DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
2. The information disclosure statement (IDS) submitted on 03/12/24 was filed and entered. The submission is in compliance with the provisions of 37 CFR 1.97 and has been considered by the Examiner.
Election/Restrictions
3. Applicant’s election, without traverse, of Group I and sequences 1 and 333, in the reply filed on 01/27/26, is acknowledged.
Claim Status
4. The amendment, filed 01/27/26, has been entered. Claims 1-2, 5-6, 9-10, 13, 15-17, 19, 21-22, 25, 27, 29-31, 33-34, 37, and 39-46 are pending. Claims 3-4, 7-8, 11-12, 14, 18, 20, 23-24, 26, 28, 32, 35-36, and 38 are cancelled. Claim 46 is newly added. Claims 30, 31, 33, 34, 37, 39, 40 and 41 are amended. Claims 42-45 have been withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 01/27/26. Claims 1-2, 5-6, 9-10, 13, 15-17, 19, 21-22, 25, 27, 29-31, 33-34, 37, 39-41, and 46 are under examination.
Claim Objections
5. Claim 2 is objected to because of the following informalities: repeated words. Claim 2 lists Oryza sativa japonica (rice) twice and Arabidopsis thaliana three times. Appropriate correction is required.
6. Claim 5 is objected to because of the following informalities: repeated word. Claim 5 lists CINV1 twice. Appropriate correction is required.
7. Claims 2, 15, 19 and 21 are objected to because of the following informalities: improper recitation of species names. Latin names of microorganisms are properly recited with the genus name (i.e. first part of binomial identifier) capitalized and species name (i.e. second part of binomial identifier) in lower case, with both in italics, and having the genus name spelled out upon first usage, in order to be understood without requiring reference to the specification (i.e. see MPEP 2173.05(s); claims are to be complete in themselves). Thus, for example, “S. cerevisiae” is properly written “Saccharomyces cerevisiae” upon its first usage and “S. cerevisiae” thereafter; and “Pichia pastoris” is properly written as “Pichia pastoris”. Appropriate correction for all species and genera is required.
Improper Markush Grouping Rejection
8. Claims 17 and 40 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
Therefore, the Markush groupings of (A) SEQ ID NO: 1 to SEQ ID NO: 14 (see claim 17) and (B) SEQ ID NO: 315, 332-335 and 342 (see claim 40) are each improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the alternatives defined by the Markush grouping are structurally distinct as evidenced by their unique sequence identifiers (see Sequence listing).
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims (although note that the Restriction Requirement remains intact) and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim Rejections - 35 USC § 112
9. 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.
10. Claims 2, 5, 9, 10, 13, 15, 16, 17, 19, 30-31, 33-34, 37, 39, 41 and 46 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 2 is indefinite because of the use of parentheses. Although parenthesis may be appropriate when defining an abbreviation or acronym, the inclusion of parentheses for phrases or generic terms, raises uncertainty as to whether the feature in the parentheses is optional or always present. Thus, clarification is required to ascertain the metes and bounds of these claims.
Claim 5 recites the limitation "the invertase" in line 1. There is insufficient antecedent basis for this limitation in the claim because there is no recitation of an invertase in claim 1. Thus, clarification is required.
Claim 9 depends from claim 8, which has been cancelled. Further, claim 9 is indefinite because it is unclear if the serines and threonines are required to be O-mannosylated (and if so what amount) based on the phrase “are capable of” (as opposed to “are”). Thus, the metes and bounds of claim 9 cannot be ascertained and clarification is required.
Claim 10 is indefinite because it is unclear if “a fusion protein” (in line 1) is referring to the same fusion protein found in claim 6, or to a different one. If the former, then the limitation should read “the fusion protein”; but if the latter, then the limitation should better distinguish the two fusion proteins. Regardless, clarification is required.
Claims 13, 15, and 17 each depend from claim 1 and each recite the limitation "the GPI anchored protein". There is insufficient antecedent basis for this limitation in each claim because there is no recitation of GPI in claim 1. Further, the abbreviation GPI is not defined in the claim 1 or in claims 13, 15, or 17 (i.e. see claim 6), also making these claims unclear. Thus, correction and/or clarification is required.
