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 .
Response to Amendment
Applicant’s remarks and amendments filed 12/15/2025, in response to the non-final rejection mailed 9/24/2025, are acknowledged and have been fully considered.
Applicant’s amendment to the claims is acknowledged. This listing of the claims replaces all prior versions and listings of the claims. By the amendment, claims 35, 49, 50, 51, 53, and 56 are amended and claims 58 and 59 are newly added. Claims 35-36, 38-48, and 56-57 are withdrawn as being directed to non-elected inventions.
Claims 49-55 and 58-59 are pending and have been examined on the merits.
Response to Arguments
Applicant’s arguments in the remarks filed 12/15/2025 are acknowledged and have been fully considered. Any previous rejection or objection not mentioned herein is withdrawn.
Applicant’s arguments with respect to the rejections of claims 49-55 under 35 U.S.C. § 103 as being obvious over Jennewein '724 (US 2018/0305724) in view of Furrer et al. ("Export of the siderophore enterobactin in Escherichia coli: involvement of a 43 kDa membrane exporter." Molecular Microbiology vol. 44, 5 (2002): 1225-34) and Jennewein '707 (WO 2019020707) have been fully considered but are not persuasive.
As an initial matter, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Applicant argues that Jennewein '724 relates to export of "desired oligosaccharides" from genetically modified microbial host cells through expression of sugar export proteins, particularly transporters of the SET family and related proteins and that although sialylated oligosaccharides are mentioned among possible targets, the reference provides no experimental data, no identified transporter, and no demonstration that such molecules can be exported or that their production or efflux can be improved.
In response, the Examiner notes that Jennewein ‘724 teaches a cell genetically modified for the production of many different oligosaccharides including several species of sialylated oligosaccharide ([0019]) including inter alia, “lacto-N-sialylpentaose LSTa, LSTb, LSTc, disialyllacto-N-tetraose, and disialyllacto-N-neotetraose”, which are sialylated oligosaccharides.
Further, the previous Office Action communicated that Jennewein ‘724 teaches modified cells comprising recombinant glycosyltransferases, including sialyltransferases (see e.g. [0027]). Jennewein ‘724 also teaches that possible membrane proteins for exporting a desired oligosaccharide may comprise a siderophore exporter from among those recited in [0026], wherein the recited exporting proteins includes the E. coli protein YbdA. Thus, Jennewein ‘724 teaches that the genetic modifications to the host cells can be selected from enzymes including sialyltransferases and from membrane exporters including the oligosaccharide exporter YbdA, which is undisputedly a siderophore exporter (albeit not identified explicitly as such in the reference).
Applicant’s discussion of Furrer et al. has been fully considered, and it is noted that Applicant argues that “Furrer et al. (1) does not disclose export of oligosaccharides of any kind; (2) does not describe export of metabolites into the culture medium; and (3) does not identify YbdA as an oligosaccharide exporter or as improving production of carbohydrates.”.
Furrer was cited to provide evidence of the inherent and intrinsic functions of YbdA (also known as EcEntS) and to describe the existence and activity thereof as being known to the art. It is evident from both the art of record and from the instant specification that the recited claim limitation of “wherein said membrane protein comprises a siderophore exporter” encompasses the siderophore exporting membrane protein E. coli EntS, encoded by the gene ybdA. Further, “YbdA” is taught in Jennewein ‘724 as one of the membrane transporters that can be selected from to export a desired oligosaccharide when making a modified host cell.
Applicant notes that Jennewein '707 is directed to in vivo biosynthesis of sialylated oligosaccharides via recombinant expression of sialyltransferases and associated and discusses that this reference is silent regarding export or efflux of sialylated oligosaccharides. In response, it is noted that the Jennewein '707 reference was cited to demonstrate that selection of desirable genetic manipulations in host cells is a known practice in the art, that bioengineering of host cells to express heterologous (i.e. non-native) sialyltransferase results in improved cost-efficient process for producing SHMOs (pg. 3, lines 15-22), and that heterologous sialyltransferases are known to achieve desired sialic acid modifications (pg. 12, lines 29-32).
Jennewein ‘707 also teaches further genetic manipulations of the host cell in order to optimize the production of the sialylated oligosaccharide including the expression of membrane proteins including at least a functional lactose permease and membrane proteins capable of transporting sialic acids, specifically sialic acid importers (claim 15, pg 16, lines 24-30).
