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 .
Priority
This application claims benefit of priority to foreign applications PCTEP2021051479 filed 01/22/2021 and EP21185379.1 filed 07/13/2021. This application is also a 371 of PCT/EP2022/051295 filed 01/21/2022. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Amendments and Claim Status
In the reply filed 07/10/2026, Applicant amended claims 5 and 7-9. Claims 10 and 15-16 are canceled.
Claims 1-9, 11-14 and 17-20 are currently pending.
Claims 12-14, 18 and 20 remain withdrawn.
Claims 1-9, 11, 17 and 19 are under examination.
Maintained Rejection (with modifications as necessitated by amendment)
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.
Claim 1-9, 11, 17 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Pedersen et al. (WO 2019123324 A1, 06/27/2019) (IDS Reference of 07/19/2023, 108 Pages) in view of Jennewein et al. (US 20180305724 A1, 10/25/2018) (Of Record) and UniProt (A0A380PXT8_YERFR, 11/07/2018) (Of Record), as evidenced by GenBank (AF400048.1, 07/23/2016)
Regarding claims 1-2, 4, 11 and 17, Pederson et al. disclose recombinant production of biological molecules in host cells and nucleic acid constructs that allow the modification of expression of desired genes wherein the constructs can be used to produce human milk oligosaccharides (HMOs) (See entire document, Abstract). More specifically, Pederson et al. disclose the sialylated HMO 3’-sialyllactose (3’-SL) can be produced by an engineered bacteria comprising an exogenous nucleic acid molecule encoding for an α(2,3) sialyltransferase (Page 56, Lines 19-21). An exogenous nucleic acid molecule encoding for an α(2,3) sialyltransferase reads on a heterologous nucleic acid sequence encoding a sialyl-transferase. The exogenous sialyltransferase gene utilized for 3’-SL production may be obtained from any available source, e.g., those described from Neisseria meningitidis and Neisseria gonorrhoeae, including specific examples listed in Table 5 (Page 56, Lines 21-24). A specific example from Table 5 includes NST from N. meningitidis MC58 with accession number AAC44541.1 (Table 5). AAC44541.1 is the elected α-2,3-sialyltransferase.
Furthermore, the bacterium (e.g., E. coli) also comprises a sialic acid synthesis capability. For example, the bacterium comprises a sialic acid synthesis capability through provision of an exogenous UDP-GlcNAc 2-epimerase (e.g., neuC of Campylobacter jejuni (GenBank AAK91727.1; GL 15193223) or equivalent (e.g. neuC of E.coli S88 (GenBank YP _002392936.1; GI: 218560023), a Neu5Ac synthase (e.g., neuB of C. jejuni (Gen Bank AAK91726.1; Gl:15193222) or equivalent, (e.g. Flavobacterium limnosediminis sialic acid synthase, Gen Bank GL559220424), and/or a CMP-Neu5Ac synthetase (e.g., neuA of C. jejuni (GenBank AAK91728.1; Gl:15193224) or equivalent, (e.g. Vibrio brasiliensis CMP-sialic acid synthase, GenBank GI: 493937153).
Bacteria producing sialylated HMO's comprise one or more exogeneous sialyltransferases, which are encoded by the coding DNA of an expression cassette of the invention that is present in the host cells either as plasmid-borne or genome-integrated. Preferably, at least one of the one or more sialyltransferase-coding DNA sequences is operably linked to a glp promoter described herein, preferably PglpF. Non-limited examples of useful sialyltranferases are listed in Table 5 (Page 58, Lines 8-22).
The sialic acid synthesis capability from the genes disclosed above, which produces CMP-Neu5AC, reads on a biosynthetic pathway for making a sialate sugar nucleotide. In a specific embodiment, Pederson et al. disclose plasmid MAP1214 comprising MDO PglpF-NeuA PglpF-neuB PglpF-neuC PglpF-nst (Table 6). The MDO portion of plasmid MAP1214 represents the background strain which is Escherichia coli K12 DH1 (Page 61, Line 15).
Pederson et al. additionally disclose the construct of the invention may encode an enzyme or a sugar transporter protein which are normally expressed by the host bacterial cell that naturally comprises in its genome genes encoding said enzyme or sugar transporter protein (Page 28, Lines 24-27).
Pederson et al. do not disclose a heterologous nucleic acid sequence encoding an MFS polypeptide of SEQ ID NO: 1 or a functional homologue thereof that shares 90% sequence identity to instant SEQ ID NO: 1.
However, Jennewein et al. disclose a method for the production of oligosaccharides in genetically modified bacterial host cells (See entire document, Abstract), specifically human milk oligosaccharides (Paragraph [0016]). The genome of the often used fermentation model organism E. coli encodes more than 500 distinct transporter proteins (Paragraph [0006]). The E. coli transport protein SetA was even described to transfer the human milk oligosaccharide 3-fucosyllactose, resulting in an improved production of said compound during fermentation of a recombinant E. coli strain overexpressing setA (Paragraph [0011]).
