DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Receipt of Arguments/Remarks filed on 12/05/2025 is acknowledged. Claims 52-55 and 57-92 are pending. Claims 52, 55, 57, 66, 67, 68, and 71 were amended. Claim 56 was canceled. New claims 90-92 were added. Claims 79-89 are withdrawn.
Withdrawn Objections/Rejections
The objections to the specification and are withdrawn.
The rejections under 35 U.S.C. § 112(b) are withdrawn.
New and modified rejections necessitated by amendment
Claim Rejections - 35 USC § 112
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 67 and 68 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Regarding written description, 35 U.S.C. 112(a) and the first paragraph of pre-AlA 35 U.S.C. 112 require that the "specification shall contain a written description of the invention ...." This requirement is separate and distinct from the enablement requirement. Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010). To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention (MPEP § 2163(I)).
MPEP 2163(II)(A)(3)(a)(i and ii) states that the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus.
A "representative number of species" means that the species which are adequately described are representative of the entire genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., .759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014). Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
Claim 67 recites a polypeptide sequence having at least 80% sequence identity to SEQ ID NO:01 and having N-acetylneuraminate synthase activity. Claim 67 additionally recites a polypeptide sequence having at least 80% sequence identity to SEQ ID NOs: 02, 03, or 04, and having N-acylneuraminate cytidylyltransferase activity. Claim 68 recites a polypeptide sequence having at least 80% sequence identity to SEQ ID NO:05 and having L-glutamine-D- fructose-6-phosphate aminotransferase activity. Claim 68 also recites a polypeptide sequence having at least 80% sequence identity to SEQ ID NO:06 and having glucosamine-6-phosphate N-acetyltransferase activity.
There is not sufficient written description support for a polypeptide sequence with 80% identity to any of SEQ ID NOs: 1 and 3-7 that retains the claimed functions, as there is not a disclosed structure-function relationship for the claimed sequences.
There is no disclosure of which positions or residues can or cannot be mutated, deleted, or truncated in any of these sequences while still maintaining protein function. 80% identity encompasses a wide range of potential sequences, and it would not be clear to a skilled artisan which of these potential variants, for each of SEQ ID NOs: 1 and 3-7, would maintain the claimed functions. For example, SEQ ID NO: 1 has 349 amino acids. This means that anywhere from 1-69 amino acids could vary within the scope of 80% identity. Given that there are 19 alternative amino acids that could be substituted at any of these positions, 80% identity encompasses millions of potential amino acid sequences.
The disclosure has support for the specifically disclosed sequences (SEQ ID NOs: 1 and 3-7). However, there are a vast number of sequences encompassed within 80% identity, and as there are not examples in the specification of a representative number of variants, it is not clear that the inventors had possession of the full scope of the claimed invention at the time of filing.
For these reasons, claims 67 and 68 fail to comply with the written description requirement.
Claim Rejections - 35 USC § 102
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 52-55, 57-65, 70-78, and 90-92 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Pedersen et al., WO 2019/123324 and as evidenced by Stroud et al., Proceedings of the National Academy of Sciences; 104(5):1445-6.
Regarding claim 52, Pedersen teaches constructs and modified bacterial cells for the production of human milk oligosaccharides, including sialylated oligosaccharides (Pedersen p. 1 “Field of the Invention”; p. 56 lines 1-10). Pedersen teaches that the cells are modified for expression of multiple coding DNA sequences via integration of the multiple coding DNA sequences into the genome of the cell or via plasmids (vector stably transformed into the cell) and that the nucleic acid constructs may be integrated in the genome of the host cell or into a plasmid as a single copy or as multiple copies (Pedersen p. 34 lines 1-30). Pedersen teaches strain MAP425 for sialylated oligosaccharide production, which comprises heterologous neuBCA via integration into the E. coli genome and also comprises neuBCA from a multicopy number plasmid, as well as two chromosomally integrated copies of the heterologous gene nst (Pedersen p. 82 Ex. 15; Table 6). Thus, Pedersen teaches a cell modified for expression of multiple coding sequences encoding one or more proteins catalyzing the same chemical reaction (two coding sequences encoding neuBCA, two coding sequences encoding nst), wherein the sequences are heterologous and are integrated into the genome or on a vector transformed into the cell.
Regarding claim 53, Pedersen teaches that at least one of the proteins is involved in the pathway for production of sialylated oligosaccharides: neuB is a Neu5Ac synthase, neuC is UDP-GlcNAc 2-epimerase, neuA is CMP-Neu5Ac synthetase, and nst is an α-2,3-sialyltransferase (Pedersen p. 58 lines 1-15; Table 9).