With regards to claim 19, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 19 recites the broad recitation “a yeast cell”, and the claim also recites “a Pichia species” which is the narrower statement of the same limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. Thus, clarification is required.
Claim 30 recites the limitation "the engineered eukaryotic cell" in lines 1-2. There is insufficient antecedent basis for this limitation in the claim because claim 1 is not limited to eukaryotic cells. Thus, clarification is required.
Claim 41 is indefinite based on the limitation “…wherein the fusion protein comprises a nucleotide sequence…” because a fusion protein, by definition, is a sequence of amino acids and therefore cannot comprise a nucleotide sequence (i.e. structurally different). Thus, clarification is required.
Other dependent claims do no clarify the issues identified above; therefore, clarification is required to remove scope ambiguity and ascertain the metes and bounds of the claims.
Claim Rejections - 35 USC § 112
11. 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.
12. Claims 1-2, 5-6, 9-10, 13, 15-17, 19, 21-22, 25, 27, 29-31, 33-34, 37, 39-41, and 46 are rejected under 35 U.S.C. 112(a) 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, at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
Instant claims are drawn to an engineered host cell comprising an integrated coding sequence of a fusion protein comprising a catalytic domain of a heterologous glycosyl hydrolase; and an integrated coding sequence of a heterologous protein of interest (POI); wherein the engineered host cell does not endogenously express the glycosyl hydrolase and the POI; and wherein the glycosyl hydrolase is anchored on the surface of the engineered host cell; wherein an anchoring domain of the GPI anchored protein comprises an amino acid sequence that is at least 70% identical to one of SEQ ID NO: 1 to SEQ ID NO: 14; and wherein the fusion protein comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence selected from SEQ ID NOs: 315, 332-335, and 342; and wherein the nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the nucleotide sequence of SEQ ID ON: 314. Consequently, it is the Office' s position that (1) the claim(s) constitute(s) a "broad generic claim” based on the generically claimed host cells, integrated coding sequences, glycosyl hydrolases, heterologous proteins, and/or the lack of guidance regarding “variants” (i.e. which 1%-30% of amino acids may be substituted within a claimed sequence); and/or polynucleotides back-translated (i.e. integrated coding sequences) from these polypeptide sequence variants; and (2) the claimed genus has substantial variation because of the numerous options and combinations permitted. Therefore, it is the Office’s position that the engineered host cells and integrated coding sequences have not been described with sufficient particularity, such that one skilled in the art would recognize that Applicant had possession of the claimed invention, at the time of filing, because of (A) a lack of a correlation, known or disclosed, between the claimed functional requirements and the structures that meet those requirements; and/or (B) a lack of a representative number and variety of species to constitute possession of the full scope of the claimed genus.
For example, the specification appears to describe engineered Pichia pastoris first modified to express recombinant ovalbumin and subsequently modified to express a fusion protein comprising a PGCW14 promoter, a secretion signal, and an SUC2-Tir4 construct wherein the DNA sequence for the expression cassette and the corresponding amino acid sequence are disclosed as SEQ ID NO: 314 and 315, respectively (see Example 2; and Figure 4). However, the specification does not adequately describe any engineered host cells except for Pichia pastoris and does not adequately provide a nexus between the limited results for P. pastoris and the breadth and diversity of the host cells claimed (e.g. all prokaryotes, all eukaryotes, all plants, all fungi, all yeasts, etc.). The specification does not adequately describe the surface expression and anchoring of glycosyl hydrolases, other than SUC2 invertase from Saccharomyces cerevisiae and does not adequately provide a nexus between the limited results for SUC2 and the breadth and diversity of glycosyl hydrolases, in general, or invertases from Kluyveromyces lactis, Cyberlindnera jadinii, Oryza sativa japonica (rice), Arabidopsis thaliana, Rattus norvegicus (rat), Oryctolagus cuniculus (rabbit), and/or Homo sapiens, in particular. The specification does not adequately describe wherein the invertase is encoded by a gene selected from MAL1, invertase (INV1), cytosolic invertase 1 (CINV1), CIN2, INVA, INVE, and sucrase-isomaltase (SI) gene; or an inducible promoter selected from an AOX1, DAK2, PEX11, FLD1, FGH1, DAS1, DAS2, CAT1, MDH3, HAC1, BiP, RAD30, RVS161-2, MPP10, THP3, TLR, GBP2, PMP20, SHB17, PEX8, PEX4, or TKL3 promoter; and/or a terminator selected from an AOX1, TDH3, MOX, RPS25A, or RPL2A terminator. The specification does not adequately describe overexpression of egg protein, except for recombinant ovalbumin, and does not describe a nexus between the limited results for ovalbumin and other egg proteins including ovomucoid, lysozyme ovoglobulin G2, ovoglobulin G3, α-ovomucin, β-ovomucin, ovotransferrin, ovoinhibitor, ovoglycoprotein, flavoprotein, ovomacroglobulin, ovostatin, cystatin, avidin, ovalbumin related protein X, and ovalbumin related protein Y, in particular. The specification does not adequately describe anchoring domains for surface expression, other than the GPI-protein Tir4 from Saccharomyces cerevisiae and does not adequately provide a nexus between the limited results for Tir4 and the breadth and diversity of anchoring domains claimed including all GPI-anchored proteins in general, or Dan1 or Sed1, in particular. The specification does not adequately describe wherein the anchoring domain of the GPI anchored protein further comprises an MFalpha signal peptide.
With specific regards to the sequence variants (see claims 17 and 40), the specification does not adequately describe a nexus between SEQ ID NOs: 314 and 315 and the elected SEQ ID NO: 1 and/or SEQ ID NO: 333. In addition, the specification does not disclose a correlation between the necessary structure of the integrated coding sequence (i.e. critical subsequences of the back-translated polynucleotide that must be retained in a 70% variant of SEQ ID NO: 1 and/or in an 85-99% variant of SEQ ID NO: 333 and/or critical subsequences of the polynucleotide for 85-99% variants of SEQ ID NO: 314) of the fusion protein, and the claimed function to be maintained (i.e. surface displayed protein anchored on a particular host cell). Thus, the specification does not define sufficient structural features commonly possessed by all members of the claimed genus because, while the description of an ability of a molecule (e.g. integrated coding sequence) to code for a sequence variant, might generically describe that molecule's function, it does not describe the molecule itself. Therefore, a definition by function does not suffice to define the genus because it is only an indication of what the integrated coding sequence does, rather than what it actually is and even one of skill in the art cannot visualize or recognize the necessary structures by only knowing generic encoding characteristics of a partial structure of amino acids. Accordingly, the specification does not provide substantive evidence for possession of this large and variable genus, encompassing the use of a potentially massive number of integrated coding sequences, claimed only by functional characteristics. Consequently, it is the Office’s position that even one of skill in the art would not conclude that Applicant was in possession of the entire genus claimed.
In addition, the specification does not provide adequate written description to identify the broad genus of the claims because, inter alia, it does not describe a sufficient number and/or a sufficient variety of representative species to reflect the breadth and variation within the claimed genus. It is noted that the genus of these host cells mixed-and-matched with these integrated coding sequences is expected to be large and highly variable and thus a person of skill in this art would need to know the structure of the particular integrated coding sequence in the particular host cell. The specification, as best, describes only one species (i.e. example) of Pichia pastoris first modified to express recombinant ovalbumin and subsequently modified to express a fusion protein comprising a PGCW14 promoter, a secretion signal, and an SUC2-Tir4 construct wherein the DNA sequence for the expression cassette and the corresponding amino acid sequence are disclosed as SEQ ID NO: 314 and 315. Therefore, it is the Office’s position that even one of skill in the art would not conclude that Applicant was in possession of the entire genus claimed because, inter alia, the skilled artisan would not accept the disclosure of the one example of one yeast species using a fully defined expression cassette having SEQ ID NO 314 for encoding SEQ ID NO: 315, as representative in number or variety, to demonstrate possession of the entire genus of all host cells and all integrated coding sequences (e.g. back-translated from partial structures of sequence variants) having glycosyl hydrolases and anchoring domains, as encompassed by the claims as written.