Additionally, UniProt discloses A0A380PXT8_YERFR, a sugar efflux transporter protein with gene name setA, that shares 98.7% sequence identity to instant SEQ ID NO. 1. Sequence alignment provided below wherein Qy represents instant SEQ ID NO: 1 and Db represents A0A380PXT8_YERFR disclosed by UniProt.
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Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to utilize the setA gene disclosed by UniProt in the genetically modified cell of Pederson et al. motivated by the desire to create a genetically modified cell capable of producing HMOs at a high level because Jennewein et al. disclose the use of setA in a recombinant cell resulted in the improved production of an HMO and the setA disclosed by UniProt was a known and effective setA protein disclosed by the prior art.
Regarding claim 3, it appears, absent evidence to the contrary, that the presence of the specific MFS polypeptide would inherently provide this effect. Therefore, the genetically modified cell of Pederson et al./UniProt meets this limitation.
Regarding claims 5 and 19, it appears as though SEQ ID NO: 3 and AAC44541.1 refer to the same sequence. The instant Specification states the gene that is genomically integrated is a gene encoding a α-2,3-sialyltransferase, for example, NST of Neisseria meningitidis (Genbank protein accession number AAC44541.1 or SEQ ID NO: 3) (Page 22, Lines 31-33). Thus, it appears as though SEQ ID NO: 3 and AAC44541.1 refer to the same sequence. As discussed above regarding claim 1, Pederson et al. disclose a specific example of an α(2,3) sialyltransferase from Table 5 being NST from N. meningitidis MC58 with accession number AAC44541.1.
Regarding claim 6, as discussed above regarding claim 1, Pederson et al. disclose the bacterium comprises a sialic acid synthesis capability wherein that capability is provided via nueA from C. jejuni with GenBank accession number AAK91728.1, nueB from C. jejuni with GenBank accession number AAK91726.1 and nueC from C. jejuni with GenBank accession number AAK91727.1 (Page 58, Lines 6-15). It is noted the instant Specification states CMP-Neu5Ac synthesis enzymes are neuBCA genes (Page 40, Line 1). The Specification further states neuBCA is a gene cluster consisting of neuA, neuB and neuC (Page 15, Lines 15-18). Thus, the disclosure of Pederson et al. of the bacterium comprising a sialic acid synthesis capability wherein that capability is provided via nueA from C. jejuni with GenBank accession number AAK91728.1, nueB from C. jejuni with GenBank accession number AAK91726.1 and nueC from C. jejuni with GenBank accession number AAK91727.1, reads on a biosynthetic pathway for making a sialate sugar nucleotide wherein the sialate sugar nucleotide is CMP-Neu5Ac.
Regarding claim 7, as discussed above regarding claim 1, Pederson et al. disclose the bacterium comprises a sialic acid synthesis capability wherein that capability is provided via nueA from C. jejuni with GenBank accession number AAK91728.1, nueB from C. jejuni with GenBank accession number AAK91726.1 and nueC from C. jejuni with GenBank accession number AAK91727.1 (Page 58, Lines 6-15).
GenBank accession number AAK91728.1 (nueA) refers to a protein ID of an amino acid sequence that has been translated from a nucleic acid sequence. The nucleic acid sequence encoding protein AAK91728.1 shares 100% sequence identity to instant SEQ ID NO: 16. A sequence alignment has been provided below where Qy represents instant SEQ ID NO: 16 and Db represents the nucleic acid sequence encoding the amino acid sequence of protein AAK91728.1.
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GenBank accession number AAK91726.1 (nueB) refers to a protein ID of an amino acid sequence that has been translated from a nucleic acid sequence. The nucleic acid sequence encoding protein AAK91726.1 shares 100% sequence identity to instant SEQ ID NO: 12. A sequence alignment has been provided below where Qy represents instant SEQ ID NO: 12 and Db represents the nucleic acid sequence encoding the amino acid sequence of protein AAK91726.1.
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GenBank accession number AAK91727.1 (neuC) refers to a protein ID of an amino acid sequence that has been translated from a nucleic acid sequence. The nucleic acid sequence encoding protein AAK91727.1 shares 100% sequence identity to instant SEQ ID NO: 14. A sequence alignment has been provided below where Qy represents instant SEQ ID NO: 14 and Db represents the nucleic acid sequence encoding the amino acid sequence of protein AAK91727.1.