In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). Further, the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981).
In this case, Jennewein ‘724 discloses that the glycosyltransferase is selected from, inter alia, a sialyltransferase, that potential endogenous sugar export proteins comprise, inter alia, YbdA (a membrane protein) from E. coli, which, according to Furrer et al. (and via sequence evidence from the instant disclosure) encodes EntS having SEQ ID NO:9 of the instant application. Jennewein teaches that by expressing one or more of the named oligosaccharide exporters, large amounts of the synthesized oligosaccharide is obtainable from the medium ([0016]). Further, both Jennewein ‘724 and Jennewein ‘707 teach that industrially desired oligosaccharides include sialylated oligosaccharides, which have commercial applications.
The examined claims are drawn to products, i.e. host cells, and not methods. It is noted that for product claims, a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use (in this case producing a sialylated oligosaccharide), then it meets the claim. The host cells taught broadly in Jennewein ‘724 includes cells that produce sialylated oligosaccharide and are genetically modified to do so (e.g. expressing a recombinant sialyltransferase according to the alternatives presented in [0027]).
Applicant argues that that the cited teachings of the prior art would not have led one of ordinary skill to arrive at a host cell expressing a siderophore exporter that improves production and/or efflux of sialylated oligosaccharides. Applicant further argues that the Office Action does “not identify any disclosure that would provide a reasonable expectation of success that a siderophore exporter-studied only in the context of siderophore transport-would improve efflux of sialylated oligosaccharides.” This argument is not found persuasive.
As discussed on pages 15-17 of the previous Office Action, Jennewein ‘724 teaches a finite number of possible membrane proteins from which to choose to solve the problem of exporting the oligosaccharide from the host cell. The membrane transport proteins taught in Jennewein ‘724 include the elected siderophore exporter having a sequence identical to YbdA. To one of ordinary skill, the selection of any of the membrane proteins taught in the ‘724 reference, would have been a matter of testing and optimizing within the conditions taught in the prior art. Because the ‘724 reference teaches a finite and relatively short list of possible oligosaccharide exporter proteins ([0026]), it would have been predictable and reasonable to try any of these transporters described therein, including YbdA as recited in the instant invention, with the predictable result of secreting desired oligosaccharides. See MPEP § 2143(E).
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). See also MPEP 2141.II.C, which states that "A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton."KSR, 550 U.S. at 421, 82 USPQ2d at 1397. "[I]n many cases a person of ordinary skill will be able to fit the teachings of multiple patents together like pieces of a puzzle."Id. at 420, 82 USPQ2d at 1397. Office personnel may also take into account "the inferences and creative steps that a person of ordinary skill in the art would employ."Id. at 418, 82 USPQ2d at 1396.
In the instant case, a host cell having all of the claimed features clearly falls within the broad disclosure of Jennewein ‘724, however, there is not a single reduction to practice in the Jennewein ‘724 of such a species. Therefore, although Jennewein ‘724 cannot be said to anticipate the claimed host cells, the claimed subject matter would have been envisioned from the teachings therein by one having ordinary skill and knowledge of the art.
Furrer et al. provides practical teachings establishing that the YbdA membrane protein taught in Jennewein ‘724 is the same as that which is so instantly claimed. Proteins having the same sequence have the same function, as ultimately, the sequence is what determines activity. As previously discussed, Jennewein ‘707 establishes motivation for one of ordinary skill to seek to produce commercially desirable sialylated oligosaccharides, while the genetic modifications to produce sialylated oligosaccharides are found fully within the teachings of Jennewein ‘724. For all of these reasons, it would have been obvious to arrive at the claimed cells having a sialyltransferase and one or more of the claimed exporters, particularly YbdA or EcEntS.
In regards to the reasonable expectation of success, YbdA is one of the useful oligosaccharide exporters named explicitly in Jennewein ‘724. There is no teaching in the references that suggests that the named exporters would not all be functional in the manner and methods described therein. Further, one of ordinary skill would be reasonably capable of testing each and every of the named transporters in Jennewein ‘724 and thus the “discovery” of the claimed efflux effects provided by YbdA (and likewise provided by additional exporters recited in Jennewein ‘724, including SetB, SetC, Yhhs, MhpT, YebQ, EcFucP, and llImrA as further discussed below) would have been expected when following the teachings of the cited reference.
