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 7/15/2026 is acknowledged. Claims 1-10 were canceled. New claims 11-30 were added. Claims 11-30 are pending.
It is noted that claims 29 and 30 do not have a proper status identifier, i.e. “(New)”. However, as the remarks state that claims 11-30 are added, claims 29 and 30 are being treated as newly added claims.
Information Disclosure Statement
The information disclosure statement filed 9/23/2026 fails to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. The references not considered by the examiner are lined through on the IDS form.
Withdrawn Rejections
The rejections of claims 9 and 10 on the ground of nonstatutory double patenting are withdrawn in view of claim amendments.
New objections and rejections necessitated by amendment
Claim Objections
Claim 11 is objected to because of the following informalities: claim 11 recites “the genetically engineering microbial cell” in line 4. This should instead read “the genetically engineered microbial cell”. Appropriate correction is required.
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 11-30 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.
In the instant case, claim 11 recites a lactose permease variant with a sequence identity of 70% to E. coli wild-type lactose permease LacY and comprises a basic amino acid residue in at least one of amino acid positions 292, 293 and 294 with respect to the lactose permease as represented by SEQ ID NO: 1. There is not sufficient written description support for a protein having 70% sequence identity with the claimed substitutions which maintains the claimed function, i.e. a reduced internalization of lactose as compared to E. coli wild-type LacY. SEQ ID NO: 1, or the WT E. coli LacY sequence, has 417 amino acids. This means that ~125 amino acids may differ from the WT sequence within the scope of 70% identity, in addition to other modifications such as insertions or deletions. This is a vast number of potential amino acid sequences.
Claim 1 recites that positions 292, 293, and 294 are substituted with a basic amino acid residue. Table 3 of the instant specification recites 6 residues which are irreplaceable while maintaining enzyme function. Table 4 of the instant specification recites 9 amino acid residues which are not essential for lactose transport, some of which result in no change to transport activity when mutated. The only disclosure of a LacY variant with reduced internalization of lactose are substitutions at positions 292, 293, and 294 to R, K, or H (instant specification p. 12 lines 19-17). It is additionally noted that of these, there is only experimental data for L293R showing decreased lactose internalization (instant specification Ex. 4; Fig. 5). However, these examples and recitation of 6 residues which cannot be mutated are not representative of the entire genus of proteins with a sequence 70% identical to SEQ ID NO: 1, as 70% identity encompasses ~125 potential amino acid substitutions plus other modifications. A skilled artisan would not have been aware of which of the vast number of variant sequences would have the claimed activity based on the disclosure.
Similarly, claims 13-15 are directed to variants with 80, 90, or 95% identity to the WT E. coli LacY permease, i.e. SEQ ID NO: 1. With 80% sequence identity, ~83 amino acid residues can vary from WT; with 90% identity, ~42 amino acid residues can vary from WT; and with 95% identity, ~21 amino acid residues can vary from WT; in addition to any other modifications such as insertion and deletion of residues. As discussed above, only 3 residue mutations are specifically claimed, and only L293R is exemplified as having the claimed function of decreased lactose internalization. While there are 6 residues indicated as irreplaceable, this is not sufficient to indicate which of the vast number of amino acid sequences encompassed by 80, 90, or 95% identity to SEQ ID NO: 1 would have the claimed function.
For these reasons, it is not clear that the applicant was in possession of the entire scope of the invention at the time of filing.
Claims 12 and 16-30 are included in this rejection because they depend on a rejected claim and do not clarify the issue.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 11-30 are rejected under 35 U.S.C. 103 as being unpatentable over Beauprez et al., US 2018/0066294 A1, in view of Sahin‐Tóth et al., Protein Science. 1993 Jun;2(6):1024-33, and as evidenced by Zhang, Journal of molecular evolution. 2000 Jan;50(1):56-68.
Regarding claim 11, Beauprez teaches a method of producing an oligosaccharide of interest by providing a genetically engineered microbial cell that resists lactose killing (p. 1 para. 1). Beauprez teaches that the engineered microbes take up lactose and convert lactose to human milk oligosaccharides (p. 5 para. 68). Beauprez teaches cultivating the microbe in the presence of exogenous lactose in a medium (p. 6 para. 83; p. 11 para. 148) under conditions wherein the microbe can intracellularly synthesize the oligosaccharide (p. 5 para. 68).
Beauprez teaches a genetically engineered microbial cell for the production of an oligosaccharide of interest (p. 1 para. 1). Beauprez teaches that the microbial cell comprises a lactose transporter, which may be a lactose permease such as lacY (p. 3 para. 50; p. 4 para. 56; p. 9 para. 126). Beauprez teaches modifying E. coli lacY to develop a mutant (variant) strain which expresses lactose permease and resists lactose killing (p. 10 para. 140-141). Beauprez teaches selecting microorganisms with variant lactose transporters (i.e. lacY) which retain at least 50% of lactose influx compared to the wild type transporter, i.e. reduced internalization of lactose (p. 3 para. 51).