With regards to the state of the art, genetically modifying yeast host cells for surface expression of anchored proteins was still under development and thus necessarily unpredictable, as evidenced by, for example, Phienluphon et al. 2019 (Identification and evaluation of novel anchoring proteins for cell surface display on Saccharomyces cerevisiae; Applied Microbiology and Biotechnology 103: 3085-3097). Phienluphon teaches yeast cell surface display technology is emerging as a valuable and powerful platform but the activities and efficiency of the surface display proteins require further improvement and development of anchoring proteins (e.g. page 3085, Introduction). Phienluphon teaches that one challenging task for the development of yeast cell surface display technology is to search for an ideal anchoring protein, which both facilitates efficient transport of target proteins to the yeast cell surface and yields large amounts of displayed proteins and that other requirements include the ability to attach the target protein onto yeast cell wall without disturbing the activity or stability of the displayed protein (e.g. see page 3092, Discussion). Phienluphon teaches that not even computational predictions were able to predict the functional activities of anchoring proteins with 100% accuracy due to the nature of proteins from different species, the conformational change after fusion with target proteins, and/or the failure to translocate the fusion protein to ER and Golgi complex (e.g. see page 3095, right column).
Furthermore, with specific regards to the integrated coding sequences (i.e. nucleic acids) back-translated from partial structures of 70-99% polypeptide sequence variants, even one of skill in this art cannot envision the structure of a corresponding nucleotide sequence by only knowing what it encodes, as evidenced by the art, for example, see Edelman et al. 2001 (Degeneracy and complexity in biological systems; PNAS 98(24): 13763-13768). In summary, a specific protein sequence is easily determined from a known nucleic acid sequence, because the known sequence of nucleotides (i.e. a nucleic acid sequence; e.g. SEQ ID NO: 314) produces one and only one corresponding protein sequence (i.e. a sequence of amino acids; e.g. SEQ ID NO: 315); but, the inverse is not true because a specific sequence of nucleotides cannot be ascertained from a known sequence of amino acids since more than one distinct codon (i.e. set of three nucleotides) may code for a particular amino acid. Thus, a description of the amino acid per se, does not provide sufficient written description of the codon encoding that amino acid because the one-to-one correspondence is unidirectional, i.e., from codon forward to amino acid, but not from an amino acid back-translated to a codon. Thus, the specification does not adequately describe the structures of the numerous nucleic acid sequences claimed by their capacity to encode the claimed protein sequences and/or the variations thereof.
Therefore, neither the specification nor the state of the art provides sufficient written description to support the genus encompassed by the claims. Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.). Accordingly, Applicant has not satisfied the requirements as set forth under 35 U.S.C. 112(a).
Claim Rejections – 35 USC § 112
13. Claims 1-2, 5-6, 9-10, 13, 15-17, 19, 21-22, 25, 27, 29-31, 33-34, 37, 39-41, and 46 are rejected under 35 U.S.C. 112(a) because the specification, while being enabling for engineered Pichia pastoris host cells comprising SEQ ID NO: 314; the specification does not reasonably provide enablement for all host cells comprising all integrated coding sequences (including sequence variants) of all fusions of glycosyl hydrolases and anchoring domains. 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 use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required, are set forth in In re Wands, 8 USPQ2d 1400. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art and (8) the breadth of the claims. Although all the factors were considered, the most relevant ones are discussed below. In the instant case:
Nature of the invention: The nature of the invention is an engineered host cell comprising an integrated coding sequence of a fusion protein comprising a catalytic domain of a heterologous glycosyl hydrolase; and an integrated coding sequence of a heterologous protein of interest (POI); wherein the engineered host cell does not endogenously express the glycosyl hydrolase and the POI; and wherein the glycosyl hydrolase is anchored on the surface of the engineered host cell; wherein an anchoring domain of the GPI anchored protein comprises an amino acid sequence that is at least 70% identical to one of SEQ ID NO: 1 to SEQ ID NO: 14; and wherein the fusion protein comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence selected from SEQ ID NOs: 315, 332-335, and 342; and wherein the nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the nucleotide sequence of SEQ ID ON: 314. Therefore, the nature of the invention is a chemical case, where there is natural unpredictability in performance of certain species or sub-combinations other than those specifically enumerated; see MPEP 2163. Accordingly, it is the Office’s position that undue experimentation would be required to practice the full scope of the claimed invention, with a reasonable expectation of success, because it would not be predictable from the disclosure of one particular species what other species may or may not work; see MPEP 2164.03.
