation.
Additionally, the “solid cancers” include small-cell lung cancer, liver cancer, neuroblastoma, neuroglioma, and leukemia, wherein “leukemias” are traditionally not considered “solid cancers”.
For at least these reasons, claim 9 is rejected on the grounds of being indefinite.
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. In light of the 35 USC 112b issues above, the interpretation of claims 1-9 will be clearly provided herein.
Claim 1 is drawn to an attenuated recombinant West Nile virus (WNV) comprising an envelope (E) protein, wherein:
(a) the full-length amino acid sequence of the E protein has at least 98% amino acid sequence identity to SEQ ID NO: 1; and
(b) when the amino acid sequence of said E protein is aligned with SEQ ID NO: 1, said amino acid sequence of said E protein comprises an amino acid substitution at each residue aligned with positions 138, 172, 173, 276, and 312 of SEQ ID NO: 1.
Claim 2 is drawn to the attenuated recombinant WNV according to claim 1, wherein the amino acid substitutions at the residues aligned with positions 138, 172, 173, 276, and 312 of SEQ ID NO: 1 are E138K, Y172V, T173A, K276M, and A312V, respectively, relative to SEQ ID NO: 1.
Claim 3 is drawn to the attenuated recombinant WNV according to claim 1, wherein, relative to SEQ ID NO:1:
(i) the amino acid at the residue aligned with position 138 of SEQ ID NO: 1 is Lysine (Lys/K), arginine (Arg/R), or histidine (His/H)
(ii) the amino acid at the residue aligned with position 172 of SEQ ID NO: 1 is Valine (Val/V), Methionine (Met/M), isoleucine (Ile/I), leucine (Leu/L), or Alanine (Ala/A);
(iii) the amino acid at the residue aligned with position 173 of SEQ ID NO: 1 is Alanine (Ala/A), Valine (Val/V), isoleucine (Ile/I), leucine (Leu/L), or Methionine (Met/M);
(iv) the amino acid at the residue aligned with position 276 of SEQ ID NO: 1 is Methionine (Met/M), Valine (Val/V), isoleucine (Ile/I), leucine (Leu/L), or Alanine (Ala/A);
(v) the amino acid at the residue aligned with position 312 of SEQ ID NO: 1 is Valine (Val/V), isoleucine (Ile/I), leucine (Leu/L), or Methionine (Met/M).
Claim 4 is drawn to the attenuated recombinant WNV according to claim 1, wherein the attenuated recombinant WNV is incapable of infecting the central nervous system (CNS) following peripheral administration.
Claim 5 is drawn to the attenuated recombinant WNV according to claim 4, wherein the attenuated recombinant WNV replicates in Vero cells and, following peripheral administration to an immunocompetent mammal, induces an anti-WNV antibody response in said mammal.
Claim 6 is drawn to the attenuated recombinant WNV according to claim 5, wherein the attenuated recombinant WNV is capable of replicating in and causing cell death of a tumor or cancer cell.
Claim 7 is drawn to the attenuated recombinant WNV according to claim 1, further comprising a heterologous nucleic acid encoding a CD86 polypeptide, wherein said WNV comprising said CD86 polypeptide is capable of replicating in Vero cells and expressing said CD86 polypeptide, wherein said expressed CD86 polypeptide activates T-cells.
Claim 8 is drawn to the attenuated recombinant WNV according to claim 1, wherein said WNV comprises a heterologous nucleic acid inserted at the junction between the nucleotide sequence encoding the E protein and the nucleotide sequence encoding non-structural protein 1 (NS1) in the viral genomic RNA.
Claim 9 is drawn to the attenuated West Nile virus according to claim 7, wherein the CD86 is human CD86, and wherein said WNV can be used as an immunotherapy for cancers selected from small-cell lung cancer, liver cancer, neuroblastoma, neuroglioma, and leukemia.