In response to applicant's argument that the expression of the siderophore exporter resulted in improved production and/or efflux of the sialylated oligosaccharides, the fact that the inventor has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious. See Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985).
Applicant further argues that the specification as filed demonstrates that expression of a siderophore exporter results in improved production and/or efflux of sialylated oligosaccharides relative to control cells, and thus provides evidence of the unpredictability of the art.
In regards to the cited experimental evidence, it is noted that the cited portions of the specification ([0167]-[0176]; [0594]-[0617]; [0620]-[0624]) describe a number of possible proteins that provide the increased efflux of sialylated oligosaccharides, including the aforementioned YbdA, but also various members of the major facilitator superfamily (MFS), the sugar efflux transporter (SET) family, the Multidrug/Oligosaccharidyl-lipid/Polysaccharide Flippase Superfamily (MOP); the resistance, nodulation and cell division superfamily (RND); and the ABC superfamily (see e.g. Tables 1 and 2). In [0595], it is stated that “The membrane proteins with SEQ ID NOs 02, 03, 04, 06, 07, 09, 10, 11, 14, 15, 16, or 18 in TU 01, SEQ ID NO 10 in TU 03 or SEQ ID NOs 20 and 21 in their native transcriptional operon structure showed that they are able to enhance 6′-SL production that is being produced in a 6′-SL production host expressing a sialyllactose pathway with α-2,6-sialyltransferase ST1” (see FIG. 2 and Table 3). From this section and Table 1, the Examiner notes that SEQ ID NO: 2 is EcSetB, SEQ ID NO: 3 is EcSetC, SEQ ID NO: 07 is Yhhs, SEQ ID NO: 09 is ECEntS/YbdA, SEQ ID NO: 10 is MhpT, SEQ ID NO: 11 is YebQ, which are each cited as equivalent alternatives for the oligosaccharide exporter in the cited portion ([0026]) of Jennewein ‘724. Additionally, SEQ ID NO: 14 is EcFucP and SEQ ID NO: 15 is ImrA of Lactococcus lactis, both of which are recited in [0049] of Jennewein ‘724. It is thus evident that the improved efflux is not provided only by YbdA, but also by additional exporters taught in Jennewein ‘724 and described in the instant disclosure.
Further, in [0621], it is demonstrated that membrane proteins “with SEQ ID NO 19 in TU 02, SEQ ID NOs 66 and 68 in TU08, SEQ ID NOs 19 and 99 in TU 13, SEQ ID NOs 100, 19, 57, 60 and 74 in TU 14, SEQ ID NOs 102, 103, 105, 106, 108, 109, 110, 111, 114, 115, 117, 118, 119 and 121 in TU 15, SEQ ID NO 66 in TU 16, SEQ ID NO 71 in TU 17, SEQ ID NOs 47, 55 and 75 in TU 18, SEQ ID NOs 19 and 68 in TU 21, SEQ ID NO 80 in TU 22, SEQ ID NOs 70, 71, 72, 74 and 80 in TU 25, SEQ ID NOs 75 and 81 in TU 26 and SEQ ID NO 80 in TU 27 showed that they are able to enhance 6′-SL production that is being produced in a 6′-SL production host” (see FIGs 8 and 9).
Therefore, when considering the large breadth of the described results, there is no convincing evidence that these are critical results attributed to the selection of a particular siderophore exporter. Instead this appears to be a general result obtainable with many membrane transporters, including several of the alternative proteins taught in Jennewein ‘724, in addition to YbdA, when so tested in the manner described in the instant specification.
Thus, the arguments are not considered persuasive and the claims remain rejected by the cited combination of Jennewein ‘724 in view of Furrer et al. and Jennewein ‘707.
Claim Rejections - 35 USC § 103
(modified as necessitated by Applicant’s amendments)
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 49-55 and 58-59 are rejected under 35 U.S.C. 103 as being unpatentable over Jennewein ‘724 (US PGPub 2018/0305724) in view of Furrer et al. (“Export of the siderophore enterobactin in Escherichia coli: involvement of a 43 kDa membrane exporter.” Molecular microbiology vol. 44,5 (2002): 1225-34) and Jennewein ‘707 (WO2019020707, published 1/31/2019 and filed 7/25/2018).
