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 .
Election/Restrictions
Applicant’s election without traverse of Group I (i.e., a genetically modified filamentous fungus comprising at least one cell capable of producing immune-active molecules) and “antigen” (species of immune active molecule) in the reply filed on 05/08/2026 is acknowledged.
Claims 12, 27, 29, and 31 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species and invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 05/08/2026.
Status of Claims
Claims 1-6, 9-10, 12, 14, 18, 21, 25-27, 29, 31, 33, 38, and 41 are currently pending.
Claims 1-6, 9-10, 14, 18, 21, 25-26, 33, 38, and 41 are under consideration, as claims 12, 27, 29, and 31 are withdrawn.
Priority
The present application claims status as a 371 (National Stage) of PCT/IB2022/060813 filed on 11/10/2022. Acknowledgment is made of applicant’s claim for benefit under 35 U.S.C. 119(e) of Provisional application No. 63/278,112, filed on 11/11/2021. The present application and all claims are being examined with an effective filing date of 11/11/2021. In future actions, the effective filing date may change due to amendments or further review of priority documents.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 07/03/2024 and 11/03/2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 41 is 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 insertion of the recited transcription units into the recited genomic loci of Thermothelomyces heterothallica C1, does not reasonably provide enablement for insertion of the transcription units into the recited genomic loci throughout the full scope of the ascomycetous filamentous fungi encompassed by the claim. 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 the invention commensurate in scope with these claims.
The specification fails to enable the claim (or the full scope of the claim) if a person of ordinary skill in the art would be faced with an undue burden of experimentation when trying to implement the invention based on the disclosure. In re Wands (858 F.2d 731 at 737, 8 USPQ2d 1400 at 1404 (Fed. Cir. 1988)) sets forth a non-exclusive list of factors by which this burden of experimentation may be judged to be due or undue; factors that are germane to the instant case include the breadth of the claims, nature of the invention, the amount of direction provided by the inventor, the existence of working examples and the state of the prior art.
Claim 41 recites the genetically modified ascomycetous filamentous fungus of claim 1, wherein each of the transcription units is inserted into at least one locus within the fungal genome, wherein the locus is selected from the group consisting of cellobiohydrolase (cbh1), β-glucosidase (bgl8), cellobiose dehydrogenase (cdh), chitinase (chi1), a glycoside hydrolase family 6 gene (GH6), a glycoside hydrolase family 61 gene (GH61), and a carbohydrate-binding WSC gene. In summary, the nature of the invention is that the transcription units may be inserted into any of the recited genomic loci in any ascomycetous filamentous fungus. Accordingly, claim 41 is unduly broad with respect to insertion of the transcription units into the recited genomic loci.
The specification identifies the recited loci in T. heterothallica C1 and provides CRISPR RNAs designed to target those loci in the C1 genome. The working examples, however, are limited to T. heterothallica C1 strains. Although the claim broadly encompasses ascomycetous filamentous fungi of numerous genera and species, the specification does not establish that each of the specifically recited loci is present, identifiable, and suitable for insertion of the claimed transcription units throughout that full scope. Nor does the specification provide sufficient guidance for identifying and targeting the corresponding loci in ascomycetous filamentous fungi other than T. heterothallica C1.
The only direction and working example(s) provided by the disclosure relate to insertion of transcription units into the recited loci in Thermothelomyces heterothallica C1. The specification identifies the recited loci and discloses CRISPR RNAs designed to target those loci in the C1 genome. The specification, however, does not provide direction or working examples demonstrating that the recited loci are present, identifiable, and suitable for targeted insertion in the full scope of the claimed ascomycetous filamentous fungi, which encompasses numerous genera and species. Applicant provides no additional direction or working examples showing how to identify the corresponding loci or successfully target those loci in fungal species other than T. heterothallica C1.