Claim Rejections - 35 USC § 112(a); First Paragraph
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 1-9 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. The claim(s) contains 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The written description requirement is separate and distinct from the enablement requirement. To satisfy the written description requirement, the specification must reasonably convey to one skilled in the relevant art that the inventor had possession of the claimed invention as of the filing date. Possession may be shown by a description of the complete structure of the claimed invention, a representative number of species falling within the scope of a claimed genus, or relevant identifying characteristics sufficient to show that the inventor had possession of the claimed subject matter.
Claim(s) 1-9 recite an attenuated recombinant West Nile virus (WNV) comprising an envelope (E) protein, wherein:
(a) the full-length amino acid sequence of the E protein has at least 98% amino acid sequence identity to SEQ ID NO: 1; and
(b) when the amino acid sequence of said E protein is aligned with SEQ ID NO: 1, said amino acid sequence of said E protein comprises an amino acid substitution at each residue aligned with positions 138, 172, 173, 276, and 312 of SEQ ID NO: 1. Further claims narrow the possible substitutions at the recited residues, and also claim functional properties with the mutations (e.g. wherein said mutations allow the WNV to retain antigenicity and replication capacity while being useful as a live-attenuated vaccine).
The specification describes SEQ ID NO: 1 and SEQ ID NO: 2, and describes one five-site mutant made in the WNV B956 background, having E138K, Y172V, T173A, K276M, and A312V substitutions. The specification also describes a WNV engineered to express human CD86, designated DS1-H2-1, and a WNV expressing mouse CD86, designated DS1-M2-1. The human CD86 fragment was inserted between the regions of the WNV genome which comprise the E and NS1 regions of the WNV polyprotein. The disclosed in vivo tumor work concerns the use of DS1-H2-1 in human neuroblastoma and human small cell lung cancer xenograft models, and DS1-M2-1 in a mouse neuroblastoma model (¶[0013-0032][0067-0090]). However, the scope of the claims is not limited to the embodiments described in the specification, namely the five site substitutions, the B956 WNV background, mouse and human CD86, or the disclosed cancer/tumor models. The claims broadly encompass any WNV background, additional E protein mutations due to the 98% identity limitation, any substitution at the five noted residues, any CD86, and both solid and non-solid cancer types. Additionally, this breadth is tied into the resulting WNV being attenuated at any level. The specification does not describe a sufficient number of species representative of the claimed scope. The specification also does not describe structural features common to the claimed genus which would allow one skilled in the art to recognize which additional species fall within the scope of the claimed invention. Instead, one skilled in the art would be required to select additional WNV E protein variants, substitutions at the recited positions, WNV backbones, and cancer types not described in the specification and determine whether those additional embodiments satisfy the recited limitations.
The claimed viruses are defined, at least in part, by the recited function of being attenuated while retaining replication and immunogenicity, wherein the “attenuation” appears to be defined, at least in part, by the ability of the virus to no longer invade the CNS from the periphery while still remaining non-toxic to the rest of the host. Additionally, the WNV is claimed to functionally be useful as a vaccine and potentially have oncolytic/immunogenic value. However, the specification does not establish a correlation between the disclosed structural features and the recited function sufficient to identify the additional WNV variants with the claimed E protein mutations falling within the scope of the claim. The specification describes one specific example of one WNV with a specific set of mutations at the claimed residues which exhibits the attenuation claimed, but does not identify structural features common to the broader claimed genus which would allow one skilled in the art to recognize other members of the genus. Instead, the specification notes that excessive amino acid mutations in the E protein can affect viral replication and survival, and that mutations unrelated to neurotoxicity do not achieve the desired neurotoxicity attenuation. The disclosure of the desired function, without a sufficient description of the claimed genus, does not demonstrate possession of the full scope of the claim.