Beauprez does not teach that the variant of the E. coli lactose permease LacY has a sequence identity of at least 70% to the wildtype and comprises basic amino acid residues in positions 292, 293, or 294 of SEQ ID NO: 1.
Regarding claim 11, Sahin-Toth teaches mutagenesis of residues in the transmembrane helix IX region of E. coli lactose permease LacY (Sahin-Toth Abstract). Amino acid positions 292, 293, and 294 are in the transmembrane helix IX region of LacY (see instant specification Table 2). Sahin-Toth teaches that the transmembrane helix IX region is important for the lactose transport activity of LacY (Sahin-Toth p. 1025 para. 1-2). Sahin-Toth teaches replacing the leucine residue at positions 292, 293, and 294 with cysteine, which results in a decrease in lactose transport (Sahin-Toth Fig. 2). Instant SEQ ID NO: 1 is the wildtype sequence of E. coli LacY. As Sahin-Toth teaches the wildtype E. coli LacY sequence, it is expected that the LacY sequence of Sahin-Toth would be identical, i.e., have at least 70% identity, to instant SEQ ID NO: 1.
Conservative amino acid substitutions, wherein an amino acid is substituted for a different amino acid with similar physiochemical properties, are known in the art, and a conservative substitution is expected to have minimal impact on the protein function (see Zhang “Introduction”). Non-conservative substitutions, wherein an amino acid is substituted for an amino acid with different physiochemical properties, are expected to result in a change to protein function. Leucine (the amino acid at positions 292, 293, and 294 in WT LacY) is a neutral, nonpolar, small amino acid, while the basic amino acids (R, H, and K) are positively charged, polar, and relatively large (Zhang Fig. 1). Therefore, given the teachings of Sahin-Toth that a non-conservative substitution of L to C results in a change in lacY function, specifically decreased lactose transport, it would be expected that another non-conservative substitution to a basic amino acid at these residues would also change the function of lacY and cause a decrease in transport activity.
Given the teachings of Sahin-Toth and general knowledge in the art of amino acid substitutions, it would have been obvious for a skilled artisan to substitute a basic amino acid residue at any of positions 292, 293, or 294 of E. coli LacY. Sahin-Toth teaches that making a non-conservative substitution of cysteine at these residues results in decreased lactose transport activity. Thus, it would have been obvious to make a different non-conservative substitution of a basic amino acid residue that has different physiological properties than the native leucine at any of positions 292, 293, or 294, which would also be expected to alter the activity of the LacY protein.
Further, as Beauprez teaches using E. coli expressing a LacY variant with decreased lactose transport in a method of producing an oligosaccharide, it would have been obvious for person having ordinary skill in the art to use an E. coli strain with LacY modified to have a substitution of a basic amino acid residue at positions 292, 293, or 294 in a method for this same purpose.
A skilled artisan would have been motivated to substitute a basic amino acid residue at positions 292, 293, or 294 of LacY in E. coli because Sahin-Toth teaches making substitutions at these positions, and teaches that a non-conservative substitution at these positions results in decreased lactose transport. A person having ordinary skill in the art would have been motivated use this modified E. coli in a method of producing an oligosaccharide because Beauprez teaches using E. coli with LacY modified to have decreased lactose transport in a method for producing oligosaccharides of interest. Thus, it would be considered beneficial to use a strain with LacY substitutions at positions which result in decreased lactose transport in a method for producing oligosaccharides. As a substitution of a basic amino acid at residues 292, 293, or 294 would be expected to alter the function of the enzyme, and Sahin-Toth teaches that non-conservative substitutions at these positions result in decreased lactose transport, a skilled artisan would have been motivated to use a strain with these substitutions in the method of Beauprez.
A person having ordinary skill in the art would have had a reasonable expectation of success in doing so because Sahin-Toth teaches that non-conservative substitutions at positions 292, 293, and 294 result in decreased lactose transport for E. coli , and thus it could be reasonably expected that a different non-conservative substitution to a basic amino acid reside, would similarly change the function of LacY. As modified E. coli having decreased lactose transport are known to be used in methods of producing oligosaccharides as taught by Beauprez, a skilled artisan could reasonably expect success in using a different E. coli strain with modified LacY for such a method.
Regarding claim 12, Beauprez teaches that the microbial cells produce the oligosaccharides of interest and the oligosaccharides are accumulated and measured by HPLC, i.e. recovered from the cell or culture medium for analysis (p. 7 para. 92; p. 11 para. 149).