Regarding the state of the prior art, references of record demonstrate that certain individual genomic loci have been identified and used for targeted insertion in particular fungal species. For example, Emalfarb et al. teaches targeted insertion at the β-glucosidase (bgl8) locus in Thermothelomyces heterothallica, while other prior art (Mantyla et al., WO 9727306 A1, cited in PTO-892) teaches use of the cellobiohydrolase (cbh1) locus in Trichoderma species. However, these references are directed to particular loci in particular fungal species and do not demonstrate that each of the specifically recited loci is present, identifiable, and suitable for targeted insertion throughout the full scope of the claimed ascomycetous filamentous fungi. Accordingly, the state of the prior art does not provide sufficient guidance to reduce the amount of experimentation required to practice the full scope of the claimed invention.
Accordingly, a person of ordinary skill in the art would be required, for each additional fungal genus or species, to determine whether a recited locus or corresponding homolog is present, identify its genomic sequence and location, develop suitable targeting reagents, and determine whether insertion at that locus permits viable fungal growth and production of the claimed immune-active molecules. In view of the breadth of ascomycetous filamentous fungi encompassed by claim 41 and the C1-specific nature of the guidance and working examples, the required experimentation would be undue. Therefore, the specification does not enable the full scope of claim 41.
Claim Rejections - 35 USC § 103
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 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 1-6, 9-10, 14, 18, 21, 25-26 and 38 are rejected under 35 U.S.C. 103 as being unpatentable over Wakai et al. ("Modified expression of multi-cellulases in a filamentous fungus Aspergillus oryzae." Bioresource technology 276 (2019): 146-153, cited in the IDS), Philippidis, A. ("Off Message: Dyadic Fights COVID-19 with a Fungus: Dyadic applies novel C1 Technology Platform based on Thermothelomyces heterothallica to develop its vaccine against the coronavirus and emerging variants." GEN Edge 3.1 (2021): 346-353, cited in the IDS), and Espinosa et al. ("In-solution buffer-free digestion for the analysis of SARS- CoV-2 RBD proteins allows a full sequence coverage and detection of post- translational modifications in a single ESI-MS spectrum." BioRxiv, p. 1-61, cited in the IDS).
Regarding claims 1-6, Wakai et al. teaches a genetically modified filamentous fungus, Aspergillus oryzae, comprising fungal cells engineered to simultaneously produce multiple different recombinant proteins. Wakai et al. specifically describe an engineered A. oryzae strain that simultaneously produces cellobiohydrolase, endoglucanase, and β-glucosidase by chromosomal integration of genes encoding the respective proteins (Abstract; p. 147, left column, final two paragraphs). Wakai et al. further teaches that the three recombinant proteins are expressed from separate expression cassettes. In section 2.2, Wakai et al. describes individual cellulase cassettes comprising different promoter, cellulase-gene, and terminator combinations, including the CBHI, EGI, and BGL cassettes. Wakai et al. further states that the marker plasmid and the three cellulase cassettes were simultaneously introduced into A. oryzae, and that the target genes were integrated into the chromosomal DNA of each transformant (p. 148, right column, sections 2.2 and 2.3). Thus, Wakai et al. teaches at least two different recombinant proteins produced from at least two different transcription units in a genetically modified filamentous fungal cell.
Wakai et al. also teaches modifying the relative production levels of the different recombinant proteins by selecting promoter/terminator combinations and controlling integrated gene copy number. Wakai et al. teaches that transcription levels increased with gene copy number, that the transcription level per copy differed according to the promoter used, and that promoter strength and copy number could be used to design and balance the expression levels of multiple genes (p. 151, left and right columns, discussion of Figs. 2 and 3; p. 152, left column, immediately preceding section 3.3). Wakai et al. does not expressly teach that the simultaneously produced recombinant proteins are immune-active molecules or that their amounts are in a ratio from about 1:1 to about 1:10.
