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 .
Application Status
This action is written in response to applicant’s correspondence received on 2/18/2026. Claims 1-8, 10-15, 17, 21, 23-24, and 26-29 are pending. Claims 1 and 12 have been amended. Claims 28-29 are newly added. Claims 9, 16, 18-20, 22, and 25 have been previously cancelled. All pending claims are currently under examination.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow. This Office Action is Final.
Claim Rejections - 35 USC § 112 – Maintained/Updated in Response to Amendments
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.
Claims 1-8, 10-15, 17, 21, 23-24, and 26-29 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Regents of the University of California v. Eli Lilly & Co, 119 F.3d at 1568, 43 USPQ2d at 1406.
Regarding claim 1, claim 1 recites isolated mutant filamentous fungal cells comprising a coding sequence encoding a protein under control of a promoter regulated by transcription factors. The transcription factor is recited to comprise a sequence having at least 90% homology to SEQ ID NOs 1-4 and 123-124. Claim 1 further recites that the native transcription factor gene and/or genes are modified to produce the mutant rendering the mutant at least 95% deficient in the production of the one or more native transcription factors.
With regards to the subject matter encompassed in claim 1, claim 1 broadly encompasses modifications to native transcription factor genes, where the modifications have the overall effect of either knocking out or partially suppressing the production of the one or more transcription factors (i.e., the modified transcription factor genes are 95-100% deficient in production of the native transcription factors). Such modifications reasonably include, for instance, gene deletions to render mutants completely deficient in the transcription factors. As claim 1 is drawn to modifications in the “gene” and not the transcription factors themselves, claim 1 also reasonably encompasses mutations to non-coding regions of the genes, such as the promoter elements. Thus, claim 1 reasonably encompasses mutations in the cis-acting promoter elements of the genes of the recited transcription factors. Thus, claim 1 encompasses the genus of “modifications,” where the modification is located anywhere within the native transcription factor genes. This claim language is problematic because the Applicant does not appear to have identified any regions within the genes which would lead to “95%” deficiency in the production of the transcription factors. The Applicant has only performed gene deletion studies, where the transcription factor gene is mutated by deletion to remove production of the native transcription factor in its entirety (i.e., 100% modification by complete deletion of the transcription factor gene). The Applicant has not identified, for instance, regions of the promoter such as cis-acting elements which could be targeted to render partially deficient expression of the transcription factors (95% deficient production of the transcription factors) because the Applicant has not characterized the promoter or its regulatory elements, or other aspects of the genes which affect their expression (e.g., UTR regions).
Furthermore, the Applicant has only performed gene deletions in T. reesei. As discussed below, it is known in the art that different strains and species of fungal cells can comprise gene variants/promoter variants which affect the expression of the same gene product. The Applicant has therefore not characterized the genus of “filamentous fungal cell” because they have not offered representative species of this genus owing to the unpredictability of the genus as a whole (see below).
Regarding the guidance provided in the specification, the Applicant has offered Examples 1-29 in their specification (pages 42-79). Examples 1-4 recite an overview of culturing techniques (pages 42-46). Example 5 recites an RNAseq assay to identify genes (pages 46-48). Examples 6-10 recite targeted gene deletion strains of Trichoderma reesei (pages 48-59). Examples 11-13 recite lysozyme productivity assays in select strains of the Applicant’s cells (pages 60-62). Examples 14-23 recite plasmid/strain construction plasmids and gene deletion strains (pages 62-72). Examples 24-29 recite protein titer studies, cellulase-minus phenotypes, and transcription factor deletion strain studies (pages 62-79). Thus, overall, the specification has offered strains of T. reesei cells where three transcription factors, SEQ ID NOs 1, 3, and 123 (nucleic acid sequences), or their respective amino acid sequences (SEQ ID NOs 2, 4, and 124) have been completely deleted in various strain backgrounds, where the protein production of the strains has been evaluated. The specification has not recited studies related to mutational analysis of transcription factor genes or characterized the promoters of the genes sufficiently to identify targets of the genes to render 95% deficient production of the transcription factors in T. reesei, let alone the genus of “filamentous fungal” cells.
With regards to the guidance provided in the specification concerning methods and strategies to modify genes, the specification recites known strategies for gene targeting (pages 29-31). For instance, the specification recites that fungal cells can be constructed by the introduction of substitutions and deletions, where nucleotides can be inserted or removed to introduce stop codons, remove start codons, or introduce frame-shift mutations using site-directed mutagenesis (page 29, second paragraph). The specification further identifies methods to disrupt genes by insertional elements, and gene conversion (page 29, paragraphs 3-4). These methods have to total effect of the complete deficiency of a target gene, and do not encompass “95%” deficiency methods, where mutations are made in the gene rendering partial expression of the recited transcription factors.