Regarding claim 54, Pedersen teaches that bacteria producing sialylated human milk oligosaccharides (HMOs) comprise one or more heterologous sialyltransferases (Pedersen p. 58 lines 16-22). The strain MAP425 comprises nst, which is a heterologous α-2,3-sialyltransferase (Pedersen Table 9).
Regarding claim 55, Pedersen teaches that the multiple coding DNA sequences comprise multiple copies of the same DNA sequence and multiple coding DNA sequences encoding one protein, i.e. two copies of nst; neuBCA sequences integrated into the genome and neuBCA sequences introduced as a plasmid in the same cell (Pedersen p. 82 Ex. 15).
Regarding claim 57, Pedersen teaches that coding DNA sequences may be presented to the cell in one or more gene expression modules that are integrated into the cell’s genome or presented on a vector (plasmid) to be stably transformed into the cell (Pedersen p. 34 lines 1-30).
Regarding claims 58 and 59, Pedersen teaches that at least one of the proteins is involved in the synthesis of the nucleotide-activated sugar CMP-sialic acid (CMP-Neu5Ac), as NeuA is a CMP-Neu5Ac synthetase (Pedersen p. 58 lines 1-15).
Regarding claim 60, Pedersen teaches a cell (MP245) modified to express three lgtA and two galTK genomic copies (Pedersen p. 81 Ex. 13). galTK is a β-1,3-galactosyltransferase (Pedersen Table 9). This cell therefore comprises multiple coding DNA sequences integrated into the cell’s genome encoding proteins catalyzing the same chemical reaction (three lgtA copies) and further expresses a galactosyltransferase.
Regarding claim 61, Pedersen teaches HMO-producing bacteria which do not have inherent lactose transport ability are modified with exogenous lactose transporter genes that are provided on a plasmid vector or integrated into the host chromosome (Pedersen p. 52 lines 16-27). Pedersen teaches that the nucleic acid constructs of the invention may be integrated in the genome of the host cell or into a plasmid as as multiple copies (Pedersen p. 34 lines 1-30). Pedersen teaches that an exogenous lacY may be provided (Pedersen p. 52 lines 25-26). LacY is a major facilitator superfamily (MFS) membrane transporter (see Stroud et al. Abstract).
Regarding claim 62, Pedersen teaches that the sialylated oligosaccharide is a milk oligosaccharide, or HMO (Pedersen p. 1 “Field of the Invention”).
Regarding claim 63, Pedersen teaches that the cell, E. coli, comprises a fucosylation pathway comprising phosphomannose isomerase, phosphomannomutase, mannose-1-phosphate guanylyltransferase, GDP-mannose-4,6-dehydratase, GDP-fucose synthase (Pedersen p. 51 lines 6-16).
Regarding claim 64, Pedersen teaches that the cell comprises a galactosylation pathway with a galactosyltransferase (Pedersen p. 81 Ex. 13).
Regarding claim 65, Pedersen teaches that the cell comprises an N-acetylglucosaminylation pathway with a gene encoding N-acetylglucosaminyltransferase (Pedersen p. 59 lines 1-10).
Regarding claims 70 and 71, Pedersen teaches that the E. coli cell comprises a deficient (partially inactivated) sialic acid catabolic pathway by introducing a mutation in the endogenous nanA (N-acetylneuraminate lyase) (Pedersen p. 57 lines 8-10). Strain MAP245 is constructed from E. coli MDO, which has a deletion of nanKETA (Pedersen Table 6).
Regarding claims 72-73, Pedersen teaches that the cell uses a precursor for synthesizing HMOs, including sialylated oligosaccharides, and that the precursors can be produced naturally by the host cell or imported into the cell from the medium (Pedersen p. 33 lines 16-20).
Regarding claim 74, the limitation, “wherein the cell produces” is a functional limitation of the cell according to claim 52. Any cell with the structure recited in claim 52 is considered to be capable of performing this function. Therefore, the cell taught by Pedersen is capable of producing oligosaccharides as set forth in claim 74.
Regarding claim 75, Pedersen teaches that the cell is a bacterium, E. coli (Pedersen p. 56 lines 14-17).
Regarding claim 76, Pedersen teaches a cell with eliminated synthesis of colanic acid by deletion of wcaJ (Pedersen p. 53 lines 9-15). E. coli MDO, which is used to construct MAP245, has a deletion of wcaJ (Pedersen Table 6).