Breadth of the claims: The broadest reasonable interpretation of the claims covers numerous host cells (e.g. all yeast, all fungi, all plants, all bacteria, all protists, etc.) comprising numerous integrated coding sequences (e.g. DNA) including those back-translated from only partial structures thereof (i.e. sequence variations) for all fusions of glycosyl hydrolases and anchoring domains. However, without guidance on which of the structural components are required (i.e. which host cells, which enzymes, which anchoring domains, which amino acids must be conserved, which nucleotides must be conserved) to maintain their claimed functions (i.e. surface expression and anchoring on a particular host cell wall), undue experimentation would be required to determine which of the numerous structural options, alone and in combination, actually work. Accordingly, undue experimentation would be required to practice the full scope of the claimed invention, with a reasonable expectation of success, because while enablement is not precluded by the necessity for routine screening, if a large amount of screening is required, the specification must provide a reasonable amount of guidance with respect to the direction in which the experimentation should proceed and such guidance has not been provided in the instant specification (see below).
Amount of direction provided by Inventor and Existence of Working Examples: The specification appears to disclose an engineered Pichia pastoris first modified to express recombinant ovalbumin, and then subsequently modified to express a fusion protein comprising a PGCW14 promoter, a secretion signal, and an SUC2-Tir4 construct wherein the DNA sequence for the expression cassette and the corresponding amino acid sequence are disclosed as SEQ ID NO: 314 and 315, respectively (see Example 2; and Figure 4). However, the specification does not sufficiently disclose any engineered host cells except for Pichia pastoris and does not adequately provide a nexus between the limited results for P. pastoris and the breadth and diversity of the host cells claimed (e.g. all prokaryotes, all eukaryotes, all plants, all fungi, all yeasts, etc.). The specification does not sufficiently disclose the surface expression and anchoring of glycosyl hydrolases, other than SUC2 invertase from Saccharomyces cerevisiae, and does not adequately provide a nexus between the limited results for SUC2 and the breadth and diversity of glycosyl hydrolases, in general, or invertases from Kluyveromyces lactis, Cyberlindnera jadinii, Oryza sativa japonica (rice), Arabidopsis thaliana, Rattus norvegicus (rat), Oryctolagus cuniculus (rabbit), and/or Homo sapiens, in particular. The specification does not sufficiently disclose wherein the invertase is encoded by a gene selected from MAL1, invertase (INV1), cytosolic invertase 1 (CINV1), CIN2, INVA, INVE, and sucrase-isomaltase (SI) gene; or an inducible promoter selected from an AOX1, DAK2, PEX11, FLD1, FGH1, DAS1, DAS2, CAT1, MDH3, HAC1, BiP, RAD30, RVS161-2, MPP10, THP3, TLR, GBP2, PMP20, SHB17, PEX8, PEX4, or TKL3 promoter; and/or a terminator selected from an AOX1, TDH3, MOX, RPS25A, or RPL2A terminator. The specification does not sufficiently disclose overexpression of egg protein, except for recombinant ovalbumin, and does not describe a nexus between the limited results for ovalbumin and other egg proteins including ovomucoid, lysozyme ovoglobulin G2, ovoglobulin G3, α-ovomucin, β-ovomucin, ovotransferrin, ovoinhibitor, ovoglycoprotein, flavoprotein, ovomacroglobulin, ovostatin, cystatin, avidin, ovalbumin related protein X, and ovalbumin related protein Y, in particular. The specification does not sufficiently disclose anchoring domains for surface expression, other than the GPI-protein Tir4 from Saccharomyces cerevisiae and does not adequately provide a nexus between the limited results for Tir4 and the breadth and diversity of anchoring domains claimed including all GPI-anchored proteins in general, or Dan1 or Sed1, in particular. The specification does not sufficiently disclose wherein the anchoring domain of the GPI anchored protein further comprises an MFalpha signal peptide. With specific regards to the sequence variants (see claims 17 and 40), the specification does not adequately disclose a nexus between SEQ ID NOs: 314 and 315 and the elected SEQ ID NO: 1 and/or SEQ ID NO: 333. In addition, the specification does not disclose a correlation between the necessary structure of the integrated coding sequence (i.e. critical subsequences of the back-translated polynucleotide that must be retained in a 70% variant of SEQ ID NO: 1 or in an 85-99% variant of SEQ ID NO: 333 and/or critical subsequences of the polynucleotide for 85-99% variants of SEQ ID NO: 314) of the fusion protein, and the claimed function to be maintained (i.e. surface displayed protein anchored on host cell).