The specification further recites that anti-sense and/or RNAi can be used to target or reduce the expression of the recited transcription factors (page 29 final paragraph to page 30, first two paragraphs). While it may be true that such methods can partially reduce the expression of a transcription factor, claim 1 is drawn to modifications of the transcription factor “gene” for the overall effect of a partial or complete deficiency of the production of the transcription factor, and not the introduction of other molecules to partially knockdown its expression (i.e., RNA molecules).
Finally, the specification further recites that random mutagenesis or specific mutagenesis can be used to construct the mutant strains (page 30, third paragraph). Random mutagenesis by definition generates random mutations, and are therefore inherently unknown to the user. Simply reciting that a user could randomly identify a cell and then screen for useful mutations is not equivalent to the Applicant having possession or knowledge of what said mutations would be. Furthermore, while “specific” mutagenesis is recited, no specific mutations are identified in the specification to generate partially deficient expression of the transcription factors which would yield 95% deficient production of the transcription factors, as the examples are drawn to complete gene deletions (page 30, third paragraph).
With regards to genetic variability, variations in promoter regions of the same gene are known in the art to produce expression level variability. For example, Ronald (Ronald J et al. PLoS Genet. 2005 Aug;1(2):e25) is a research article that focuses on regulatory variation in the fungal cells S. cerevisiae (Title, Abstract, and throughout). As an initial matter, it is understood that S. cerevisiae, while being a fungal cell, is not a filamentous fungal cell as recited in claim 1. However, absent evidence to the contrary, there is no reason to expect that the teachings of Ronald with respect to regulatory changes in variants would not apply to different fungal eukaryotes such as filamentous fungi. Ronald teaches that naturally occurring variations within the same species are known to affect gene expression (Abstract). Ronald further teaches that local regulatory variations occurred in nearly a quarter of yeast genes between divergent strains (Abstract). Ronald further teaches that local regulatory variations/cis-regulatory variations occur as a result in polymorphisms in the promoter regions, where such variations can occur in transcription factor binding sites (Abstract). Thus, Ronald teaches that gene expression can be highly variable within the same gene across strains, where mutations in certain promoter regions can affect the expression in ways which must be empirically determined (Abstract). However, the Applicant has not identified specific regions of, for instance, the promoter region of the gene to target in order to have the overall effect of “95%” deficiency of the expression of the recited transcription factors.
Similarly, Sung (Sung HM et al. Mol Biol Evol. 2009 Nov;26(11):2533-8) is a research article that focuses on the roles of trans and cis variations in yeast intraspecies evolution of gene expression (Title, Abstract, and throughout). Sung teaches that cis variations in genes across different strains of yeast significantly contribute to expression divergence. (Abstract). Thus, Sung teaches that variations in the promoter sequences of genes can have significant effects on the expression level of gene products, and that such sequence divergences in cis-regulatory transcription factor binding sites of the promoter and their effects must be empirically determined, as evidenced by the fact that such sequence divergences and their correlation to expression patterns require genome-wide studies such as those performed by Sung (Introduction, first paragraph and Results pages 2536-2538). The Applicant has not characterized regulatory elements within the promoter regions of the recited genes, and was therefore not in possession of mutations which may have the overall effect of rendering 95% deficient production/expression of the recited transcription factors.
Finally, Thompson (Thompson DA et al. FEBS Lett. 2009 Dec 17;583(24):3959-65) is a research article which focuses on cis and trans fungal regulatory elements (Title, Abstract, and throughout). Thompson teaches that regulatory divergence is a known phenomenon in fungal cells, that little is known about the adaptive role of regulatory evolution, and that empirical studies and experimentation are required to fully understand regulatory divergence throughout different species of fungi (Abstract). Importantly, Thompson teaches that, while cis-regulatory elements are often conserved in closely related species, they are not always conserved even between and across species (page 3, fourth paragraph). Thompson teaches that:
“Many cis-regulatory elements are conserved in closely related species. In some cases, the specific site and its location in the promoter is conserved, a feature exploited for motif identification using alignments of orthologous regulatory regions. In other cases, gain and loss of cis-regulatory motifs, and the potential for corresponding changes in transcription factor binding, occur on relatively short time scales (on the order of 5 – 20 my), both within and between species. Doniger et al. estimated that, of the lineage-specific binding-site losses within sensu stricto Saccharomyces, over half correspond to newly emerged binding sites in the same regulatory regions. Turnover of one binding site in a promoter for a functionally equivalent one can explain how gene expression can be maintained despite change in regulatory sequences,” (page 3, fourth paragraph).