Jennewein ‘724 pertains to genetically modified microbial host cells and methods of using the host cell for producing a desired oligosaccharide, wherein the modified host cell comprises at least one recombinant glycosyltransferase, and at least one nucleic acid sequence coding for a protein enabling the export of the oligosaccharide (Abstract).
Jennewein ‘724 teaches a cell genetically modified for the production of sialylated oligosaccharide ([0017], “a genetically modified microbial host cell that comprises at least one recombinant glycosyltransferase”; and [0019]), wherein the host cell may comprise a polynucleotide encoding an enzyme for sialylated oligosaccharide synthesis (see [0019]: wherein the desired oligosaccharide includes, inter alia, sialylated oligosaccharides, e.g. “lacto-N-sialylpentaose LSTa, LSTb, LSTc, disialyllacto-N-tetraose, disialyllacto-N-neotetraose”, and [0027], stating that the recombinant glycosyltransferase comprises a sialyltransferase).
Further, Jennewein ‘724 teaches that the host cell is genetically modified for at least one of i) overexpression of an endogenous membrane protein, ii) expression or overexpression of a homologous membrane protein, and/or iii) expression or overexpression of a heterologous membrane protein ([0017]-[0020], including: “the host cell comprises: at least one homologous or heterologous nucleic acid sequence coding for a protein enabling the export of a desired oligosaccharide into the culture medium, wherein said host cell has been modified such that the expression of the homologous or heterologous nucleic acid sequence is overexpressed or under control of a promoter enabling the overexpression of the nucleic acid sequence”). Jennewein ‘724 teaches that possible membrane proteins for exporting a desired oligosaccharide may comprise a siderophore exporter ([0026]: the recited membrane exporting proteins includes the E. coli protein YbdA, which is a siderophore exporter, as evidenced by the instant specification describing SEQ ID NO:9, see row 9 of Table 1 on page 83). Jennewein teaches that by expressing an oligosaccharide exporter, large amounts of the synthesized oligosaccharide is obtainable from the medium, as it is not bound to a surface protein or in the host cell ([0016]).
Regarding claim 50, Jennewein ‘724 teaches a host cell having a membrane export protein wherein said membrane protein is SEQ ID NO: 9, or a sequence having at least 80% sequence identity to SEQ ID NO: 9 ([0026], wherein the oligosaccharide exporter is a protein selected from “at least one of the following: SetA, SetB, SetC, YdeA, Cmr, YnfM, MdtD, YfcJ, YhhS, EmrD, YdhC, YbdA… of E. coli”). Therefore Jennewein ‘724 teaches providing a sequence encoding the oligosaccharide exporter protein YbdA (also referred to as EcEntS in the instant specification, Table 1), which corresponds to sequence SEQ ID NO:9 herein, and therefore Jennewein ‘724 suggests a host cell modified for the production of oligosaccharides wherein the membrane protein comprises a siderophore exporter having the sequence of SEQ ID NO:9. An alignment of SEQ ID NO:9 and the protein encoded by the E. coli gene YbdA is included with this Action as an appendix.
In regards to claim 51, Jennewein ‘724 teaches that the host cell comprises a microbial host cell ([0060]): “A ‘microbial’ host cell according to the invention, and as generally understood, means any microorganism, including bacteria, fungi and archaea, which is generally suitable for cultivation in large amounts, and which can be genetically modified according to the invention in order to produce a desired oligosaccharide”).
Claim 53 recites that the sialylated oligosaccharide which is produced may include sialyllacto-N-tetraose a (LSTa); sialyllacto-N-tetraose b (LSTb); sialyllacto-N-neotetraose c (LSTc) or disialyl-lacto-N-tetraose (DS-LNT), which are disclosed as desired products according to the methods of Jennewein ‘724 ([0019], the desired oligosaccharide includes, inter alia, sialylated oligosaccharides, which include lacto-N-sialylpentaose, LSTa, LSTb, LSTc, and disialyllacto-N-tetraose).