The specification also describes WNV carrying CD86 between the E and NS1 protein coding regions. However, the claims are not limited to those constructs. The claims also encompass constructs that differ in the heterologous gene which may be within the WNV, and where it may be inserted. While the claims are also drawn to the insertion of CD80, the specification does not describe actual reduction to practice of CD80 or any fragment thereof inserted anywhere in the WNV genome. The specification does not note where in the WNV genome a heterologous gene may be inserted, as the entire WNV is encoded as a polyprotein that is post-translationally processed into the individual viral proteins; therefore, it is unclear if the heterologous gene can only be inserted into an intergenic region, if it can replace one or more WNV proteins, or if it can be inserted into non-coding regions of the WNV genome. The specification does not describe representative examples across that scope or identify structural features sufficient to show possession of the broader group of constructs.
The specification describes the use of specific WNV to treat solid tumor in vivo models. However, claims 6-7 and 9 broadly encompass that the WNV, both with and without an additional heterologous gene, may be used in the treatment of cancers, including solid and non-solid cancers. The specification does not describe representative embodiments across that scope or otherwise demonstrate possession of the broader claimed method, as the examples are limited to tumor data for human neuroblastoma and human small cell lung cancer xenografts and mouse neuroblastoma. The disclosure of these examples does not reasonably convey possession of all WNV compositions which can be used in the methods claimed to treat any type of cancer, such as any liver cancer, leukemia, neuroglioma, or any other cancer encompassed by the claims.
Accordingly, the disclosure does not reasonably convey to one skilled in the art that the inventor had possession of the full scope of the subject matter recited in claims 1-9 at the time the application was filed.
Claims 1-9 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the disclosed B956 West Nile virus (WNV) construct having the E138K, Y172V, T173A, K276M, and A312V substitutions in the envelope (E) protein, and for the disclosed CD86-harboring WNV constructs evaluated in the limited tumor models, does not reasonably provide enablement for the broader scope of any recombinant attenuated WNV with any substitution in the E protein at the noted locations with the percent identity claimed, comprising any further heterologous gene insert, for any cancer treatment therapeutic. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
The legal considerations that govern enablement determinations pertaining to undue experimentation have been set forth in In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). The factors to be considered include: (1) the breadth of the claims; (2) the nature of the invention; (3) the state of the prior art; (4) the level of one of ordinary skill; (5) the level of predictability in the art; (6) the amount of direction provided by the inventor; (7) the existence of working examples; and (8) the quantity of experimentation needed to make or use the invention based on the content of the disclosure. The factors are considered as a whole in determining whether any necessary experimentation would have been undue.
Nature of the invention and breadth of the claims. The claimed invention is directed to attenuated recombinant West Nile viruses having an E protein with at least 98% identity to SEQ ID NO:1 and also comprising substitution mutations at residues 138, 172, 173, 276, and 312, along with viruses having broad alternative substitutions, foreign genes, CD86/CD80, and cancer treatment or immunotherapy utility.
The specification describes one B956-based WNV construct having E138K, Y172V, T173A, K276M, and A312V substitutions in the E protein. The specification reports that this construct replicated in tested cell lines and tumor tissues and did not infect the host central nervous system (CNS) following peripheral administration (¶[0067-0078]). The specification also describes human and mouse CD86 insertions into the WNV between the coding regions for E and NS1 in the WNV genome (¶[0072-0080]). However, claims 1-9 are not limited to these disclosed embodiments. The claims also encompass additional, uncharacterized E proteins which differ due to the 98% sequence identity limitation and any substitution at the five noted locations. The claims further encompass any mutations which retain “similar structure and properties” to the E138K, Y172V, T173A, K276M, and A312V substitutions. Further dependent claims require attenuated neurotoxicity, retained antigenicity and replication capability, vaccine utility, and oncolytic/immunogenic utility across the broader claimed scope. The claims also encompass any heterologous gene inserted at any location in the WNV genome, and also encompass cancer immunotherapy which goes beyond the scope of the given examples and tumor models. The claimed scope therefore extends beyond the embodiments described in the specification.