Philippidis teaches use of the filamentous fungal C1 expression platform, based on Thermothelomyces heterothallica, for production of recombinant immune-active molecules. Philippidis describes production in C1 of SARS-CoV-2 RBD, full spike protein, RBD fused to SpyTag, full spike fused to SpyTag, RBD-Fc, monoclonal antibodies, and other vaccine candidates (Discussion beginning “At Dyadic, we listened to the Israelis and the Europeans”; and discussion beginning “We made the spike RBD.”).
Espinosa et al. likewise teaches expression of a SARS-CoV-2 viral antigen in the filamentous fungus Thermothelomyces heterothallica. Espinosa et al. describe a construct encoding residues 333–527 of the SARS-CoV-2 spike protein RBD, cloned into a C1 expression vector under a C1 endogenous promoter and transformed into a low-protease C1 strain (p. 11).
Before the effective filing date of the claimed invention, the teachings of Wakai et al. of genetically modifying filamentous fungi to express multiple recombinant proteins using multiple transcription units, in combination with the teachings of Philippidis of employing Thermothelomyces heterothallica C1 as a recombinant protein production platform for expression of recombinant immune-active molecules, including coronavirus receptor-binding domain proteins and other viral antigens, and the teachings of Espinosa of recombinant Thermothelomyces heterothallica strains producing SARS-CoV-2 spike protein antigens, including receptor-binding domain proteins, would have made it obvious to one of ordinary skill in the art to employ the recombinant Thermothelomyces heterothallica C1 platform of Philippidis and Espinosa in the recombinant expression system of Wakai to produce recombinant immune-active molecules, including antigens, specifically viral antigens, coronavirus antigens, and coronavirus receptor-binding proteins, with a reasonable expectation of success because both Philippidis and Espinosa demonstrate successful recombinant production of such immune-active molecules using the Thermothelomyces heterothallica C1 platform. It further would have been obvious to determine and adjust the relative amounts of the simultaneously produced immune-active molecules through routine selection of promoter strength and gene copy number, as expressly taught by Wakai et al. The claimed range of about 1:1 to about 1:10 therefore encompasses relative production levels obtainable through the balancing and optimization of multiple-gene expression taught by Wakai et al. The selection of a workable ratio within that range would have involved routine optimization of a result-effective variable absent evidence that the claimed range produces an unexpected result. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Regarding claims 9-10, as described above, Wakai et al. teaches simultaneous production of three different recombinant proteins (CBHI, EGI, and BGL) in a single genetically modified filamentous fungus through three separate expression cassettes and Philippidis/Espinosa teach the recombinant production of SARS COV-2 RBD antigens. Furthermore, Philippidis expressly teaches that the Thermothelomyces heterothallica C1 expression platform is readily adaptable for rapid production of a wide variety of recombinant SARS-CoV-2 proteins, explaining that “whatever sequence you want to put into a cell, we can do it fast” and describing the production of multiple SARS-CoV-2-derived proteins, including spike protein, receptor-binding domain (RBD), RBD-Fc, spike-SpyTag, and spike nanoparticles. Philippidis further explains that the platform was developed to enable rapid, scalable responses to emerging vaccine needs and that additional “generation two or three” constructs and new gene sequences were continually being developed (pg. 8).
Before the effective filing date of the claimed invention, the teachings of Wakai et al. of simultaneously expressing multiple recombinant proteins in a genetically modified filamentous fungus, together with the teachings of Philippidis and Espinosa regarding recombinant production of SARS-CoV-2 RBD antigens using Thermothelomyces heterothallica, would have made it obvious to one of ordinary skill in the art to simultaneously express three SARS-CoV-2 RBD antigens corresponding to different viral variants. Because Philippidis teaches that the expression platform is readily adapted by substituting the nucleotide sequence encoding the desired recombinant protein and emphasizes its suitability for rapidly producing newly developed SARS-CoV-2 constructs, selecting different RBD coding sequences corresponding to different SARS-CoV-2 variants would have amounted to the predictable substitution of one known RBD sequence for another while using the same established recombinant expression platform, with a reasonable expectation of success (see MPEP 2144.06 Substituting equivalents known for the same purpose). Therefore, the invention as a whole would have been prima facie obvious before the effective filing date of the claimed invention.