Regarding claim 54, Jennewein ‘724 teaches that a host cell may be further transformed to comprise at least one nucleic acid sequence coding for a protein facilitating or promoting the import of substrate required for oligosaccharide synthesis, wherein the protein is selected from the group consisting of lactose transporter ([0034] and [0043]-[0044]). Specifically, Jennewein ‘724 teaches, in an embodiment, that the genetically modified host cell may comprise a nucleic acid sequence coding for a functional lactose permease protein, preferably LacY ([0034]). Jennewein ‘724 also teaches that the host cell may further comprise at least one homologous or heterologous nucleic acid sequence coding for a protein enabling the import of a precursor of a desired oligosaccharide ([0043]).
Claim 55 recites that the host cell is transformed and comprises an additional enzyme having one of the indicated activities. Jennewein ‘724 teaches that the host cell may further comprise the overexpression of an enzyme having, inter alia, glucosamine-1-phosphate acetyl transferase and/or glucose-1-phosphate uridylyltransferase activity ([0036]: “increased UDP-N-acetylglucosamine and UDP-galactose production capability comprises the overexpression of one or more genes encoding for proteins comprising the following activities … glucosamine-1-phosphate acetyl transferase,… glucose-1-phosphate uridylyltransferase”).
Regarding claim 58, Jennewein ‘724 teaches that the enzyme expressed in the host cell may comprise an α-2,6-sialyltansferase ([0027]).
Regarding claim 59, Jennewein ‘724 teaches that the host cell may comprise the oligosaccharide exporter YbdA/EntS.
However, Jennewein ‘724 does not explicitly describe in one embodiment a host cell comprising a polynucleotide encoding an enzyme for sialylated oligosaccharide synthesis, wherein the host cell is genetically modified to overexpress or express a membrane protein, and wherein the membrane protein comprises a siderophore exporter.
In addition, Jennewein ‘724 does not explicitly teach that the host cell comprises a catabolic pathway for selected mono-, di- or oligosaccharides which is at least partially inactivated, the mono-, di-, or oligosaccharides being involved in and/or required for the synthesis of sialylated oligosaccharide, as recited in claim 52.
Furrer et al. (“Export of the siderophore enterobactin in Escherichia coli: involvement of a 43 kDa membrane exporter.” Molecular microbiology vol. 44,5 (2002): 1225-34. doi:10.1046/j.1365-2958.2002.02885.x) describes an Escherichia coli membrane protein P43, encoded by ybdA in the chromosomal region of genes involved in enterobactin synthesis (Abstract; Fig. 1). Furrer states that “These data establish that P43 is a critical component of the E. coli enterobactin secretion machinery and provides a rationale for the designation of the previous genetic locus ybdA as entS to reflect its relevant biological function” (Abstract, last sentence; see also Fig. 3; pg. 1227, last paragraph). From the sequence provided in Fig. 1, the entS protein of Furrer is greater than 98% identical to that of the EcEntS protein having SEQ ID NO:9 described in the instant application. Thus, under the B.R.I. as would be understood by one of ordinary skill in the art, the recited claim limitation of “wherein said membrane protein comprises a siderophore exporter” encompasses siderophore exporting membrane proteins such as E. coli EntS, encoded by the gene ybdA, which is taught in Jennewein ‘724 as one of the membrane transporters that can be selected to export a desired oligosaccharide.
Jennewein ‘707 (WO2019020707) pertains to methods and cells for producing sialylated oligosaccharides, wherein a genetically engineered cell is used for producing said sialylated oligosaccharide (pg. 3, lines 20-29, claim 1). Jennewein ‘707 teaches that sialylated human milk oligosaccharides (SHMOs) are metabolically useful and are difficult to synthesize or obtain in large quantities (pg. 1, line 14 - pg. 2, line 10). Jennewein ‘707 describes that one difficulty in producing sialylated oligosaccharides comes from the fact that genes encoding sialyltransferases are barely expressed in prokaryotic microorganisms commonly used for large scale fermentation methods (pg. 2, lines 11-23). Thus, Jennewein ‘707 teaches that genetic bioengineering of host cells to express heterologous (i.e. non-native) sialyltransferase can result in a cost-efficient process for producing SHMOs (pg. 3, lines 15-22). Jennewein ‘707 teaches that “In an embodiment, the genetically engineered cell comprises a heterologous sialyltransferase being capable of possessing α-2,3-sialyltransferase activity, and the human milk oligosaccharide is LNT. The thus produced sialylated oligosaccharide is LST-a.” (pg. 12, lines 29-32).