Accordingly, the scope of the claims is extremely broad compared to the guidance and exemplification provided in the specification. Therefore, the only way to determine if any given combination of options does indeed work, is the empirical testing of each and every combination encompassed (i.e. after the fact). Consequently, based on the almost unfathomable number of possibilities, a non-routine amount of experimentation would be required to practice the full scope of the invention, with a reasonable expectation of success, because testing such a vast number of options would be easily recognized by the skilled practitioner to be disproportionately demanding and thus rise to the level of non-routine.
State of the Prior Art and Level of Predictability in the Art: With regards to the state of the art, genetically modifying yeast host cells for surface expression of anchored proteins was still under development and thus necessarily unpredictable, as evidenced by, for example, Phienluphon et al. 2019 (Identification and evaluation of novel anchoring proteins for cell surface display on Saccharomyces cerevisiae; Applied Microbiology and Biotechnology 103: 3085-3097) which teaches yeast cell surface display technology is emerging as a valuable and powerful platform but the activities and efficiency of the surface display proteins require further improvement and development of anchoring proteins (e.g. page 3085, Introduction). Phienluphon teaches that one challenging task for the development of yeast cell surface display technology is to search for an ideal anchoring protein, which both facilitates efficient transport of target proteins to the yeast cell surface and yields large amounts of displayed proteins and that other requirements include the ability to attach the target protein onto yeast cell wall without disturbing the activity or stability of the displayed protein (e.g. see page 3092, Discussion). Phienluphon teaches that not even computational predictions were able to predict the functional activities of anchoring proteins with 100% accuracy due to the nature of proteins from different species, the conformational change after fusion with target proteins, and/or the failure to translocate the fusion protein to ER and Golgi complex (e.g. see page 3095, right column).
Furthermore, with specific regards to the integrated coding sequences (i.e. nucleic acids) back-translated from partial structures of 70-99% polypeptide sequence variants, even one of skill in this art cannot envision the structure of a corresponding nucleotide sequence by only knowing what it encodes, as evidenced by the art, for example, see Edelman et al. 2001 (Degeneracy and complexity in biological systems; PNAS 98(24): 13763-13768). In summary, a specific protein sequence is easily determined from a known nucleic acid sequence, because the known sequence of nucleotides (i.e. a nucleic acid sequence; e.g. SEQ ID NO: 314) produces one and only one corresponding protein sequence (i.e. a sequence of amino acids; e.g. SEQ ID NO: 315); but, the inverse is not true because a specific sequence of nucleotides cannot be ascertained from a known sequence of amino acids since more than one distinct codon (i.e. set of three nucleotides) may code for a particular amino acid. Thus, a description of the amino acid per se, does not provide sufficient written description of the codon encoding that amino acid because the one-to-one correspondence is unidirectional, i.e., from codon forward to amino acid, but not from an amino acid back-translated to a codon. Accordingly, a non-routine amount of experimentation would be required to practice the full scope of the invention, with a reasonable expectation of success, because testing such a vast number of options would be easily recognized by the skilled practitioner to be disproportionately demanding (i.e. undue).