State of the prior art and predictability of the art. At the time the application was filed, it was known that certain mutations generated in the E protein of WNV did not attenuate WNV like they did other flaviviruses. Kaiser et. al. (Kaiser JA, et. al. NPJ Vaccines. 2019 Dec 5;4:50.) evaluated WNV containing the E138K mutation after noting said mutation in Japanese encephalitis virus (JEV) attenuated said virus. However, the WNV E138K mutant retained virulence in mice, showed increased E-protein variation, and included reversion at this residue. Given the results from their studies, Kaiser concluded that an attenuating mutation in one related flavivirus could not predictably translate to another flavivirus, such as WNV.
Vandergaast et. al. (Vandergaast R, et. al. Viruses. 2014 Apr 9;6(4):1637-53.) constructed WNV infectious clones carrying inserted reporter sequences. Vandergaast found that certain inserted sequences reduced viral fitness, and that portions of an inserted sequence were lost during virus recovery or serial passage. The insertion site of Vandergaast was the Capsid (C)/Capsid Anchor (CA) junction of the viral polyprotein, and Vandergaast also noted that previous studies with insertions at the 3’ UTR were also similarly unstable. Given these findings, the art was apprised as to the unpredictable nature of foreign gene insertion into the WNV, and that the virus did not predictably tolerate insertion at all sites in the viral genome.
Bonaldo et. al. (Bonaldo MC, et. al. Virol J. 2007 Oct 30;4:115.) teaches that insertion of a heterologous reporter gene in between the E and NS1 genes of a flavivirus required specific stem-anchor and NS1 design features to preserve the polyprotein processing and viable virus production. Bonaldo also reported variation in genetic stability, including loss of foreign sequence in certain recombinant viruses after passage. Bonaldo was able to show that their resultant virus remained immunogenic and was able to not only generate an immune response against the flavivirus, but the heterologous transgene product as well. This art indicates that an inserted foreign gene is not predictably compatible with the E/NS1 regions merely because a single construct may be recovered.
Ehrlich et. al. (Ehrlich M, et. al. Cancers (Basel). 2021 Feb 24;13(5):939.) teaches that with the oncogene-enhanced anabolic nature of cancer-cell metabolism, this attenuation of antiviral defenses contributes to viral replication and to the selectivity of oncolytic viruses (OVs) towards malignant cells. However, Ehrlich also points out that the treatment of immunodeficient cancer cells with OVs depends on the identity of the OV, and that the difference in outcomes of combined OV and DNA methyltransferase inhibitors (DNMTis) supports the notion of tailoring therapy combinations to the distinct properties of the OV. The teachings of Ehrlich therefore support that results in one cancer model do not establish comparable activity in unrelated cancer types.
The specification itself also notes that “Our research has proven that excessive amino acid mutations in the E protein affect the virus's replication or survival, and amino acid mutations not related to neurotoxicity do not achieve neurotoxicity attenuation effects.”(¶[0031]). The art was not sufficiently predictable to support extrapolation from the disclosed five site B956 construct to the more broadly claimed E-protein sequence genus, WNV comprising foreign transgene genus, and cancer treatment genus. Accordingly, the results obtained using the limited disclosed embodiments would not have reasonably established that the broader claimed scope could be practiced without further experimentation.
Level of skill in the art/Working Examples/Guidance in the Specification. One skilled in the art would have been familiar with infectious WNV clone construction, sequence analysis, viral culture techniques, serial passage of cells/viruses, replication assays of cells/viruses, neurovirulence testing, and different in vivo tumor models. However, the ability of those methods does not establish that one would know which additional E-protein variants, gene inserts, or tumor settings would satisfy the claimed limitations without further experimentation.
The specification provides working examples for one defined five site substitution E protein mutant, the insertion of CD86 into the WNV genome at the E/NS1 junction, and limited neuroblastoma and small cell lung cancer studies with the WNV (¶[0067-0090]). It does not provide working examples for additional E protein variants within the claimed 98% identity scope which comprise any combination of substitution mutations at the five locations within the E protein, any CD80 construct within any WNV, other foreign transgenes inserted anywhere within the WNV, or the broader cancer treatment scope as provided for in instant claims 6 and 9.