Thus, Jennewein ‘707 teaches a host cell, including E. coli, having expression of a sialyltransferase for producing sialylated oligosaccharides.
Jennewein ‘707 also teaches further genetic manipulations of the host cell in order to optimize the production of the sialylated oligosaccharide including the expression of membrane proteins including at least a functional lactose permease and membrane proteins capable of transporting sialic acids (claim 15, see also pg 16, lines 24-30: “the at least one genetically engineered cell comprises at least one selected from the group consisting of a functional lactose permease, a functional fucose permease and a functional sialic acid transporter (importer)”).
In regards to claim 52, Jennewein ‘707 further teaches that in one embodiment (that of Example 1), to prevent intracellular degradation of N-acetylneuraminic acid the genes encoding N-acetylglucosamine-6- phosphate deacetylase (nagA) and glucosamine-6-phosphate deaminase (nagB) as well as the whole N-acetylneuraminic acid catabolic gene cluster, encoding Nacetylmannosamine kinase (nanK), N-acetylmannosamine-6-phopsthate epimerase (nanE), N-acetylneuraminic acid aldolase (nanA) and the sialic acid permease (nanT) were deleted from the genome of the E. coli BL21 (DE3) used to produce the sialyltransferase-expressing host cell.
Therefore, Jennewein ‘707 also teaches inactivation of genes involved in the catabolism of the mono-, di-, or oligosaccharides involved in and/or required for the synthesis of sialylated oligosaccharide (particularly those for N-acetylneuraminic acid) in order to prevent the degradation of the sialylated oligosaccharides.
Regarding claim 58, Jennewein ‘707 teaches that preferably, the at least one sialylated oligosaccharide produced by the method disclosed therein is 3'- sialyllactose, 6'-sialyllactose, LST-a, LST-b, LST-c or DSLNT (pg. 21, lines 6-9). Jennewein ‘707 also discloses that the expressed sialyltransferase can be an α-2,6-sialyltansferase (pg. 6, lines 22-25).
Therefore, to one of ordinary skill in the art, before the effective filing date of the claimed invention, it would have been prima facie obvious to modify the host cells taught in Jennewein ‘724 expressing or overexpressing at least one homologous or heterologous membrane protein enabling the export of a desired oligosaccharide into the culture medium, in which the membrane proteins includes siderophore exporters (e.g. YbdA as evidenced in Furrer), by also selecting and expressing a sialyltransferase for producing sialylated oligosaccharides as taught in Jennewein ‘707 (WO2019020707), for the expected benefits of producing metabolically useful sialylated oligosaccharides in a cost effective manner as taught in Jennewein ‘707, and having increased export of the oligosaccharide into the fermentation medium as taught in Jennewein ‘724.
One of ordinary skill would have been motivated by the teachings of both references to produce a cell having a sialyltransferase for producing metabolically useful sialylated oligosaccharide, as these are known beneficial compounds found in human milk which are traditionally difficult and/or expensive to obtain as taught in Jennewein ‘707.
Jennewein ‘724 describes the selection of membrane transport proteins for the secretion of synthesized oligosaccharides into the fermentation media. There had been a recognized problem or need in the art, as the synthesis of sialylated oligosaccharides was a known costly and ineffective process, according to Jennewein ‘707. Thus, in view of the combination of teachings from each of these references, one would have been motivated to include an oligosaccharide-exporting membrane protein as this results in the product being obtainable from the fermentation media, eliminates having to lyse cells, and results in an overall improved fermentation process.
MPEP § 2143(E) states that one “rationale to support a conclusion that the claim would have been obvious is that "a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely that product [was] not of innovation but of ordinary skill and common sense. In that instance the fact that a combination was obvious to try might show that it was obvious under § 103."KSR, 550 U.S. at 421, 82 USPQ2d at 1397”. In this case, Jennewein ‘724 teaches a finite number of possible membrane transport proteins from which to choose to solve the problem of exporting the oligosaccharide from the host cell. The membrane transport proteins taught in Jennewein ‘724 include the elected siderophore exporter having a sequence identical to YbdA. Thus, to one of ordinary skill in the art, the selection of any of the membrane proteins taught in the ‘724 reference, for obtaining a cell expressing a siderophore exporter capable of exporting sialylated oligosaccharides produced by host cell having expressing a sialyltransferase would have been a matter of testing and optimizing within the conditions taught in the prior art.