Relative Skill of Those in the Art: The relative level of skill of those in the art is deemed to be high (e.g. PhD level); however, even one of skill in the art could not predictably extrapolate the teachings in the specification, limited to one example of engineered Pichia pastoris first modified to express recombinant ovalbumin, and then subsequently modified to express a fusion protein comprising a PGCW14 promoter, a secretion signal, and an SUC2-Tir4 construct wherein the DNA sequence for the expression cassette and the corresponding amino acid sequence are disclosed as SEQ ID NO: 314 and 315 to all of the other host cells, integrated coding sequences, and sequence variants mixed and matched, yet with the same functional properties, as broadly as is claimed. The skilled artisan simply cannot envision the structures required, thus conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method used to determine such structures or to test for such properties, after the fact. Therefore, even one of skill in the art, would have to engage in undue experimentation to determine which options and combinations of options actually retain the necessary functional properties and thereby carry out the full scope of the invention.
Quantity of Experimentation Necessary Based on Content of the Disclosure: The specification does not enable the genus because where the results are unpredictable, the disclosure of a single species usually does not provide an adequate basis to support generic claims. This is because it is not obvious from the disclosure of one particular species, what other species will work; see MPEP 2164.03. One of skill in the art would neither expect nor predict the appropriate functioning of the numerous combinations, and accordingly, without such guidance, the experimentation left to those skilled in the art is unnecessarily and improperly extensive and undue. It is noted that providing methods for determining the functional properties, would not reduce the amount of experimentation required because the functional properties still must be determined empirically. Therefore, the scope of enablement provided to one skilled in the art is not commensurate with the scope of protection sought by the claims.
Therefore, in view of the lack of guidance and direction provided by Applicant there would be undue experimentation required to practice the claimed invention, with a reasonable expectation of success, absent a specific and detailed description in Applicant's specification of how to effectively make and/or use the full scope of the claimed invention. Thus, Applicant has not satisfied the requirements as set forth under 35 U.S.C. 112(a).
Claim Rejections - 35 USC § 102
14. 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.
15. The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections 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.
16. Claims 1, 22, 25, 27 and 29 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Clubb et al. 2012 (WO 2012/118900).
Clubb teaches genetically modified Gram positive microorganisms (i.e. host cells) comprising encoding nucleic acid constructs (i.e. integrated coding sequences) engineered to display heterologous proteins (i.e. proteins of interest) on their surfaces comprising fusion proteins comprising cellulase enzymes and scaffoldin proteins anchored to their cell walls (i.e. on the surface of the host cell) and wherein the cellulolytic enzyme is a glycosyl hydrolase (e.g. [0007-0009, 0018, 0045, 0055, 0078]; and Figures 1 and 2; meeting limitations found in instant claims 1, 22, 25 and 27).
With regards to “…wherein a growth rate of the engineered host cell in a media containing sucrose as a primary carbon source is higher than a growth rate of a control host cell, wherein the control host cell is identical to the engineered host cell, except the control cell does not express the glycosyl hydrolase” in dependent claim 29, it is noted that the limitation does not add a structural element to the product claims and thus has been interpreted as functional property thereof (see MPEP 2112.01) and/or the intended use thereof (see MPEP 2144.07).
Accordingly, Clubb anticipates the invention as claimed.
Claim Rejections - 35 USC § 102
17. Claims 1, 6, 9-10, 13, 15-16, 19, 25, 27, 29-30, 37, and 39 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Argyro et al. 2018 (WO 2018/167670 A1).
Argyro teaches recombinant yeast host cells (i.e. engineered host cells) comprising heterologous nucleic acid molecules encoding chimeric (i.e. fusion) cell-associated proteins (i.e. proteins of interest) including glycosidase (i.e. glycosyl hydrolase) tethered (i.e. anchored) to the cell wall (i.e. surface displayed) and having a linker and wherein the tether is a glycosylphosphatidylinositol (GPI) anchor including an SED1 anchor (see pages 2-3, 15; Table 1; and Argyro claims 22-38; meeting limitations found in instant claims 1, 6, 13, 16, 19, 25, and 27). Argyro teaches the TT (i.e. anchoring protein) may be any one of several sequences including both full length proteins and fragments having 100 or more amino acids (i.e. see pages 3-4, 20-23; meeting limitations found in instant claims 6 and 9-10). Argyro teaches the TT may come from Saccharomyces cerevisiae and a suitable host cell is Pichia pastoris (e.g. see page 13; and Table 1; meeting limitations found in instant claims 15 and 21). Argyro teaches additional genetic modifications may be made to produce secreted proteins (e.g. see Table 1; meeting limitations found in instant claim 30, 37, and 39). Argyro teaches the use of native and/or heterologous promoters (e.g. see Argyro claims 47-50) and the use of terminators (e.g. see Argyro claims 51-56) and the use of heterologous signal sequences (e.g. see Argyro claims 57-60). Argyro teaches the use of invertase (e.g. see Table 1).
