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 .
DETAILED ACTION
Claim Status
The amendment on April 13, 2026 is acknowledge. Claims 1-27 are currently pending. Claims 13, 15-16, 20, 23, 25 and 27 are cancelled. Claim 26 has been withdrawn. There is no new or amended claim.
Elections/Restrictions
Applicant’s election without traverse of group I (claims 1-12, 14, 17-19, 21-22 and 24) in reply filed on April 12, 2026 is acknowledged. Claims 26 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 1-12, 14, 17-19, 21-22, 24 are being examined on the merits herein.
Priority
Acknowledgment is made of applicant's claim for foreign priority based on an application filed in on March 11, 2021. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 102
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 (i.e., changing from AIA to pre-AIA ) 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.
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.
Claims 1, 3, 12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Li et al. (Published April 28, 2011; hereafter Li; PTO-892).
Li teaches N-glycosylation of proteins is catalyzed by the OST enzyme complex, in which Stt3p plays a central role.
Li teaches a promoter replacement strategy, the native Afstt3 promoter was used to generate a Afstt3 conditional inactive mutant, CPR-stt3.
Li teaches the repression of Afstt3 causes a reduction of N-glycosylation in Aspergillus fumigatus, reduction of high mannose-type sugar chains on some proteins, cell-wall defect caused by reduced N-glycosylation.
Li also teaches the A. fumigatus Afstt3 gene contains five introns and its 2603 bp ORF encodes a protein consisting of 743 aa. The predicted AfStt3 shows an identity of 65% with the S. cerevisiae Stt3p, deleting the Afstt3 gene by replacement of Afstt3 with pyrG and unsuccessful attempts of trying to obtain any null mutant strain after several rounds of screening.
Li teaches “considering that S. cerevisiae STT3 is an essential gene (Yoshida et al., 1995; Zufferey et al., 1995), it is likely that Afstt3 is also essential for A. fumigatus”.
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.
Claims 2, 14, 17-19, 24 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. (Published April 28, 2011; hereafter Li; PTO-892) in view of Saloheimo et al. (11th PEGS Europe, November 18-22, 2019; hereafter Saloheimo; PTO-892) as applied to claims 1, 3, 12 above.
Li teaches all the limitations of claim 1 as fully disclosed above and incorporated herein.
However, Li does not teach at least one cell comprises at least one exogenous polynucleotide encoding the protein of interest as claim 2.
Li does not teach the ascomycetous filamentous fungus is of the species Thermothelomyces heterothallica (also denoted Myceliophthora thermophila) as claim 14.
Li does not explicitly teach the protein of interest is selected from the group consisting of an antigen, therapeutic protein, antibody, enzyme, vaccine and structural protein as claim 17.
Li does not teach the protein of interest is a secreted protein as claim 18.
Li does not teach delete one or more genes encoding an endogenous protease as claim 19.
Li does not teach a method for producing a heterologous protein having reduced or no N-glycans, the method, culturing the ascomycetous filamentous fungus under conditions suitable for expressing the heterologous protein and recovering the heterologous protein as claim 24.
Saloheimo teaches filamentous Fungus Myceliophthora thermophilica C1, glycoengineering, generation of humanized protein-glycan structures, engineering a G0-glycan producing C1, Fc-fusion protein, Vaccine antigen, mAbY production, protein secreted to media, which is pertinent to claims 2, 14, 17-19, 24. See slides 1, 4, 7.
Saloheimo teaches C1 protease library in Pichia pastoris, C1 lineage of protease deficient strains, total protease extracellular protease activity is greatly reduced in C1 protease strains and improvement of stability of target proteins, target protein spiked into the culture supernatant of the protease deletion strains, vaccine antigen and Fc-fusion protein, which is pertinent to claims 19, 24. See slide 9-13.