The specification provides the desired results for the disclosed constructs, but does not identify a general rule for selecting additional amino acid changes while retaining viable replication and attenuation. Nor does it provide guidance for determining which foreign genes can be inserted between E and NS1 while maintaining stability of the virus and foreign insert, or which cancers will respond to the claimed WNV-oncolytic immunotherapy approach.
Quantity of experimentation necessary. To practice the full scope of claims 1-9, one skilled in the art would need to prepare additional E protein variants, recover candidate recombinant WNV, assess replication to determine if said WNV are attenuated, perform genetic analysis after multiple passages to determine the genetic stability of the claimed heterologous gene inserts, test neuroinvasion or neurotoxicity after peripheral administration of said WNV, and determine if the WNV candidate virus would remain antigenic, oncolytic, and useful for virotherapeutic techniques. Such experimentation would not merely involve the routine application of known methods to embodiments reasonably expected to work. Instead, one skilled in the art would need to prepare and test additional embodiments to determine whether they satisfy the claimed functional attenuation of the resulting WNV, and if said WNV could be safely and effectively used in oncolytic virotherapy techniques. Although the individual methods used to prepare and test candidate embodiments may have been known in the art, the relevant inquiry is not whether one skilled in the art could perform the required assays. The relevant inquiry is whether the specification provides sufficient guidance to identify and practice the embodiments falling within the full scope of the claims without undue experimentation. Although the individual assays for each step may have been known, the specification fails to provide sufficient guidance to practice the full claimed scope without undue experimentation.
Amgen. The Supreme Court has explained that a specification need not describe with particularity how to make and use every embodiment within a claimed class. However, the disclosure must enable one skilled in the art to make and use the full scope of the claimed invention. A reasonable amount of experimentation may be permissible depending on the nature of the invention and the underlying art. Amgen Inc. v. Sanofi, 598 U.S. 594, 610-13 (2023).
In the instantly claimed invention, the specification describes a single five site WNV E protein mutant and limited CD86 constructs, but the claims encompass a materially broader E protein sequence, vector, and therapeutic genus. The specification does not identify a general quality or provide sufficient guidance that would allow one skilled in the art to practice that broader scope without undue experimentation.
Conclusion. For the reasons discussed above, the specification does not enable one skilled in the art to make and/or use the full scope of the invention recited in claims 1-9 without undue experimentation.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 follows:
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 1-7 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Pugachev et. al. (US20120288520A1; Pub. 11/15/2012; hereafter “Pugachev”) in view of Yu (US20200215133A1; Pub. 07/09/2020; hereafter “Yu”) as evidenced by Borisevich et. al. (Borisevich VG, et. al. Polyprotein. UniProtKB/Swiss-Prot: Q5MXE3. 01/2004; hereafter “Borisevich”) and Lanciotti et. al. (Lanciotti R, et. al. Polyprotein precursor [West Nile virus]. GenBank: AAF20092.2. 12/07/2000; hereafter “AAF20092.2”).