With regards to “…wherein a growth rate of the engineered host cell in a media containing sucrose as a primary carbon source is higher than a growth rate of a control host cell, wherein the control host cell is identical to the engineered host cell, except the control cell does not express the glycosyl hydrolase” in dependent claim 29, and “… wherein a fusion protein… provides greater glycosyl hydrolase activity …” in claim 10; it is noted that these limitations do not add a structural element to the product claims and thus have been interpreted as a functional property thereof (see MPEP 2112.01) and/or the intended use thereof (see MPEP 2144.07).
Therefore, Argyro anticipates the invention as claimed.
Claim Rejections - 35 USC § 102
18. Claims 1-2, 5-6, 9-10, 13, 15-16, 19, 21-22, 25, 27, 29-30, and 37 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Phienluphon et al. 2019 (Identification and evaluation of novel anchoring proteins for cell surface display on Saccharomyces cerevisiae; Applied Microbiology and Biotechnology 103: 3085-3097).
Phienluphon teaches genetically modify yeast surface display systems (i.e. engineered host cells), including both Saccharomyces cerevisiae and Pichia pastoris, comprising encoded fusion proteins of passenger proteins (i.e. proteins of interest) attached to GPI-anchored cell wall proteins and green fluorescent proteins and b-glucosidases (i.e. a glycosyl hydrolase) made with vectors comprising a yeast invertase secretion signal (SSsuc2), polyhistidine tag (6xHis), yeast enhanced green fluorescent protein (yEGFP), a (G4S)3 linker, and a multiple cloning site (see abstract; page 3086, left column; and page 3087 Strains and Plasmid construction; Figure 2; and Table 1; meeting limitations found in claims 1, 2, 5, 6, 13, 15, 19, 21, 22, 27, and 37). Phienluphon teaches the use of full length agglutinin, Cwp1p, Cwp2p, Sed1; and Flo1; (see page 3086, left column; meeting limitations found in instant claims 1, 6, 10 and 16). Phienluphon teaches the sequences contain at least 30% serine/threonine content (see abstract; meeting limitations found in instant claims 6 and 9). Phienluphon teaches the anchoring proteins can be N-terminal or C-terminal (e.g. see page 3094; meeting limitations found in instant claim 25). Phienluphon teaches examples for secreted proteins (e.g. see Table 1; meeting limitations found in instant claim 30).
With regards to “…wherein a growth rate of the engineered host cell in a media containing sucrose as a primary carbon source is higher than a growth rate of a control host cell, wherein the control host cell is identical to the engineered host cell, except the control cell does not express the glycosyl hydrolase” in dependent claim 29, and “… wherein a fusion protein… provides greater glycosyl hydrolase activity …” in claim 10; it is noted that these limitations do not add a structural element to the product claims and thus have been interpreted as a functional property thereof (see MPEP 2112.01) and/or the intended use thereof (see MPEP 2144.07).
Accordingly, Phienluphon anticipates the invention as claimed.
Potentially Allowable Subject Matter
19. In the interest of compact prosecution, it is noted that SEQ ID NO: 314 and 315 appear to be free of the art.
Conclusion
20. No claims are allowed.
21. Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY MAILLE LYONS whose telephone number is (571)272-2966. The examiner can normally be reached on Monday-Friday 8 am to 5 pm EST. 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, Dan Kolker can be reached on (571)-272-3181. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
22. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MARY MAILLE LYONS/Examiner, Art Unit 1645 March 9, 2026