Saloheimo teaches C1 glycan structure is more mammalian like than typically in yeasts, native C1 glycans are mostly high mannose type (Man3-Man9) including some hybrid glycans, less engineering steps needed for C1 and stable genome - defined glycan structure is stable from culture to culture and batch to batch, mammalian glycan forms G0, G0F, G2 and G2F, which is pertinent to claims 2, 14, 17-19, 24. See slide 14.
Saloheimo teaches Man3 is the most important precursor of G0 glycans, and two approaches for high man3, deletion of alg3 and over expression of mannosidase I and deletion of alg3 and alg11, which is pertinent to claims 2, 14, 17-19, 24. See slide 15.
Saloheimo teaches the alg11 gene was deleted from an alg3 deletion strain. Simultaneously heterologous GNT1 and GNT2 were expressed from the alg11 locus. Saloheimo also teaches G0 glycan levels of up to 95% have been reached with this strategy. In addition to G0, only Man3 and GlcNAcMan3 remain in the glycan pattern, which is pertinent to claims 2, 14, 17-19, 24. See slide 17-18.
Saloheimo teaches strains were made where two different lipase variants were expressed in addition to GNT1 and GNT2 in alg3-alg11 deletion background, total glycosylation level (sum of peaks) increased~4x (flippase1) or ~9x (flippase2), glycan pattern remained 93-95% G0 glycans, which is pertinent to claims 19, 21, 24. See slide 19.
Saloheimo teaches production of biologics in C1, fermentations for mAbY production, initial culture volume, vessel volume, SDS gel analysis of the mAbY antibody purified from the fermentations by protein A affinity chromatography, antibody titer, mass spectrometry analysis showed that both chains were intact, the binding properties of C1 produced mAbY were compared to the CHO produced mAbY in a Biacore T200 assay and the C1-produced mAbY and CHO produced mAbY showed virtually indistinguishable binding kinetics, which is pertinent to claim 24. See slides 20-26.
It would be obvious to one of skill in the art to modify the teachings of Li, thereby arriving at the invention of claims 2, 14, 17-19, 24. Since the ascomycetous filamentous fungi of Li (Aspergillus fumigatus) and Saloheimo (Chysosporium lucknowense also known as Myceliophthora thermophilica) were shown to be effective for producing proteins with reduced N-linked glycosylation it would have been obvious to substitute these known equivalents; see MPEP 2144.06.
See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.
Claims 4-5, 7-8 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. (Published April 28, 2011; hereafter Li; PTO-892) in view of Saloheimo et al. (11th PEGS Europe, November 18-22, 2019; hereafter Saloheimo; PTO-892) as applied to claims 1, 3, 12 above, and further view of Barke et al. (Published October 2011; hereafter Barke; PTO-892).
Li teaches all the limitations of claim 1 as fully disclosed above and incorporated herein.
However, neither prior art teaches an amino acid sequence having at least 75% identity to the amino acid of Thermothelomyces heterothallica STT3, the Thermothelomyces heterothallica STT3 comprises the amino acid of SEQ ID NO: 27, the CWH8 comprises an amino acid sequence having at least 75% identity to the amino acid of Thermothelomyces heterothallica CWH8, the Thermothelomyces heterothallica CWH8 comprises the amino acid of SEQ ID NO: 28 as claims 4-5, 7-8, respectively.
Barke teaches genomic Accession codes, assembly and annotation data for Myceliophora thermophila (Thermothelomyces thermophilus) and Thielavia terrestris are available through JGI MycoCosm Genome Portal at http://jgi.doe.gov/fungi and at DDBJ/EMBL/GenBank under chromosome accession numbers CP003002-CP003008 and CP003009 CP003014, respectively. The transcriptome data are available under GEO accession number GSE27323”. See for example Barke et al. 2011.
Barke teaches Gene IDs: 11509028 and 11512155, both in the genome of Thermothelomyces thermophilus, genomic DNA: CP003003 (strain ATCC 42464 / BCRC 31852 / DSM 1799). The Gene IDs: 11509028 and 11512155 encode the amino acid sequences of SEQ ID NOs: 27, 28, respectively, which is pertinent to claim 4-5, 7-8.