The Prior Art
Pugachev teaches recombinant flaviviruses and vaccine compositions thereof that can be used in the prevention and treatment of flavivirus infection, wherein said vaccines comprise recombinant flaviviruses with attenuating mutations (entire document; see abstract.) Pugachev teaches the art was apprised to WNV E protein sequences, such as West Nile virus strain NY99-flamingo 382-99 (GenBank Accession Number AF196835, which encodes polyprotein AAF20092.2)(¶[0054]). Alignment of AAF20092.2 shows 94.01% sequence identity to SEQ ID NO:1, and also shows the following amino acids are equivalents according to the alignment below (Query: SEQ ID NO:1; Sbjct: AAF20092.2):
AAF20092.2
SEQ ID NO:1
138
138
176
172
177
173
280
276
316
312
Query 1 FNCLGMSNRDFLEGVSGATWVDLVLEGDSCVTLMSKDKPTIDVKMMNMEAANLADVRSYC 60
FNCLGMSNRDFLEGVSGATWVDLVLEGDSCVT+MSKDKPTIDVKMMNMEAANLA+VRSYC
Sbjct 291 FNCLGMSNRDFLEGVSGATWVDLVLEGDSCVTIMSKDKPTIDVKMMNMEAANLAEVRSYC 350
Query 61 YLASVSDLSTRAACPTMGEAHNEKRADPAFVCKQGVVDRGWGNGCGLFGKGSIDTCAKFA 120
YLA+VSDLST+AACPTMGEAHN+KRADPAFVC+QGVVDRGWGNGCGLFGKGSIDTCAKFA
Sbjct 351 YLATVSDLSTKAACPTMGEAHNDKRADPAFVCRQGVVDRGWGNGCGLFGKGSIDTCAKFA 410
Query 121 CTTKATGWIIQKENIKYEVAIFVHGPTTVESHG----KIGATQAGRFSITPSAPSYTLKL 176
C+TKA G I KENIKYEVAIFVHGPTTVESHG ++GATQAGRFSITP+APSYTLKL
Sbjct 411 CSTKAIGRTILKENIKYEVAIFVHGPTTVESHGNYSTQVGATQAGRFSITPAAPSYTLKL 470
Query 177 GEYGEVTVDCEPRSGIDTSAYYVMSVGAKSFLVHREWFMDLNLPWSSAGSTTWRNRETLM 236
GEYGEVTVDCEPRSGIDT+AYYVM+VG K+FLVHREWFMDLNLPWSSAGST WRNRETLM
Sbjct 471 GEYGEVTVDCEPRSGIDTNAYYVMTVGTKTFLVHREWFMDLNLPWSSAGSTVWRNRETLM 530
Query 237 EFEEPHATKQSVVALGSQEGALHQALAGAIPVEFSSNTVKLTSGHLKCRVKMEKLQLKGT 296
EFEEPHATKQSV+ALGSQEGALHQALAGAIPVEFSSNTVKLTSGHLKCRVKMEKLQLKGT
Sbjct 531 EFEEPHATKQSVIALGSQEGALHQALAGAIPVEFSSNTVKLTSGHLKCRVKMEKLQLKGT 590
Query 297 TYGVCSKAFKFARTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNP 356
TYGVCSKAFKF TPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNP
Sbjct 591 TYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNP 650
Query 357 FVSVATANSKVLIELEPPFGDSYIVVGRGEQQINHHWHKSGSSIGKAFTTTLRGAQRLAA 416
FVSVATAN+KVLIELEPPFGDSYIVVGRGEQQINHHWHKSGSSIGKAFTTTL+GAQRLAA
Sbjct 651 FVSVATANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKSGSSIGKAFTTTLKGAQRLAA 710
Query 417 LGDTAWDFGSVGGVFTSVGKAIHQVFGGAFRSLFGGMSWITQGLLGALLLWMGINARDRS 476
LGDTAWDFGSVGGVFTSVGKA+HQVFGGAFRSLFGGMSWITQGLLGALLLWMGINARDRS
Sbjct 711 LGDTAWDFGSVGGVFTSVGKAVHQVFGGAFRSLFGGMSWITQGLLGALLLWMGINARDRS 770
Query 477 IAMTFLAVGGVLLFLSVNVHA 497
IA+TFLAVGGVLLFLSVNVHA
Sbjct 771 IALTFLAVGGVLLFLSVNVHA 791
Pugachev teaches a YF17D/WNV chimeric virus comprising the WNV NY99 prM/E region and describes ChimeriVax-WN04 E protein variants intended to reduce viscerotropism (excessive viral replication in peripheral organs) while retaining immunogenicity (¶[0063][0068-0069][0097]; Tables 3-4; reference claims 1-3). Pugachev teaches at Table 3 residues in the WNV E protein which may be mutated, namely E138, Y176, T177, K280, and A316, and their corresponding mutations in the attenuated Japanese Encephalitis virus mutant, namely E138K, Y176V, T177A, K280M, and A316V (Table 3; ¶[0098]). Table 4 of Pugachev shows some of the WNV E protein mutants and combinations thereof which were generated, and Pugachev teaches that the mutations in WNV can be a combination of substitutions, such as E138K, Y176V, T177A, K280M, and A316V (¶[0047][0054][0067][0069]). Table 4 identifies ChimeriVax-WN04 E#7 as WN02 plus the E138, E176, E177, and E280 changes; WN02 already includes A316V (¶[0097-0100]; See legend for Table 3.) As shown in the table and alignment above, Pugachev disclosed E#7 substitution pattern corresponds to E138K, Y172V, T173A, K276M, and A312V relative to SEQ ID NO:1 (instant claims 2-3). Pugachev further reports that E#7 was viable, was selected for further testing, and had favorable attenuation and immunogenicity characteristics (¶[0101-0105]; Tables 4-5). In hamsters, E#7 was among the variants producing reduced viremia while maintaining neutralizing antibody responses and protection after wild-type WNV challenge (Table 5; instant claims 4-5).