Regarding claim 14, as described above, Espinosa et al. teaches expressing the recombinant SARS-CoV-2 receptor-binding domain in a low-protease background Thermothelomyces heterothallica C1 strain. Specifically, Espinosa et al. state that the RBD sequence was codon-optimized for expression in a low-protease-background C1 strain and further explain that the engineered C1 host expression system has a very significant reduction of the protease load, thereby “minimizing degradation” of recombinant proteins during fermentation (p. 11 and p. 28). Also described above, it would therefore have been obvious to employ the reduced-protease filamentous fungal host of Espinosa et al. in the recombinant multi-expression fungal system of Wakai et al., as modified by Philippidis, specifically because reducing protease activity was known to improve the stability and yield of recombinant proteins produced by filamentous fungi.
Regarding claim 18, Wakai et al. teach the genetically modified filamentous fungus Aspergillus oryzae. Aspergillus oryzae is a member of the subphylum Pezizomycotina. Therefore, Wakai et al. teaches the filamentous fungus recited in claim 18.
Regarding claim 21, as described above, Espinosa et al. and Philippidis expressly teach expression of the recombinant SARS-CoV-2 receptor-binding domain in the filamentous fungus Thermothelomyces heterothallica. Applicant identifies SEQ ID NO:1 as genomic DNA of Thermothelomyces heterothallica. No evidence has been presented that the disclosed C1 strain lacks the claimed sequence identity.
Regarding claim 25, Espinosa et al. teach that the recombinant immune-active molecule comprises a signal peptide for secretion. Specifically, Espinosa et al. describe constructing an expression cassette encoding a C1 endogenous signal sequence operably linked to the SARS-CoV-2 receptor-binding-domain antigen, followed by a GlySer linker and C-tag. The recombinant construct was expressed in Thermothelomyces heterothallica C1, and the recombinant RBD protein was recovered from the culture supernatant, demonstrating secretion of the recombinant antigen (p. 11, construction of the expression cassette; p. 12, purification from culture supernatant). Accordingly, it would have been obvious to include a secretion signal peptide as part of the recombinant immune-active molecule in the fungal expression system of Wakai et al., as modified by Philippidis, in order to direct secretion of the expressed antigen.
Regarding claim 26, Espinosa et al. teaches expression of a SARS-CoV-2 receptor-binding-domain (RBD) viral antigen in the engineered Thermothelomyces heterothallica C1 expression system using a 1 L fed-batch bioreactor (p. 11). Espinosa et al. further teaches that the engineered C1 host was developed as an industrial recombinant protein production platform capable of producing several recombinant proteins at yields greater than 10 g/L (p. 28). Because the expressed RBD is a recombinant protein produced in the disclosed C1 host, and the claimed minimum production level of 0.1 g/L is substantially below the production capability of the host platform, it would have been obvious that the fungal expression system would be capable of producing at least the claimed amount of viral antigen.
Regarding claim 38, as described above, Wakai et al. teach simultaneous introduction of multiple independent transcription cassettes into Aspergillus oryzae and chromosomal integration of the target genes (Sections 2.2 and 2.3). It would have been obvious to one of ordinary skill in the art to integrate the different transcription units into different loci within the fungal genome, as integration of multiple independently introduced expression cassettes into separate chromosomal loci was a routine genetic engineering technique for obtaining stable expression of multiple recombinant genes.
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Philippidis, A. ("Off Message: Dyadic Fights COVID-19 with a Fungus: Dyadic applies novel C1 Technology Platform based on Thermothelomyces heterothallica to develop its vaccine against the coronavirus and emerging variants." GEN Edge 3.1 (2021): 346-353, cited in the IDS) and Sperandio et al. (Fungal co-cultures in the lignocellulosic biorefinery context: A review. International Biodeterioration & Biodegradation 142: 109-123, cited in the IDS).