Regarding claims 77-78, Pedersen teaches a cell according to claim 52. The limitations in claims 77-78 “capable of synthesizing” are functional limitations of the cell according to claim 52. Any cell with the structure recited in claim 52 is considered to be capable of performing this function. Therefore, the cell taught by Pedersen is capable of synthesizing a mixture of oligosaccharides according to claims 77 and 78.
Regarding claim 90, Pedersen teaches that two coding DNA sequences according to claim 52, for example heterologous neuBCA, may be present on expression cassettes integrated into the E. coli genome and present on a from a multicopy number plasmid/vector transformed into the cell (Pedersen p. 82 Ex. 15).
Regarding claims 91-92, Pedersen teaches that the multiple heterologous coding sequences of claim 52 comprise two coding DNA sequences encoding the same proteins, neuBCA and nst, and are heterologous to the host cell genome (Pedersen p. 82 Ex. 15).
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim 66 is rejected under 35 U.S.C. 103 as being unpatentable over Pedersen as applied to claims 52-55, 57-65, 70-78, and 90-92 above, in view of Zhu et al., Biotechnology letters; 39(2):227-34.
Pedersen teaches the cell of claim 52, as set forth above. Pedersen does not teach that the cell is modified for enhanced synthesis or supply of phosphoenolpyruvate (PEP) as set forth in claim 66.
Regarding claim 66, Zhu teaches a recombinant E. coli strain for the production of N-Acetyl-D-neuraminic acid (Neu5Ac) using N-acetylglucosamine (GlcNAc) and phosphoenolpyruvate (PEP) as substrates (Zhu “Abstract”). Zhu teaches that Neu5Ac is an important medical precursor and food additive, making economical production of Neu5Ac critical (Zhu pg. 227 para. 1). Zhu teaches that intracellular PEP supply is crucial for Neu5Ac production (pg. 227 para. 2) and that PEP is synthesized by PEP synthase, ppsA, and PEP carboxykinase, pck (Zhu pg. 228 para. 1). Zhu teaches an E. coli strain overexpressing ppsA and pck, which resulted in increased PEP synthesis and improved production of Neu5Ac (Zhu pg. 228 para. 1).
It would have been obvious to a skilled artisan, before the effective filing date, to combine the teachings of Pedersen and Zhu, creating a recombinant bacterial strain with enhanced synthesis of PEP. Zhu teaches a genetically modified strain for enhancing Neu5Ac production, which is involved in the production of sialylated oligosaccharides (Pedersen p. 57 lines 5-10). It would have been obvious to a person having ordinary skill in the art that a cell for producing sialylated oligosaccharides such as the cell taught by Pedersen could be further modified to enhance the production of PEP and thereby enhance Neu5Ac precursor production.
A person of ordinary skill in the art would have been motivated to modify the cell of Pedersen and enhance the synthesis of PEP because enhanced PEP synthesis results in greater production of Neu5Ac, which is an important precursor for sialylated oligosaccharide production (Zhu pg. 228 para. 1). Thus, it would be considered advantageous to increase the production of this precursor in a cell engineered for the purpose of oligosaccharide production in order to improve the yield of sialylated oligosaccharides.
A skilled artisan would have a reasonable expectation of success in creating a cell for sialylated oligosaccharide production with enhanced PEP production, as techniques for modulating metabolic pathways to optimize oligosaccharide production are known in the art as taught by both Pedersen and Zhu. As Zhu teaches enhanced PEP production leads to increased Neu5Ac production, and this is a necessary precursor for sialylated oligosaccharide synthesis, a skilled artisan could reasonably expect success in modulating PEP production in a cell taught by Pedersen for the same purpose of enhanced Neu5Ac accumulation.
Claim 67 is rejected under 35 U.S.C. 103 as being unpatentable over Pedersen as applied to claims 52-55, 57-65, 70-78, and 90-92 above, in view of Gunawan et al., Journal of Biological Chemistry; 280(5):3555-63, as evidenced by NCBI NeuA and NCBI NeuB.
Pedersen teaches the cell of claim 52, as set forth above. Regarding claim 67, Pedersen teaches strain MAP245, which comprises two coding sequences encoding Campylobacter jejuni NeuA, (Pedersen p. 67 Table 9, p. 82 Ex. 15). The NeuA sequence of Pedersen, GenBank AAK91728.1, is 100% identical to instant SEQ ID NO: 3 (Pedersen p. 58 lines 13-14; see NCBI NeuA ref and sequence alignment in OA appendix). MAP245 additionally comprises two copies of nst, which is an a-2,3-sialyltransferase (Pedersen Table 6).