While Pugachev teaches a WNV E protein with the substitution mutations claimed which results in an attenuated virus, the virus of Pugachev is a chimeric virus. Additionally, the sequence of WNV E protein used by Pugachev is only 94% identical with the WNV E protein. However, these differences would be obvious to a skilled artisan given what was known in the art, as shown by the teachings of Borisevich and Yu.
Borisevich teaches a sequence 100% identical to SEQ ID NO:1 (see attached ABSS and NCBI sequence alignments with Borisevich, which provides the sequence with the WNV polyprotein Q5MXE3).
Yu teaches recombinant oncolytic flaviviruses which carry heterologous genes that result in targeting specific T cells of the immune system to therapeutic use for solid cancers (entire document; see abstract.) Yu teaches attenuation of WNV through point substitution mutations in the WNV E protein (¶[0047]). Yu describes ligating human or mouse T cell costimulatory gene fragments into attenuated WNV cFNA through restriction sites (¶[0049]), recovering recombinant virus (¶[0049-0052]), and confirming both replication and costimulator expression (¶[0052]). Yu further teaches that the recombinant flaviviruses remained genetically stable after ten Vero cell passages, retained foreign gene expression, did not lose replication capability because of the foreign gene insertion, and did not cause neuroinvasive disease in mice (¶[0051-0053]). Yu identifies CD80/86 as a T-cell stimulator that may be encoded by the foreign gene inserted into the flavivirus (reference claim 9; instant claims 7, 9). Yu describes WNV constructs carrying human or mouse genes, and their use in tumor growth inhibition and T cell infiltration, and states that a WNV oncolytic virus carrying foreign gene fragments was safe as a therapeutic drug (¶[0054-0069]; instant claim 6).
Given the art at the time of filing, arriving at a recombinant WNV which comprises an E protein with at least 98% identity to SEQ ID NO:1 while also comprising five substitution mutations would have been obvious given the teachings of Pugachev, Yu, and Borisevich. While Pugachev teaches a chimeric flavivirus with an E protein with the required substitution mutations and attenuation, Pugachev fails to teach an E protein with 98% or greater identity to SEQ ID NO:1; however, alternate sequences for WNV were known in the art at the time of filing, as taught by Borisevich. Given that Pugachev teaches the WNV with the E protein mutations as instantly claimed resulted in a stable yet attenuated virus, and given that Yu teaches an attenuated WNV with five mutations in its E protein, and given that Borisevich teaches WNV E protein with 100% identity to SEQ ID NO:1, and given that Yu teaches the WNV can be an oncolytic vector useful to treat cancers and carry heterologous genes, such as CD80, arriving at the limitations of instant claims 1-7 and 9 would be obvious to a skilled artisan given the teachings of Pugachev in view of Yu and Borisevich.
