DETAILED ACTION
Status of the Application
Claims 1, 3-7, 9-11, 15-28, 30-31, 33, 35-38, 40-41, 91-94 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment of claims 1, 3-7, 9, 11, 15-18, 22, 25-27, 31, 33, 35-38, 91, and addition of claims 92-94 as submitted in a communication filed on 5/26/2026 is acknowledged.
Claims 92 and 94 are directed to the elected invention. Claim 93 is directed in part to the elected invention. Claims 1, 3-7, 9-11, 15-28, 30-31, 33, 35-38, 40-41, 91-92, 94 and claim 93 in part are at issue and will be examined only to the extent they encompass the elected invention.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Claim Objections
Claim 5 is objected to due to the recitation of “-“. It is suggested the claim be amended to use itemization labels such as (i)-(iv), or simply remove “-“ next to each option. Appropriate correction is required.
Claim 7 is objected to due to the recitation of “…(iii) a disaccharide and/or an (iv) oligosaccharide”. The term should be amended to recite “…(iii) a disaccharide and/or (iv) an oligosaccharide”. Appropriate correction is required.
Claim 36 is objected to due to the recitation of “-“. It is suggested the claim be amended to use itemization labels such as (i)-(ii), or simply remove “-“ next to each option. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
Claims 25, 36 remain rejected and claims 37, 92-93 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. New grounds of rejection are necessitated by amendment.
Claim 25 is indefinite in the recitation of “…compared to a method wherein the cell used does not have modified or increased expression or activity of the endogenous membrane transporter protein or polypeptide having transport activity…” for the following reasons. The comparison as written can be made with a genus of methods where a genus of cells from any organism are used so long as they do not have the recited modification or increased expression. The basis for comparison is variable, thus making the determination as to what is encompassed or excluded from the scope of the claim impossible. For example, a method can be encompassed by the claim if the comparison is made with method X that uses a cell from organism Y but may not be encompassed by the claim if the comparison is made with method Y that uses a cell from organism Z. If the intended comparison is with the same method that uses a cell of the same genus/species as that of the claimed method wherein said cell does not have modified or increased expression or activity, the claim should be amended accordingly. Correction is required.
Claim 36 is indefinite in the recitation of “in a culture medium comprising a carbon source comprising a monosaccharide, disaccharide, …..lactate and pyruvate” for the following reasons. As written, it is unclear if the claim requires a culture medium where the carbon source can be any of the listed compounds (e.g., a monosaccharide, a disaccharide, citrate, lactate or pyruvate), or if the claim requires a culture medium that comprises all of the recited compounds (i.e., a monosaccharide, a disaccharide, an oligosaccharide, a polysaccharide…..citrate, lactate and pyruvate). For examination purposes, it will be assumed that the claim requires a culture medium wherein the carbon source comprises at least one of the recited compounds. Correction is required.
Claim 37 is indefinite in the recitation of “wherein a first phase of exponential cell growth is provided by adding ….followed by a second phase of cell growth, …” for the following reasons. The term “a first phase of exponential cell growth” implies that there is a second phase of exponential cell growth. The claim refers to a second phase of cell growth. Therefore, it is unclear if the method requires the exponential growth of the culture to be divided in two phases, or if the claim refers to an exponential growth phase and a cell growth phase. If the intended limitation is “wherein a first phase of cell growth is provided by adding a carbon-based substrate to a culture medium comprising a precursor, wherein said cell growth in said first phase is exponential, followed by a second phase of cell growth …”, the claim should be amended accordingly. Correction is required.
Claim 92 is indefinite in the recitation of “in comparison to a method wherein the cell used does not express the heterologous membrane transporter protein or polypeptide having transport activity…” for the following reasons. The comparison as written can be made with a genus of methods where a genus of cells from any organism are used so long as they do not express the heterologous membrane transporter protein or polypeptide having transport activity. The basis for comparison is variable, thus making the determination as to what is encompassed or excluded from the scope of the claim impossible. For example, a method can be encompassed by the claim if the comparison is made with method X that uses a cell from organism Y but may not be encompassed by the claim if the comparison is made with method Y that uses a cell from organism Z. If the intended comparison is with the same method that uses a cell of the same genus/species as that of the claimed method wherein said cell does not express the heterologous membrane transporter protein or polypeptide having transport activity, the claim should be amended accordingly. Correction is required.