Regarding claims 13-15, as discussed above, Sahin-Toth teaches the wildtype E. coli LacY sequence. It is expected that the LacY sequence of Sahin-Toth would be identical, i.e., have at least 80%, 90%, or 95% identity, to E. coli wild-type lactose permease LacY, or SEQ ID NO: 1.
Regarding claims 16-18, Beauprez and Sahin-Toth teach the method of claim 11. It would have been obvious for a skilled artisan to substitute any of residues 292, 293, or 294 with a basic amino acid residue, which includes arginine, histidine, and lysine, for the reasons discussed above. Therefore, claims 16-18 are obvious in view of the combination of Beauprez and Sahin-Toth.
Regarding claims 19-21, Beauprez and Sahin-Toth teach the method of claim 13. It would have been obvious for a skilled artisan to substitute any of residues 292, 293, or 294 with a basic amino acid residue, which includes arginine, histidine, and lysine, for the reasons discussed above. Therefore, claims 19-21 are obvious in view of the combination of Beauprez and Sahin-Toth.
Regarding claims 22-24, Beauprez and Sahin-Toth teach the method of claim 14. It would have been obvious for a skilled artisan to substitute any of residues 292, 293, or 294 with a basic amino acid residue, which includes arginine, histidine, and lysine, for the reasons discussed above. Therefore, claims 22-24 are obvious in view of the combination of Beauprez and Sahin-Toth.
Regarding claims 25-27, Beauprez and Sahin-Toth teach the method of claim 15. It would have been obvious for a skilled artisan to substitute any of residues 292, 293, or 294 with a basic amino acid residue, which includes arginine, histidine, and lysine, for the reasons discussed above. Therefore, claims 25-27 are obvious in view of the combination of Beauprez and Sahin-Toth.
Regarding claim 28, Beauprez and Sahin-Toth teach the method of claim 15. Sahin-Toth teaches that substitution of any of the residues 292, 293, or 294 of E. coli lacY results in decreased lactose transport (Sahin-Toth Fig. 2). It would have been obvious for a skilled artisan to substitute a basic amino acid reside (arginine, histidine, or lysine), in any or all of these residues, i.e., at least two, as they are all associated with decreased lactose transport, as discussed above. It would have been obvious to utilize an E. coli strain having substitutions in at least two of these positions in a method of producing oligosaccharides, for the same reasons set forth above.
Regarding claim 29, Beauprez teaches that the organisms used in the method for producing oligosaccharides synthesize nucleotide sugars, i.e. comprise at least one metabolic pathway for intracellular biosynthesis of a nucleotide activated sugar (Beauprez p. 5 para. 69). Beauprez teaches that the organisms can transfer these nucleotide sugars onto a mono-, di- or oligosaccharide by means of a glycosyltransferase enzyme, i.e. comprises at least one glycosyltransferase for transferring intracellularly a monosaccharide moiety from the nucleotide-activated monosaccharide as donor substrate to lactose or an oligosaccharide as acceptor molecule (Beauprez p. 6 para. 72).
Regarding claim 30, Beauprez teaches that the oligosaccharide produced by the engineered microorganism may be 2'-fucosyllactose (2'-FL), 3-fucosyllactose (3-FL), 2',3-
difucosyllactose (DFL), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), lacto-N-fucopentaose I (LNFP-I), lacto-N-fucopentaose II (LNFP-II), lacto-N-fucopentaose III (LNFP-III), lacto-N-hexaose (LNH), lacto-N-neohexaose (LNnH), para- lacto-N-hexaose (paraLNH), lacto-N-difucosylhexaose I, lacto-N-difucosylhexaose II, lacto-N-neodifucohexaose I, 3'-sialyllactose (3-SL), 6'-sialyllactose (6-SL) (p. 3 para. 49; p. 5 para. 68).
Response to Arguments
In view of amendments to the claims, the rejection of claims 9 and 10 under 35 U.S.C. § 102 has been withdrawn. However, upon further consideration, new grounds of rejection of claims 11-30 are made under 35 U.S.C. § 103 in view of Beauprez and Sahin-Toth as set forth above. Given these new grounds of rejection, the arguments presented regarding claims 9 and 10 rejected under 35 U.S.C. § 102 are moot. The rejections of claims 9 and 10 on the ground of nonstatutory double patenting are withdrawn in view of claim amendments.
Conclusion
Claims 11-30 are rejected.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILY F EIX whose telephone number is (571)270-0808. The examiner can normally be reached M-F 8am-5pm ET.
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/EMILY F EIX/Examiner, Art Unit 1653
/JENNIFER M.H. TICHY/Primary Examiner, Art Unit 1653