Strain MAP245 comprises two coding sequences encoding NeuB from Campylobacter jejuni (Pedersen p. 67 Table 9, p. 82 Ex. 15). Pedersen teaches that the Neu5Ac synthase may be NeuB from Campylobacter jejuni or an equivalent (Pedersen p. 58 lines 10-12).
Pedersen does not teach that the cell comprises Neisseria meningitidis NeuB with a sequence according to SEQ ID NO: 1 or at least 80% identical to SEQ ID NO: 1 (claim 67).
Regarding claim 67, Gunawan teaches the structure and function of Neisseria meningitidis NeuB, which has a sequence that is identical to instant SEQ ID NO: 1 (Gunawan “Abstract”; see NCBI NeuB ref. and sequence alignment in OA appendix). Gunawan teaches that the sialic acid synthase, NeuB, directly converts phosphoenolpyruvate (PEP) and N-acetylmannosamine (Man-NAc) into N-acetylneuraminic acid (NeuNAc, or sialic acid), and orthologous genes with the same function in other organisms include Campylobacter jejuni neuB(Gunawan p. 3555 para. 2).
It would have been obvious for a skilled artisan, before the effective filing date, to substitute the NeuB sequence of Pedersen for the Neisseria meningitidis NeuB sequence taught by Gunawan. Both of these sequences are known in the prior art and have the same function as a Neu5Ac synthase. Pedersen teaches that NeuB can be Campylobacter jejuni NeuB or an equivalent, and Gunawan teaches that known orthologous genes to Neisseria meningitidis NeuB include Campylobacter jejuni neuB. Therefore, an ordinary artisan would have found it obvious to make this substitution, with a reasonable expectation of success. This is considered a simple substitution of one known element for another with predictable results, as these genes encode proteins with the same function and are known in the art as orthologous genes.
Claims 68 and 69 are rejected under 35 U.S.C. 103 as being unpatentable over Pedersen as applied to claims 52-55, 57-65, 70-78, and 90-92 above, and further in view of Kang et al., Metabolic Engineering; 14(6):623-9, as evidenced by NCBI glmS.
Pedersen teaches the cell of claim 52, as set forth above. Pedersen additionally teaches that the bacterium comprising the capability of sialic acid synthesis may have increased production of glmS, achieved by providing additional copies of the glmS gene on a plasmid vector (Pedersen p. 58 lines 21-30). The glmS sequence of Pedersen has Accession P17169, and is 99.5% identical to instant SEQ ID NO: 6 (Pedersen p. 31 Table 3; see NCBI glmS ref. and sequence alignment in OA appendix).
Pedersen does not teach that the cell comprises two or more copies of a coding DNA sequence encoding GNA1 from Saccharomyces cerevisiae having glucosamine 6-phosphate N-acetyltransferase activity as set forth in claim 68. Pedersen does not teach that the cell is modified for reduced production of acetate as recited in claim 69.
Regarding claim 68, Kang teaches genetically engineered E. coli for the production of Neu5Ac (Kang “Abstract”). Kang teaches that NeuAc has pharmaceutical applications, requiring large scale production (Kang pg. 623 para. 1). Kang teaches that NeuAc synthesis,requires expensive substrate precursors as well as ATP to activate GlcNAc2-epimerase, which is unsuitable in large scale production, making it desirable to optimize strains and fermentation processes for NeuAc production (Kang pg. 628 “Conclusion”). Kang teaches heterologous expression of the GNA1 gene encoding GlcNAc2-epimerase from Saccharomyces cerevisiae to construct a synthetic pathway for NeuAc production in E. coli (Kang pg. 626 Section 3.1 para. 1). This GNA1 from S. cerevisiae, being from the same organism and having the same function, is expected to have the sequence according to instant SEQ ID NO: 7, which is GNA1 from S. cerevisiae. Kang teaches that the strain derepresses the feedback inhibition of glucosamine-6-phosphate synthase, increasing the accumulation of N-acetylglucosamine and pyruvate and blocking the catabolism of NeuAc, resulting in greater NeuAc production (Kang “Abstract”).
Regarding claim 69, Kang teaches that the cell is engineered to have reduced acetate production in order to provide more pyruvate for NeuAc biosynthesis (Kang pg. 627 Section 3.3 para. 1; Fig. 3).