Claim limitation “means for catalyzing the transfer of a fucose residue from GDP-fucose to the glucose (Glc) residue….” in claim 93 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The specification refers to fucosyltransferases as capable of catalyzing the transfer of a fucose residue from GDP-fucose to the glucose residue of a substrate that comprises the oligosaccharide Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4- Glc in an alpha-1,3-glycosydic linkage. While the specification discloses a limited number of fucosyltransferases, there is insufficient disclosure of structures for performing the claimed function. In addition, even if the argument is made that exemplary species of fucosyltransferases have been provided, it is unclear if the intended “means” as recited in claim 93 is limited to (i) the entire genus of enzymes capable of catalyzing the recited conversion, or (ii) the specific exemplary species whose structures have been disclosed. As such, claim 93 is indefinite and are rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. For examination purposes, it will be assumed that the claimed method requires anything that can catalyze the transfer of a fucose residue from the GDP-fucose to the glucose residue of Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4-Glc in an α-1,3-linkage. Correction is required.
Applicant may:
(a) Amend the claims so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claims, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
Claims 1, 3-7, 9-11, 15-28, 30-31, 33, 35-38, 40-41 were 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 in view of the presence of new matter. In view of Applicant’s amendment, this rejection is hereby withdrawn.
Claims 1, 3-7, 10-11, 15-28, 30-31, 33, 35-38, 40-41 remain rejected and claims 92-93 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
This rejection has been discussed at length in the prior Office action. It is maintained and further applied to claims 92-93 for the reasons of record and those set forth below.
Applicant argues that the claims have been amended to narrow the enzyme limitation. Applicant states that the claims now require a polypeptide having 90% sequence identity or more to the polypeptide of SEQ ID NO: 3 and having α-1,3-fucosyltransferase activity. Applicant states that new claims 93-94 are supported by the disclosure as filed because the specification describes fructosyltransferases having α-1,3-fucosyltransferase activity as well as their amino acid sequences.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the rejection of claims 1, 3-7, 10-11, 15-28, 30-31, 33, 35-38, 40-41 or avoid the rejection of new claims 92-93. The Examiner acknowledges the amendments made to the claims and the teachings of the specification. However, the Examiner strongly disagrees with Applicant’s contention that claims 1, 3-7, 10-11, 15-28, 30-31, 33, 35-38, 40-41 as amended and new claims 92-93 are adequately described.
For the reasons extensively discussed above, a genus of means able to catalyze the recited transfer has not been described in the specification. As explained in Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ), it is unclear as to what is encompassed or excluded by the term “means”. In the instant case, claim 93 as interpreted requires anything that can catalyze the transfer of a fucose residue in GDP-fucose to the Glc residue of a saccharide substrate that comprises Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4-Glc. Please note that as indicated above, this “means” is not limited to the polypeptide of SEQ ID NO: 3 or an enzyme having α-1,3-fucosyltransferase activity. Thus, the required means can be anything that can catalyze the recited transfer.
The Examiner acknowledges that the specification discloses a few species of the genus of enzymes that can catalyze the recited fucose transfer. However, there is a significant amount of structural variability with respect to the members of the genus of fucosyltransferases required by the claimed method. The total number of variants having at least 90% sequence identity to the polypeptide of SEQ ID NO: 3 that result from amino acid substitutions is 335!x1934/(335-34)!/34! or 1.27x1090 variants. See equation previously provided. In the instant case, there is absolutely no indication as to which modifications can be made within the polypeptide of SEQ ID NO: 3 such that the required enzymatic activity and specificity is maintained. There is no structure/function correlation or some guidance as to which variants of the polypeptide of SEQ ID NO: 3 having the recited % sequence identity are more likely to have fucosyltransferase activity and the recited specificity. As previously indicated, while one could argue that the species disclosed is representative of the structure of all the members of the genus, it is noted that the art teaches several examples of how even highly structurally homologous polypeptides can have different enzymatic activities. See the teachings of Witkowski et al., Seffernick et al. and Tang et al. previously discussed.
Therefore, for the reasons of record and those set forth above, one cannot reasonably conclude that the specification and/or the prior art adequately describes the genus of variants of the polypeptide of SEQ ID NO: 3 required by the claims and the genus of cells and modifications encompassed by the claimed method.