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Thus, the disclosure of Pederson et al. of proteins AAK91727.1, AAK91726.1 and AAK91728.1 reads on instant SEQ ID NOs: 12, 14 and 16 because, as shown above, these proteins are encoded by the nucleic acid sequences represented by SEQ ID NOs: 12, 14 and 16. Additionally, as discussed above, these proteins were inserted into a plasmid, plasmid MAP1214 comprising MDO PglpF-NeuA PglpF-neuB PglpF-neuC PglpF-nst (Table 6), wherein the MDO portion of plasmid MAP1214 represents the background strain which is Escherichia coli K12 DH1 (Page 61, Line 15). To be inserted into a plasmid, the nucleic acid sequence encoding the amino acid sequence would have to be used. Thus, the disclosure of Pederson et al. reads on this limitation.
Regarding claims 8 and 9, it is noted the instant specification states “the term, a “regulatory element” or “promoter” or “promoter region” or “promoter element” is a nucleic acid sequence that is recognized and bound by a DNA dependent RNA polymerase during initiation of transcription” (Page 25, Lines 26-28). Thus, it appears a ‘regulatory element’ is another word for a promoter. As discussed above, Pederson et al. disclose the use of the glp promoter, PglpF (Page 58, Lines 19-20).
Pederson et al. do not specifically disclose the promoter PglpF is utilized for the regulation of the MFS polypeptide.
However, as disclosed above, Pederson et al. disclose the use of the PglpF promoter before all utilized sequences in plasmid MAP1214. Plasmid MAP1214 comprises MDO PglpF-NeuA PglpF-neuB PglpF-neuC PglpF-nst (Table 6).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized the PglpF promoter to regulate the expression of the MFS polypeptide as well as it was already being used to effectively control the expression of other polypeptides of the invention.
Regarding the newly added limitation to instant claim 9 that was previously present in now canceled claim 10, Pederson et al. disclose a PglpF promoter from E. coli that shares 100% sequence identity to instant SEQ ID NO: 5 which is a nucleic acid sequence. A sequence alignment is provided below wherein Qy represents instant SEQ ID NO: 5 and Db represents the sequence disclosed by Pederson et al.
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USC § 103 – Response to Arguments
Applicant's arguments filed 07/10/2026 have been fully considered but they are not persuasive.
Applicant argued a prima facie case of obvious has not been set forth because a skilled artisan would not be motivated to combine Pedersen and Jennewein because Pedersen’s disclosure of an optional sugar transporter protein would not lead one to select the claimed MFS protein because NCBI lists over 3 million sugar transport proteins, over 61,000 MFS proteins and over 36,000 setA proteins, therefore one would not specifically select instant SEQ ID NO: 1 (Page 7 – Middle of Page 8).
The Examiner respectfully disagrees. While NCBI may disclose a multitude of options for MFS proteins, sugar transport proteins and setA proteins, it would be obvious to utilize any of the known genes for their intended purposes. Therefore, it remains the Examiner’s position that it would be obvious to utilize the setA of UniProt in the cell of Pederson, which is drawn to the production of HMOs, because Jennewein teach setA in a recombinant cell improved the production of HMOs.
Applicant also argued there would be no reasonable expectation of success when combining Pederson and Jennewein because Jennewein does not teach the use of transport proteins for the production of 3’SL, only 3’FL (Bottom of Page 8).
The Examiner respectfully disagrees. Pederson teaches a host cell for the production of 3’SL and Pederson teaches including a sugar transporter protein in the host cell for producing 3’SL. Jennewein teaches setA improved production of human milk oligosaccharides. UniProt teaches a sugar transporter protein with the gene name setA. Thus, Jennewein is not utilized to teach the production of 3’SL. Pederson teaches the use of a sugar transporter protein for producing 3’SL, therefore it would be obvious to utilize any sugar transporter protein in the host cell of Pederson, including setA disclosed by UniProt because UniProt indicates the setA is a sugar transport protein and because setA was known for increasing the production of human milk oligaosaccharies as taught by Jennewein.
Applicant further argues unexpected results and points to Page 5, Lines 9-12 and Figures 1-2 of the instant disclosure (Page 9).
It is the Examiner’s position that unexpected results are not shown. Figure 1 shows the relative production of 3’SL with Strain 1 and Strain 2 while Figure 2 shows the relative distribution of 3’SL in supernatant versus a pellet. The instant Specification states strain 1 comprises SEQ ID NO: 1 while strain 2 does not. It is noted the claims are drawn to a genetically modified cell capable of producing one or more HMOs. Thus, Figure 1 is relevant to the instant claims but it is unclear how Figure 2 shows unexpected results when Figure 2 is drawn to the distribution of 3’SL which is not what the instant claims are drawn to. Even such, Figure 1 does not show unexpected results because the production of 3’SL in Strain 1, the strain comprising SEQ ID NO: 1, is within the standard deviation of Strain 2, the strain that does not comprise SEQ ID NO: 1. Thus, it is the Examiner’s position that unexpected results are not shown.
Conclusion
Claims 1-9, 11, 17 and 19 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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/A.T.W./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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