It would have been obvious to a skilled artisan, before the effective filing date, to combine the teachings of Pedersen and Kang, creating a modified cell with two or more copies of GNA1 and reduced acetate production. Kang teaches a strain for enhanced production of the sialylated oligosaccharide precursor, NeuAc. It would have been obvious to a person having ordinary skill in the art that GNA1 could be expressed in the cell taught by Pedersen. It would have further been obvious to express two or more copies of the gene, as Pedersen teaches this technique for overexpressing other genes in the sialylated oligosaccharide synthesis pathway as discussed above. Additionally, it would have been obvious to make modifications to reduce acetate production in the cell of Pedersen given the influence of reduced acetate production on Neu5Ac production as taught by Kang.
A person of ordinary skill in the art would have been motivated to modify the cell of Pedersen and express multiple copies of GNA1, as well as reduce acetate production, as both of these modifications resulted in enhanced Neu5Ac production as taught by Kang. Efficient Neu5Ac production is desirable as this product is pharmaceutically relevant (Kang pg. 623 para. 1), and it would additionally be advantageous to increase Neu5Ac production to increase sialylated oligosaccharide production, as Neu5Ac is a precursor for sialylated oligosaccharides.
A skilled artisan would have a reasonable expectation of success in creating a cell for sialylated oligosaccharide production with GNA1 expressed and reduced acetate production, as genetic modification of pathways involved in oligosaccharide production is established in the prior art as taught by Pedersen and Kang. As Kang teaches that GNA1 expression and reduced acetate production leads to increased Neu5Ac production, and this is a necessary precursor for sialylated oligosaccharide synthesis, a skilled artisan could reasonably expect success in making these modifications to a cell taught by Pedersen for the same purpose of enhanced Neu5Ac accumulation.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 52-55, 57-78, and 90-92 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 82-86, 88-109, 111-113, 115-118 of copending Application No. 18041154 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims overlap in scope.
Regarding instant claim 52, claim 80 of copending ‘154 recites a cell for producing a di- and/or oligosaccharide, the cell comprising a pathway for production of the di- and/or oligosaccharide, wherein the cell is genetically modified for expression and/or overexpression of at least one set of multiple coding DNA sequences, wherein the multiple coding DNA sequences within one set differ in nucleotide sequence, and each encode a polypeptide, wherein the polypeptides have the same function and/or activity of interest. Claim 101 of ‘154 recites that the pathway comprises a sialylation pathway. Claim 84 of ‘154 recites that the multiple coding DNA sequences are integrated into the genome or presented on one or more vectors. Claim 112 recites that the cell may be a fungus, yeast, plant, animal, or protozoan cell, and that the coding DNA sequences in the cell of claim 80 are from Campylobacter, Haemophilus, or Pastuerella, which are bacteria. Therefore, the DNA sequences would be heterologous to the cell.
Regarding instant claims 53-55, 57-78, and 90-92, all the limitations of these dependent claims are recited in claims 82-86, 88-109, 111-113, 115-118 of copending ‘154.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 52-65, 70-78, and 90-92 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 101-110 and 112-118 of copending Application No. 18040356 in view of Pedersen et al., WO 2019/123324.
Regarding instant claim 52, copending ‘356 recites a metabolically engineered cell that produces a mixture of at least three different sialylated oligosaccharides, wherein the mixture comprises more than one mammalian milk oligosaccharide, wherein the cell is metabolically engineered for the production of the mixture, expresses a glycosyltransferase which is a sialyltransferase, is capable of synthesizing the nucleotide-sugar CMP-N-acetylneuraminic acid (CMP-Neu5Ac), expresses at least one glycosyltransferase in addition to sialyltransferase, and is capable of synthesizing one or more nucleotide-sugar(s), wherein the nucleotide-sugar(s) is/are donor(s) for the additional glycosyltransferase.
Copending ‘356 does not recite that the cell is modified for expression of multiple coding DNA sequences encoding one or more proteins that catalyze a same chemical reaction as recited in claim 52, or the limitations recited in dependent claims 55, 57, 59, 70-71, 76, and 90-92.
Regarding claims 52, 55, and 90-92, Pedersen teaches constructs and modified bacterial cells for the production of human milk oligosaccharides, including sialylated oligosaccharides (Pedersen p. 1 “Field of the Invention”; p. 56 lines 1-10). Pedersen teaches that the cells are modified for expression of multiple coding DNA sequences via integration of the multiple coding DNA sequences into the genome of the cell or via plasmids (vector stably transformed into the cell) and that the nucleic acid constructs may be integrated in the genome of the host cell or into a plasmid as a single copy or as multiple copies (Pedersen p. 34 lines 1-30). Pedersen teaches strain MAP425, which comprises heterologous neuBCA via integration into the E. coli genome and also comprises neuBCA from a multicopy number plasmid (Pedersen p. 82 Ex. 15). Thus, Pedersen teaches a cell modified for expression of multiple heterologous coding sequences encoding one or more proteins catalyzing the same chemical reaction (two coding sequences encoding neuBCA).