Claims 1, 3-7, 10-11, 15-28, 30-31, 33, 35-38, 40-41 remain rejected and new claims 92-93 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method for producing lacto-N-fucopentaose V (LNFP V), wherein said method comprises culturing an E. coli cell that has been genetically modified to (a) constitutively express the fucosyltransferase of SEQ ID NO: 3, the sucrose transporter encoded by the E. coli cscB gene, a fructokinase encoded by the Z. mobilis frk gene, a sucrose phosphorylase encoded by the B. adolescentis sucP gene, a mannose-6-phosphate isomerase encoded by the E. coli manA gene, a phosphomannomutase encoded by the E. coli manB, a mannose-1-phosphate guanyltransferase encoded by the E. coli manC gene, a GDP-mannose dehydratase encoded by the E. coli gmd gene, a GDP-fucose synthase encoded by the E. coli fcl gene, the lactose permease encoded by the E. coli lacY gene, a galactoside β -1,3-N-acetylglucosaminyltransferase encoded by the N. meningitidis lgtA gene, and an N-acetylglucosamine β-1,3-galactosyltransferase encoded by the E. coli wbgO gene, and (b) disrupt the endogenous wcaJ, thyA, lacZ, lacY, lacA, and nagB genes, does not reasonably provide enablement for (I) a method for producing any fucosylated compound that comprises Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4-[Fuc-α1,3]-Glc from GDP-fucose and a saccharide substrate comprising Gal-β1,3-GlcNAc-β1,3-Gal-β1,4-Glc (LNT), wherein said method comprises contacting GDP-fucose and LNT with any fucosyltransferase having α-1,3-fucosyltransferase activity that is a variant of the polypeptide of SEQ ID NO: 3 having the recited % sequence identity, (II) the method of (I) wherein said fucosylated compound is produced by a cell modified by any means to produce said fucosylated compound and/or said saccharide substrate, (III) a method for producing LNFP V, wherein said method comprises culturing a cell modified by any means to produce GDP-fucose and LNT, wherein said cell expresses the polypeptide of SEQ ID NO: 3, or (IV) any means to catalyze the transfer of a fucose residue in GDP-fucose to the Glc residue of a saccharide substrate that comprises Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4-Glc. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
This rejection has been discussed at length in the prior Office action. It is maintained and further applied to claims 92-93 for the reasons of record and those set forth below.
Applicant argues that the claims have been amended to narrow the scope of the enzyme genus and to address the Office’s concern regarding breadth of the previous claims. Applicant states that the amended claims do not materially extend beyond the enabled scope. Applicant states that the application discloses the polypeptide of SEQ ID NO: 3 in the sequence listing and provides a working disclosure for use of the polypeptide of SEQ ID NO: 3 to produce LNFP V. Applicant states that amended claim 1 further require variants having at least 90% sequence identity to the polypeptide of SEQ ID NO: 3 having a specific fucosyltransferase activity, thus limiting the claim to close homologs. Applicant states that the claims retain limitations directed to the production of the fucosylated compound by a cell. Applicant states that the specification identifies exemplary cellular systems and genetic modifications for producing GDP-fucose, LNT, and LNFP V, including E. coli production using the polypeptide of SEQ ID NO: 3 as encompassed by claim 91. Applicant states that claim 93 is separately enabled when properly construed under 35 USC § 112(f). According to Applicant, this claim is limited to the corresponding fucosyltransferase structures disclosed in the specification and statutory equivalents thereof. Applicant states that the enablement inquiry for claim 93 is commensurate with the scope of the § 112(f) element.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the rejection of claims 1, 3-7, 10-11, 15-28, 30-31, 33, 35-38, 40-41 or avoid the rejection of new claims 92-93. The Examiner acknowledges the amendments made to the claims and the teachings of the specification. However, the Examiner strongly disagrees with Applicant’s contention that the full scope of claims 1, 3-7, 10-11, 15-28, 30-31, 33, 35-38, 40-41 as amended and new claims 92-93 is enabled by the teachings of the specification and/or the prior art.
With regard to the enablement of claim 93, it is reiterated herein that the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. As explained in Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ), it is unclear as to what is encompassed or excluded by the term “means”. While Applicant states that claim 93 is limited to the corresponding fucosyltransferase structures disclosed in the specification and statutory equivalents thereof, it is noted that nowhere in the specification one could find a reference to the “means” recited where it is stated that the “means” are limited to the fucosyltransferases having the specific amino acid sequences disclosed, let alone a definition of “statutory equivalents thereof” so that one of skill in the art would know what is encompassed and excluded from the term “means” as recited in claim 93. In the instant case, claim 93 as interpreted requires anything that can catalyze the transfer of a fucose residue in GDP-fucose to the Glc residue of a saccharide substrate that comprises Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4-Glc. Please note that as indicated above, this “means” is not limited to the polypeptide of SEQ ID NO: 3 or an enzyme having α-1,3-fucosyltransferase activity. Thus, the required means can be anything that can catalyze the recited transfer. Applicant is reminded that invocation of 35 USC § 112(f) does not exempt an Applicant from compliance with 35 USC § 112(a). See MPEP § 2181(II)(A) and MPEP § 2181(IV).
With regard to the genus of variants of the polypeptide of SEQ ID NO: 3 having at least 90% sequence identity to the polypeptide of SEQ ID NO: 3 and the fucosyltransferase activity recited, it is reiterated herein that the number of structural variants that meet the recited % sequence identity is essentially infinite. See calculation above. The specification and the prior art are completely silent as to the structural features required in the recited variants of the polypeptide of SEQ ID NO: 3 such that the variants would have the desired enzymatic activity and specificity, or a structure/function correlation that would allow one of skill in the art to determine which variants of the polypeptide of SEQ ID NO: 3 having the recited sequence identity are more likely to have the desired function and specificity. There is no indication in the specification or the prior art as to which structural features in the polypeptide of SEQ ID NO: 3 are essential for the desired enzymatic activity and specificity. In the instant case, one of skill in the art would have to test an essentially infinite number of variants to find those that have the desired enzymatic activity and specificity in view of the lack of knowledge or guidance as to which are the structural features required in a variant as recited for such variant to have the recited function. This is not deemed routine experimentation.