Philippidis teaches a genetically modified filamentous fungal expression platform, namely the Thermothelomyces heterothallica C1 platform, to produce numerous different recombinant viral antigens, including the SARS-CoV-2 receptor-binding domain (RBD), full-length spike protein, full-length spike protein with SpyTag, and RBD-Fc, explaining that “whatever sequence you want to put into a cell, we can do it fast” and describing production of multiple vaccine candidates using the C1 platform (p. 8). Thus, Philippidis teaches genetically modified filamentous fungi comprising cells capable of producing different viral antigens. However, Philippidis does not expressly teach a cultivation comprising a mix of at least two genetically modified filamentous fungi, wherein each fungus comprises at least one cell capable of producing a different viral antigen.
Sperandio et al. teaches fungal co-cultures comprising the simultaneous cultivation of two or more fungi in the same cultivation system or bioreactor (p. 109, right column, last full paragraph; p. 118, left column, second paragraph). Sperandio et al. further teaches that co-cultivation is a recognized cultivation strategy for combining complementary biological activities by employing multiple fungal strains within the same cultivation, rather than requiring a single fungal strain to perform all desired functions (p. 109, right column, last full paragraph; p. 118, left column, third and fourth paragraphs). Sperandio additionally discloses numerous examples of co-cultures involving two different filamentous fungi cultivated together in the same cultivation system (pg. 110-111, and Table 1).
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to employ separate genetically modified Thermothelomyces heterothallica C1 fungal strains, each engineered to produce a different viral antigen, as taught by Philippidis, in a single co-culture as taught by Sperandio et al., because Sperandio teaches that co-cultivation of multiple fungal strains was a well-established cultivation strategy for combining complementary biological activities within a single cultivation system, rather than requiring a single strain to perform all desired functions. There is a reasonable expectation of success because Sperandio demonstrates that simultaneous cultivation of two or more filamentous fungi in a common cultivation system is a successful and established cultivation strategy for combining complementary biological activities. Applying this known co-culture strategy to the genetically modified fungal expression platform of Philippidis would have predictably resulted in a cultivation comprising multiple engineered filamentous fungi, each producing a different recombinant viral antigen. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art, before the effective filing date of the claimed invention.
Claim 41 is rejected under 35 U.S.C. 103 as being unpatentable over Wakai et al., Philippidis, and Espinosa et al., as applied to claim 1 above, and further in view of Emalfarb et al. (WO2020161682, cited in the IDS).
The combination of Wakai et al., Philippidis and Espinosa et al., as applied in the rejection of claim 1 above, teaches a genetically modified filamentous fungus comprising multiple transcription units for expression of different recombinant proteins, including use of Thermothelomyces heterothallica as an advantageous filamentous fungal production host for recombinant proteins such as viral antigens. However, neither expressly disclose that each transcription unit is inserted into a genomic locus selected from the group consisting of CBH1, BG18, CDH, CHI1, GH6, GH61, and WSC.
Emalfarb et al. teaches targeting heterologous expression constructs to the bg18 locus in Thermothelomyces heterothallica, identifying bg18 as a suitable genomic integration site (Example 2).
It would have been obvious to one of ordinary skill in the art at the time the claimed invention to modify the recombinant Thermothelomyces heterothallica production system made obvious by Wakai et al., Philippidis and Espinosa et al., by inserting the transcription units into the BG18 locus, as taught by Emalfarb, because Emalfarb teaches bg18 as a suitable genomic integration site in Th. heterothallica. There is a reasonable expectation of success because Emalfarb demonstrates successful recombinant protein production through targeted integration of multiple expression plasmids into Thermothelomyces heterothallica at the bg18 locus. Therefore, the invention as a whole would have been prima facie obvious before the effective filing date of the claimed invention.
Conclusion
No claim is in condition for allowance.
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/NAGHMEH NINA MOAZZAMI/ Examiner, Art Unit 1652
/ROBERT B MONDESI/ Supervisory Patent Examiner, Art Unit 1652
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