See the DNA sequence alignments below.
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814
664
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502
755
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It would be obvious to one of skill in the art to modify the teachings of Li and Saloheimo, thereby arriving at the invention of claims 4-5, 7-8. Since the genetically modified ascomycetous filamentous fungus having a reduced expression of its homologous gene of Li was shown to be effective for producing proteins with reduced N-linked glycosylation and Saloheimo taught the production of proteins of interest with reduced N-linked glycosylation by Thermothelomyces thermophilus, it would have been obvious to substitute these known equivalents; see MPEP 2144.06.
See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.
Claims 10, 21-22 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. (Published April 28, 2011; hereafter Li; PTO-892) in view of Saloheimo et al. (11th PEGS Europe, November 18-22, 2019; hereafter Saloheimo; PTO-892) as applied to claims 1, 3, 12 above, and further view of Helenius (WO 2010049177 A1; hereafter Helenius; PTO-892).
Li teaches all the limitations of claim 1 as fully disclosed above and incorporated herein.
However, neither prior art teaches the genetic modification comprises deletion or disruption of the stt3 gene such that the modified filamentous fungus fails to produce a catalytic subunit of the oligosaccharyltransferase (OST) complex as claims 10, 21-22.
Helenius teaches novel tools for the production of glycosylated proteins in host cells, glycoprotein production and protein glycosylation engineering in eukaryotes, specifically the production of human-like complex or hybrid glycosylated proteins in lower eukaryotes; filamentous fungi, preferably selected from Ascomycetes, in particular Chysosporium lucknowense (Myceliophthora thermophilica), Trichoderma reseei, A. fumigatus, etc., which is pertinent to claims 10, 21-22. See page 24-25.
Helenius teaches the host cell is a mutant for Stt3p (which is the catalytic subunit) and low mannose glycan structures, which is pertinent to claims 10, 21-22. See for example, page 35; lines 26-28, page 39; lines 10-25.
Helenius teaches, at least one subunit of the endogenous oligosaccharyl transferase, such as Stt3p, the cell is a knock out mutant of genes wbp1 and stt3, which is pertinent to claims 10, 21-22. See for example page 35; lines 17-28.
Helenius teaches one or more of the genes encoding endogenous OT subunits are knocked-out, cells are also a knock-out mutant of endogenous OT activity, in particular by knock-out of ost1 and ost2 and/or wbp1 and stt3 and/or the respective homologues thereof, which is pertinent to claim 10, 21. See for example, page 42, lines 10-25.
Helenius teaches “In the host cell, the mannosylation is suppressed in the ER and the modified cell predominantly produces LLO having Man 1-3 GlcNAc2 structures. An endogenous oligosaccharyl transferase, such as Stt3p, may have low activity for such low-mannose LLO), which is pertinent to claims 10, 21-22. See for example page 30; lines 36-40, page 31; lines 1-5.
It would be obvious to one of skill in the art to modify the teachings of Li and Helenius, thereby arriving at the invention of claims 10, 21-22. Since the ascomycetous filamentous fungi strain, Afstt3 conditional inactive mutant, CPR-stt3 of Li (Aspergillus fumigatus) and the tools for the production of glycosylated proteins in host cells by deleting endogenous oligosaccharyl transferases, such as STT3 (or its subunit Stt3p) were shown to be effective for producing proteins with reducing N-linked glycans, it would have been obvious to substitute these known equivalents; see MPEP 2144.06.
See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.
Claim 6, 9, 11 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. (Published April 28, 2011; hereafter Li; PTO-892) in view of Saloheimo et al. (11th PEGS Europe, November 18-22, 2019; hereafter Saloheimo; PTO-892) as applied to claims 1, 3, 12 above, and in further view of Janik (Published October 12, 2019; hereafter Janik; PTO-892).
Li teaches all the limitations of claim 1 as fully disclosed above and incorporated herein.