With regard to the argument that the specification identifies exemplary cellular systems and genetic modifications for producing GDP-fucose, LNT, and LNFP V, including E. coli production using the polypeptide of SEQ ID NO: 3, in support of the argument that the claims are fully enabled with regard to the cellular production of the substrate, enzyme and fucosylated product, it is reiterated herein that the modifications/cells encompassed by the claims are not limited to what is disclosed in the specification and include disruption of an unknown number of endogenous genes as well as the expression of unknown enzymes that would lead to the synthesis of precursors of the desired fucosylated compounds, such as GDP-glucose and LNT. Moreover, these modifications also encompass unknown methods to increase the expression of genes encoding biosynthetic enzymes, as well as unknown methods to inactive biosynthetic pathways of unknown metabolites that could reduce the synthesis of the desired compounds. It was not routine in the art at the time of the invention to screen by a trial and error process for any number of modifications in any cell so that the cell can synthesize a particular fucosylated compound, or it can produce GDP-fucose and/or LNT. In the absence of (i) a rational and predictable scheme for selecting those proteins most likely to have the desired functional features, (ii) a correlation between structure and α-1,3-fucosyltransferases activity with the desired specificity, and (iii) a rational and predictable scheme for determining those modifications that can be made to any cell to produce the desired compound, such as those biosynthetic enzymes that should be expressed and those endogenous genes that should be disrupted, one of skill in the art would have to test an essentially infinite number of proteins and modifications to determine which proteins have the desired functional characteristics, and which modifications could be made to achieve the desired synthesis. This is not considered routine experimentation. Therefore, contrary to Applicant’s assertions, one cannot reasonably conclude that the teachings of the specification and/or the prior art enable the entire scope of the claimed invention.
Claim Rejections - 35 USC § 102 (AIA )
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Claim 93 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tsai et al. (ACS Catalysis 9:10712-10720, 2019). This rejection is necessitated by amendment.
Claim 93 is directed in part to a method for producing a fucosylated compound, wherein said method comprises contacting GDP-fucose, a saccharide that comprises Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4- Glc, and means for catalyzing the transfer of fucose from GDP-fucose to the saccharide to obtain a fucosylated product that comprises a saccharide that comprises Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4-[Fuc-α1,3]-Glc.
Tsai et al. teach a method for producing lacto-N-fucopentose V (LNVP V) from lacto-N-tetraose (LNT) and GDP-fucose by a reaction catalyzed by a α-1,3/4-fucosyltransferase from H. pylori (FucTIII; page 10714, right column, lines 7-9; page 10713, Scheme 1, compound 3 to compound 6). Lacto-N-tetraose is a saccharide that comprises Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4- Glc and lacto-N- fucopentose V is a saccharide that comprises Gal-β1, 3-GlcNAc-β1, 3-Gal-β1, 4-[Fuc-α1,3]-Glc.(page 10713, Scheme 1, compound 3 (LNT) and compound 6 (LNVP V). Therefore, the teachings of Tsai et al. anticipate the instant claim as written/interpreted.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Allowable Subject Matter
Claim 91, which is directed to a method for producing lacto-N-fucopentaose V (LNFP V), wherein said method comprises culturing an E. coli cell that has been genetically modified to (a) constitutively express the fucosyltransferase of SEQ ID NO: 3, the sucrose transporter encoded by the E. coli cscB gene, a fructokinase encoded by the Z. mobilis frk gene, a sucrose phosphorylase encoded by the B. adolescentis sucP gene, a mannose-6-phosphate isomerase encoded by the E. coli manA gene, a phosphomannomutase encoded by the E. coli manB, a mannose-1-phosphate guanyltransferase encoded by the E. coli manC gene, a GDP-mannose dehydratase encoded by the E. coli gmd gene, a GDP-fucose synthase encoded by the E. coli fcl gene, the lactose permease encoded by the E. coli lacY gene, a galactoside β-1,3-N-acetylglucosaminyltransferase encoded by the N. meningitidis lgtA gene, and an N-acetylglucosamine β-1,3-galactosyltransferase encoded by the E. coli wbgO gene, and (b) disrupt the endogenous wcaJ, thyA, lacZ, lacY, lacA, and nagB genes, appears to be allowable over the prior art of record.
Conclusion
No claim is in condition for allowance.
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 extension fee 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 date of this final action.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
June 23, 2026