Because the ‘724 reference teaches a finite and relatively short list of possible oligosaccharide exporter proteins ([0026]), it would have been predictable to try any of these transporters described therein, including YbdA as required in the instant invention, with the predictable benefit of secreting the desired oligosaccharide. See MPEP § 2143(E).
A host cell having an exporter including YbdA and a sialyltransferase - selected from among the modifications taught in Jennewein ‘724 - would necessary possess the intrinsic function of having improved production and/or efflux of the sialylated oligosaccharide compared to a host cell without expression of the membrane protein, as recited in the amended claims, even if the prior art does not explicitly test these features. The compositions made obvious by the teachings of the cited art are likely to inherently possess the same characteristics of the claimed composition, particularly in view of the similar characteristics which they have been shown to share and by the functions of the component proteins inherently present in each, and which functions are inclusive of those appreciated in the instant disclosure as being present (see MPEP 2112.02 at Ex parte Novitski, in reference to reference-silent functioning of biological materials providing anticipation of the functions based upon the material itself - noting the reference of “Dart” therein did not appreciate the claimed function but still anticipated the function based on the inherent function of the material, and that the Applicant’s disclosure appreciating the function upon usage thereof as further evidence of the presence of the function).
The limitations of the dependent claims 50, 51, and 59 are taught in Jennewein ‘724, as set forth above. SEQ ID NO:9 of the instant invention appears to be substantially the same as the known sequence of the transporter YbdA from E. coli, as evidenced in Furrer. Further, the exemplary host cells in Jennewein ‘724 include microbial cells. Claim 59 also recites YbdA/EcEntS, which is taught in Jennewein ‘724. The providing of this specific sequence and the selection of a suitable host cell would have been obvious to one of ordinary skill in the art.
In regards to claim 52, one would have been motivated to eliminate genes involved in the catabolism of N-acetylneuraminic acid as taught in the ‘707 reference, in order to prevent the undesired degradation of the sialylated oligosaccharides.
Further, regarding claim 53, Jennewein ‘724 teaches that the desired oligosaccharide may include the sialylated species lacto-N-sialylpentaose, LSTa, LSTb, LSTc, and disialyllacto-N-tetraose) and Jennewein ‘707 teaches that the sialylated oligosaccharides include 3'- sialyllactose, 6'-sialyllactose, LST-a, LST-b, LST-c or DSLNT (pg. 21, lines 6-9). Thus, the production of at least one of these sialylated oligosaccharide would have been possible the host cell made obvious by the combination of Jennewein ‘724 and Jennewein ‘707, given that the correct precursors are available, as would have been known to one of ordinary skill in the art.
Regarding claims 54 and 55, these further limitations are taught explicitly in Jennewein ‘724 and would have thus been obvious modifications to incorporate in a host cell made obvious by the combined teachings of Jennewein ‘724 and Jennewein ‘707. These modifications would predictably result in improved performance of the host cell in the production of a sialylated oligosaccharide and one of ordinary skill in the art would have been capable of incorporating one of more of these additional genetic modifications.
Regarding claim 58, the selection and providing of an α-2,6-sialyltansferase in order to yield sialylated products including 6'-sialyllactose would have been obvious over the cited teachings of Jennewein ‘707. Both Jennewein ‘724 and Jennewein ‘707 recite that the exogenous glycotransferase may comprise an α-2,6-sialyltansferase.
From the teachings of the ‘724 and ‘707 references, it is apparent that one of ordinary skill in the art would have had a reasonable expectation of success in producing the claimed invention because each reference describes making genetic modifications for producing sialylated oligosaccharides in host microorganism cells and the ‘724 teaches optimizing the export of oligosaccharides in said microorganisms. Although not described together in one single embodiment, Jennewein ‘724 suggests that the host cells can include modifications of 1) a membrane transporter including siderophore exporters and 2) sialyltransferases. Thus, the selection and combination of the two would have reasonable expectation of success.
Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made, as evidenced by the provided references, especially in the absence of evidence to the contrary.
Conclusion
Applicant's amendment necessitated the new/modified grounds 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.M./Examiner, Art Unit 1655
/ANAND U DESAI/Supervisory Patent Examiner, Art Unit 1655