Regarding claim 57, Pedersen teaches that coding DNA sequences may be presented to the cell in one or more gene expression modules that are integrated into the cell’s genome or presented on a vector (plasmid) to be stably transformed into the cell (Pedersen p. 34 lines 1-30).
Regarding claims 58-59, Pedersen teaches that at least one of the proteins is involved in the synthesis of the nucleotide-activated sugar CMP-sialic acid (CMP-Neu5Ac) via NeuA, which is a CMP-Neu5Ac synthetase (Pedersen p. 58 lines 1-15).
Regarding claim 70, Pedersen teaches that the E. coli cell comprises a deficient sialic acid catabolic pathway by introducing a mutation in the endogenous nanA (N-acetylneuraminate lyase) (Pedersen p. 57 lines 8-10).
Regarding claim 71, Pedersen teaches that the E. coli cell comprises a deficient sialic acid catabolic pathway (Pedersen p. 57 lines 8-10).
Regarding claim 76, Pedersen teaches a cell with eliminated synthesis of colanic acid (Pedersen p. 53 lines 9-15).
It would have been obvious to a skilled artisan to modify the teachings of ‘356 and create a cell modified for expression or overexpression of multiple coding DNA sequences encoding one or more proteins that catalyze a same chemical reaction as taught by Pedersen. Both ‘356 and Pedersen are directed to genetically modified bacteria for sialylated oligosaccharide production. It would be obvious to incorporate a known technique for genetic modification, expressing multiple coding DNA sequences of a protein, in a cell as recited in claim ‘356. A skilled artisan could reasonably expect success in doing so given the teachings of Pedersen successfully utilizing a cell comprising multiple coding sequences of enzymes catalyzing the same reaction involved in sialylated oligosaccharide production. As both ‘356 and Pedersen are directed to sialylated oligosaccharide production, a skilled artisan would have found it obvious, with a reasonable expectation of success, to incorporate the additional modifications to the cell as taught by Pedersen to the cell of ‘356, as these modifications were successfully incorporated in a cell for sialylated oligosaccharide production.
Regarding instant claims 53-54, 58, 60-65, 72-75, and 77-78, all the limitations of these dependent claims are recited in claims 101-110 and 112-118 of copending ‘356.
This is a provisional nonstatutory double patenting rejection.
Claims 52-55, 57-65, 70-75, 77-78, and 90-92 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 49 and 51-55 of copending Application No. 17787115 in view of Pedersen et al., WO 2019/123324.
Regarding instant claim 52, claim 49 of ‘115 recites “a host cell genetically modified for the production of sialylated oligosaccharide, wherein the host cell comprises at least one polynucleotide encoding an enzyme for sialylated oligosaccharide synthesis”. “At least one” polynucleotide encompasses multiple coding DNA sequences or copies of a coding sequence for a protein.
The claims of ‘115 do not teach that the cell is modified for expression of multiple heterologous coding DNA sequences encoding proteins that catalyze a same chemical reaction via integration of the multiple coding DNA sequences into the cell's genome and/or into at least one vector that is stably transformed in the cell as recited in claim 52, or the limitations recited in dependent claims 55, 57, 58, 60, 63-65, 70, and 90-92.
The teachings of Pedersen regarding claim 52, 57, 58, 70, and 90-92 are set forth above.
Regarding claim 60, Pedersen teaches a cell (MP245) modified to express three lgtA and two galTK genomic copies (Pedersen p. 81 Ex. 13). galTK is a β-1,3-galactosyltransferase (Pedersen Table 9). This cell therefore comprises multiple coding DNA sequences integrated into the cell’s genome encoding proteins catalyzing the same chemical reaction (three lgtA copies) and further expresses a galactosyltransferase.
Regarding claim 63, Pedersen teaches that the cell, E. coli, comprises a fucosylation pathway comprising phosphomannose isomerase, phosphomannomutase, mannose-1-phosphate guanylyltransferase, GDP-mannose-4,6-dehydratase, GDP-fucose synthase (Pedersen p. 51 lines 6-16).
Regarding claim 64, Pedersen teaches that the cell comprises a galactosylation pathway with a galactosyltransferase (Pedersen p. 81 Ex. 13).