It would have been obvious to one of ordinary skill in the art to modify the compositions taught by Pugachev in order to incorporate a T cell costimulatory gene into an attenuated WNV platform, thereby providing a recombinant WNV capable of eliciting anti-tumor immune responses for cancer immunotherapy. One would have been motivated to do so, given the suggestion by Yu that the attenuated WNV vectors expressing T cell costimulatory molecules can function as effective oncolytic agents with retained replication and gene expression. There would have been a reasonable expectation of success, given the knowledge that SEQ ID NO:1 was a known WNV E protein sequence, as taught by Borisevich, and also given the knowledge that WNV strains could be attenuated and still viable and immunogenic with five substitution mutations to the E protein, as taught by Pugachev and Yu. Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Pugachev, Yu, and Borisevich as applied to claims 1-7 and 9 above, and further in view of Bonaldo et. al. (US20100297167A1; Pub. 11/25/2010; hereafter “Bonaldo”.)
The Prior Art
The teachings of Pugachev, Yu, and Borisevich have been set forth supra. While these teachings render obvious a WNV with five specific E138K, Y172V, T173A, K276M, and A312V substitution mutations relative to SEQ ID NO:1 in the WNV E protein and with said protein having 100% identity to SEQ ID NO:1, and while these references render obvious the use of the WNV to deliver heterologous genes, none of the references specifically teach the insertion of the heterologous gene at the E/NS1 coding interface in the WNV genome. However, the use of this as an insertion site for WNV vectors was taught in the art, as evidenced by Bonaldo.
Bonaldo teaches that a heterologous nucleic acid cassette may be inserted in the E/NS1 intergenic region of a recombinant flavivirus (entire document; see abstract; ¶[0149]). Bonaldo specifically teaches an EGFP cassette inserted at the junction between the E gene and the NS1 gene and describes including the N-terminal NS1 sequence and E stem-anchor sequence to preserve signalase processing, viral recovery, and replication (¶[0096-0097][0106][0142-0149][0176]; Figs. 17-18; reference claims 1, 7-8.) Bonaldo teaches WNV is one of the flaviviruses to which this technology can be applied (¶[0143][0154]).
It would have been obvious to place the foreign gene taught by Yu into the E/NS1 intergenic region using the disclosed cassette design of Bonaldo. Yu supplies the rationale to express a foreign T cell costimulatory gene from recombinant, attenuated WNV. Bonaldo supplies the rationale behind the specific insertion location and junction design for placing a heterologous gene between WNV E and NS1 while preserving processing and viable virus production. Therefore, arriving at the limitations of instant claim 8 would be obvious to a skilled artisan, given the teachings of Pugachev, Yu, Borisevich, and Bonaldo.
It would have been obvious to one of ordinary skill in the art to modify the compositions taught by Pugachev, Yu, and Borisevich in order to provide an oncolytic WNV vector that could deliver and express heterologous proteins, thereby providing a stable, attenuated WNV vector that could deliver therapeutic material to a target cancer cell. One would have been motivated to do so, given the suggestion by Bonaldo that the insertion location between E and NS1 in flavivirus genomes could comprise larger inserts, be stable over a number of passages in vitro, and could be applied to other flavivirus platforms using specific structural guidelines. There would have been a reasonable expectation of success, given the knowledge that these insertions were tolerated and stable at this location, as taught by Bonaldo. Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Conclusion
No claims are allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure and is listed below.
Yu L, et. al. Vaccine. 2008 Nov 5;26(47):5981-8. Epub 2008 Sep 19. Teaches WNV E protein mutations that attenuate the resulting virus. Not utilized as rejection would be redundant to those set forth supra.
Tajima S, et. al. Viruses. 2024 Aug 1;16(8):1237. Teaches WNV E protein mutations that attenuate the resulting virus. Not utilized as rejection would be redundant to those set forth supra.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RACHEL B GILL whose telephone number is (571)272-3129. The examiner can normally be reached on M to F 8:00 AM to 5:00 PM Eastern.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MICHAEL ALLEN can be reached on 571-270-3497. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/RACHEL B GILL/
Primary Examiner, Art Unit 1671
Prosecution Insights