However, neither prior art teaches reduced expression and/or activity of CWH8, reduced expression and/or activity of STT3 and CWH8, and deletion or disruption of the cwh8 gene such that the modified filamentous fungus fails to produce a functional dolichyl pyrophosphate phosphatase as claims 6, 9, 11.
Janik teaches essential role of dolichyl phosphate (DolP) as a carbohydrate carrier during protein
N-glycosylation and its importance in eukaryotes is well established, and its availability modulates the level of protein glycosylation, which is pertinent o claims 6, 9, 11.
Janik teaches homozygous disruption of the C. albicans CWH8 gene (CaCWH8) increases dolichol level, which is pertinent to claims 6, 9, 11.
Janik teaches Cwh8p protein affects transcription of genes encoding proteins presenting cis-PTase activity, which is pertinent to claims 6, 9, 11.
Janik teaches lack of CaCwh8p activity affects N-Glycosylation, which is pertinent to claims 6, 9, 11.
Janik teaches the CaCWH8 gene encodes a functional homologue of Cwh8p in S. cerevisiae, which is known for catalyze the dephosphorylation of DolPP was used to complement the cell wall defect of an S. cerevisiae cwh8D mutant caused by defective protein N-glycosylation, which is pertinent o claims 6, 9, 11.
Janik teaches CaCWH8 gene under control of the GAL1 promoter was introduced into S. cerevisiae cwh8 knockout strain. The CWH8 gene which encodes dolichyl pyrophosphate phosphatase partially restores resistance of S. cerevisiae to calcofluor white and Congo red, which is pertinent to claim 6. See for example, Figure 1.
Janik teaches N-glycosylation is also altered upon deletion of the CaCWH8 gene encoding DolPP phosphatase, bringing about similar effects in hyphae and biofilm formation, which is pertinent to claims 6, 9, 11.
Janik teaches in Candida albicans, the defective N-glycosylation in the Cacwh8D/Cacwh8D mutant altered the cell wall composition, most notably by decreasing its content of mannose, which is pertinent to claims 6, 9, 11.
Janik teaches deletion of CaCWH8, which encodes the phosphatase converting DolPP to DolP, in C. albicans affects expression of genes encoding cis-PTases and elevates de novo production of dolichol. Despite the increased activities of DPM synthase and GlcNAc transferase, the initial reactions in the N-glycosylation pathway, the N-glycosylation of the model protein Phrp was impaired. These observations suggest that the impaired N-glycosylation could result from the inhibition of the oligosaccharyltransferase activity by its final product, DolPP. The key role of N-glycosylation for the proper cell wall composition and
for the expression of pathogenic futures such as yeast-to-hyphae transition and biofilm formation in C. albicans, which is pertinent to claims 6, 9, 11. See for example Figure 9.
It would have been obvious to one of ordinary skill in the art to modify the teachings of Li and Janik, thereby arriving at the invention of claims 6, 9, 11. Since the ascomycetous filamentous fungi strains of Li (Aspergillus fumigatus) and Janik (Candida albicans, which is an ascomycetous; yeast form and multicellular filamentous form) were shown to be effective for producing proteins with reduced N-linked glycosylation. Thus, it would be an advantage and very desirable to producing proteins of interest with reduced or no N-linked glycans in industrial ascomycetous filamentous fungus, such as Myceliophthora thermophilica of Saloheimo, it would been obvious to substitute these known equivalents; MPEP 2144.06.
See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements (i.e., lower eukaryotes, such as ascomycetous filamentous fungus and conserved/homologous genes/domains involved in hypoglycosylation/reduced N-glycans of proteins of interest) were known in the art. In addition, combining these genes and filamentous fungi strain wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PRICILA HAUK TEODORO whose telephone number is (571)272-2784. The examiner can normally be reached M-F 6:15AM-3PM.
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/PRICILA NMN HAUK TEODORO/ Examiner, Art Unit 1645
/HEATHER CALAMITA/ Supervisory Patent Examiner, Art Unit 1684
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