Regarding claim 65, Pedersen teaches that the cell comprises an N-acetylglucosaminylation pathway with a gene encoding N-acetylglucosaminyltransferase (Pedersen p. 59 lines 1-10).
It would have been obvious to a skilled artisan to modify the teachings of ‘115 and create a cell modified for expression or overexpression of multiple coding DNA sequences encoding one or more proteins that catalyze a same chemical reaction as taught by Pedersen, with the same pathways and genetic modifications as taught by Pedersen. Both ‘115 and Pedersen are directed to genetically modified bacteria for sialylated oligosaccharide production. It would be obvious to incorporate a known technique for genetic modification, expressing multiple coding DNA sequences of a protein, in a cell as recited in claim ‘115. A skilled artisan could reasonably expect success in doing so given the teachings of Pedersen successfully utilizing a cell comprising multiple coding sequences of enzymes catalyzing the same reaction involved in sialylated oligosaccharide production. As both ‘115 and Pedersen are directed to sialylated oligosaccharide production, a skilled artisan would have found it obvious, with a reasonable expectation of success, to incorporate the additional modifications to the cell as taught by Pedersen, as these modifications were successfully incorporated in a cell for sialylated oligosaccharide production.
Regarding instant claims 53-54, 59, 61-62, 71, and 75, all the limitations of these dependent claims are recited in claims 49 and 51-55 of copending ‘115.
Regarding instant claims 72-73, 74, 77-78, the “wherein” clauses are directed to functional limitations of the cell of claim 52. It is expected that any cell having this same structure, including the cell of copending ‘115, is capable of performing this function.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 52-55, 57-66 and 69-78 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 54-57, 61, 63, 66-72, 74-79, and 81-82 of copending Application No. 18555663 in view of Pedersen et al., WO 2019/123324.
Regarding instant claim 52, claim 54 of copending ‘663 recites a metabolically engineered cell of a microorganism for production of a sialylated di- and/or oligosaccharide, the cell comprising a pathway for production of the sialylated di- and/or oligosaccharide, wherein the cell expresses at least one sialyltransferase, and optionally is modified in the expression or activity of at least one sialyltransferase.
Copending ‘663 does not recite that the cell is modified for expression of multiple coding DNA sequences encoding one or more proteins that catalyze a same chemical reaction as recited in claim 52, or the limitations of claims 55, 70, 76, or 90-92.
Regarding claims 52, 55, 70, 76, and 90-92, the teachings of Pedersen are set forth above.
It would have been obvious to a skilled artisan to modify the teachings of ‘663 and create a cell modified for expression or overexpression of multiple coding DNA sequences encoding one or more proteins that catalyze a same chemical reaction as taught by Pedersen. Both ‘663 and Pedersen are directed to genetically modified bacteria for sialylated oligosaccharide production. It would be obvious to incorporate a known technique for genetic modification, expressing multiple coding DNA sequences of a protein, in a cell as recited in claim ‘663. As both ‘663 and Pedersen are directed to sialylated oligosaccharide production, a skilled artisan would have found it obvious, with a reasonable expectation of success, to incorporate the additional modifications to the cell as taught by Pedersen, as these modifications were successfully incorporated in a cell for sialylated oligosaccharide production.
Regarding instant claims 53-54, 57-66, 69, 71-75, and 77-78 all the limitations of these dependent claims are recited in claims 54-57, 61, 63, 66-72, 74-79, and 81-82 of copending ‘663.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
In light of amendments to the claims, the rejection of claims 52-60, 62-65, 67, and 70-78 under 35 U.S.C. § 102 in view of Merighi has been withdrawn. However, upon further consideration, new grounds of rejection of the are made under 35 U.S.C. § 102 in view of Pedersen as set forth above. Given these new grounds of rejection, the arguments presented regarding claims rejected under 35 U.S.C. § 102 in view of Merighi are moot.
Responses to pertinent arguments are set forth below.
35 U.S.C. § 112(a)
Applicant argues that the amended claims do not require identification of permissible substitutions, and that the amended claims are tied to experimentally demonstrated enzymatic functions, not hypothetical variants. Applicant argues that the application discloses multiple NeuA enzymes with demonstrated activity despite considerable sequence divergence (SEQ ID NOs: 3-5) and that the disclosure of multiple functional NeuA enzymes spanning broad natural sequence variation reflects possession of a NeuA genus significantly broader than the narrower 80% identity claim requirement and demonstrated activity.
In response to these arguments, it is noted that, as stated in the above rejection under 35 U.S.C. § 112(a), the number of sequences having 80% identity to the claimed SEQ ID NOs: is extremely vast. While the claims do require an enzymatic function, the claims are directed to any variant of the claimed SEQ ID NOs with 80% identity and enzyme function. There are many possible variants within the scope of 80% identity that have enzymatic activity. Applicant points out the disclosure of three NeuA sequences which have considerable sequence divergence and maintain enzyme activity. However, these sequences are not representative of the large number of sequences that have 80% identity to the claimed SEQ ID NOs and enzymatic function. There are many more enzymes, which are not disclosed by the applicant, that are 80% identical and have enzyme activity.
The rejection under 35 U.S.C. § 112(a) is made because it is not clear that applicant had possession of the full scope of the claimed invention. The specification has support for the specifically disclosed sequences, SEQ ID NOs: 1 and 3-7. These sequences have been shown to possess enzyme activity, as demonstrated by applicant in Table 1 of the arguments and in the Examples of the specification. However, the disclosure of these sequences is not representative of all sequences having 80% identity and enzyme activity. Applicant’s arguments are directed to specifically disclosed sequences which have demonstrated enzyme activity, but this does not indicate that applicant was in possession of the entire genus of sequences with 80% identity to the claimed SEQ ID NOs and enzymatic function. For this reason, the rejection under 35 U.S.C. § 112(a) is maintained.
35 U.S.C. § 103
Applicant argues that claim 66 requires overexpression of genes specifically increasing PEP or glmS/GNA1 pathway flux, specifically, two or more copies of glmS or GNA1. Applicant argues that claim 66 requires multiple copies of a specific enzyme type, not merely enhanced
metabolic flux at the pathway level.
In response to this argument, it is noted that claim 66 recites “wherein the cell is modified for enhanced synthesis or supply of phosphoenolpyruvate (PEP) in comparison to a non-modified progenitor cell”. Claim 66 does not require the overexpression of any particular genes, and does not recite glmS or GNA1. Claim 52, which claim 66 depends on, teaches that the cell comprises multiple copies of a coding sequence for a protein catalyzing the same reaction. However, these can be any coding sequences. Therefore, a cell comprising two copies of a coding sequence for a protein that catalyzes the same chemical reaction (such as neuBCA or nst as taught by Pedersen), which additionally has a modification to increase PEP synthesis, meets the claim. The expression “modified” is broad and encompasses any number of changes that could be made to a cell, not just genetic modification for overexpression of particular genes. As set forth above, it is considered that Pedersen in view of Zhu renders obvious claim 66.
Applicant argues regarding claims 69 that Kang achieves reduced acetate formation by gene deletions, not by providing multiple copies of an enzyme catalyzing the same reaction, as claim 69 requires.
In response to this argument, it is noted that claim 69 does not require that the reduced production of acetate be achieved by providing multiple copies of an enzyme catalyzing the same reaction. As discussed above, although this claim depends on claim 52 which requires multiple copies of the same enzyme, this could be copies of any enzyme. Claim 69 states that the cell of claim 52 comprises a modification for reduced acetate production. Therefore, a cell which comprises two copies of a coding sequence (such as neuBCA as taught by Pedersen), and additionally comprises a modification to reduce acetate production, meets the claim. The expression “modified” is broad and encompasses any number of changes that could be made to a cell, not just the specific genetic modification to provide multiple copies of a sequence. As set forth above, it is considered that Pedersen in view of Kang renders obvious claim 69.
Applicant argues that the cells of the invention display unexpected properties such as stability. Applicant argues that the cells have unexpected performance advantages including positive effects on fermentative production and yield, higher lactose conversion, higher secretion, and higher growth speed, which are not taught by the prior art.
In response to these arguments, it is noted that the instant claims are directed to a modified cell product. Pedersen is now relied upon to teach a cell comprising multiple copies of the same enzyme sequence that are integrated into the host genome or on a plasmid as discussed in the above rejections. Regarding the unexpected properties, Pedersen teaches a cell having the same structure as the claimed cell, and any cell having an identical structure to the claimed cell must therefore have the same properties. Regarding the performance advantages, these are functional features of the claimed cell, and as the cell of Pedersen has the same structure, it is considered to be capable of performing the same functions.
Double Patenting
The rejections on the grounds of non-statutory double patenting are modified in view of claim amendments and maintained, for the reasons set forth above.
Conclusion
Claims 52-55, 57-78 and 90-92 are rejected. No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/EMILY F EIX/Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653