Thus, Thompson teaches that promoter element such as cis-regulatory elements can change within the same regulatory regions/promoters across and between species. Thompson teaches that genes which encode the same protein can have different promoter elements across species. Thus, even if the Applicant had characterized promoter elements in T. reesei, different, divergent filamentous fungal cells which encode the same protein may be under the control of promoters with different structures and/or sequence motifs/cis-regulatory elements, none of which the Applicant has characterized.
To further corroborate the diversity of fungal cells, Ward (Ward OP. Biotechnol Adv. 2012 Sep-Oct;30(5):1119-39, submitted with Applicant IDS filed 6/11/2021), a review article that teaches the production of recombinant proteins by filamentous fungi teaches that filamentous fungi are an enormously diverse and uncharacterized class of organisms (Abstract and page 1120, right column, second paragraph). Ward further teaches that not all filamentous fungi are suitable hosts for recombinant protein production (page 1120, right column, second paragraph). Ward therefore teaches that filamentous fungi are incredibly diverse and furthermore this diversity leads to a poor understanding of molecular mechanisms governing cellular interactions (Abstract, page 1120 right column, second and third paragraphs). Thus, recitation of “filamentous fungal cell” is also an uncharacterized genus recited in the claims.
Given that Thompson teaches that the same promoter can undergo gain and loss of regulatory motifs within and across species of fungi, and that a promoter is not therefore necessarily the same for the same protein across species, and that Ward teaches that fungi are a largely uncharacterized phylum of organisms, the Applicant was not in possession of the genus of “filamentous fungi” where modifications in the genes encoding the transcription factors (including the promoter regions of their genes) is encompassed by the claim.
Furthermore, regarding newly added claims 28-29, these claims recite that the modifications in the parental fungal cell line “completely deficient” in the production of the transcription factor. Such claim language includes, for instance, a complete deletion of the transcription factor gene itself as was performed by the Applicant. However, complete deletion of a gene is not the only method to mutate a gene in order to render the production of its gene product “completely deficient.”
For example, Pu (Pu N et al. Biotechnol J. 2025 Jul;20(7):e70075) is a research article which focuses on the regulatory intricacies of fungal cells (Title, Abstract, throughout). Pu teaches that:
“Eukaryotic promoters, span hundreds of base pairs, and are generally more complex and diverse than their prokaryotic counterparts… upstream activation sequences (UAS) located upstream of the promoter region is a cis-acting element capable of enhancing gene transcription. By binding to specific transcriptional activators, it recruits the co-activation complex with RNA polymerase II, thereby increasing transcriptional efficiency. Accurate identification of the UAS region is essential for hybrid promoter construction and involves systematic truncation of the promoter sequence… For P. pastoris, the prediction of the core promoter and TFBSs guided the division of the UAS into four regions, and stepwise truncation with eGFP expression was used
to define the functional UAS region,” (page 2, right column, first paragraph).
Thus, Pu teaches that eukaryotic promoters are complex regulatory elements comprising various regions which affect and control the express of a given protein by interacting with transcription factors at transcription factor binding sites (TFBSs), where furthermore characterization of such regions of the promoter as the UAS – essential for transcription – requires experimental, stepwise approaches in order to fully characterize the elements of the promoter (above).
Pu further teaches that:
“TFs [transcription factors] are proteins that regulate gene transcription and modulate gene expression. In fungal genomes, TFs typically contain DNAbinding
domains, which recognize and bind to specific DNA consensus motifs within the promoters of target genes, thereby mediating their transcriptional regulatory functions,” (page 4, right column fourth paragraph).
Thus, regarding promoters in fungal cells, Pu teaches that transcription factors are known to bind with motifs in order to carry out transcriptional regulation of genes (above). As such, fungal genes comprise regions in their promoters which are essential for the “regulatory functions” or expression of the gene product. Given that promoters are known to comprise essential regions for gene expression, it follows that ablation or elimination of such regions would render gene expression “completely deficient.” However, such mutations can be simply restricted to essential promoter elements, and do not require the deletion of the entire gene in order to have such an effect. The Applicant has only deleted the entire gene in order to render “completely deficient” production of the transcription factor, but they have not performed more refined mutational strategies by identifying regions within the promoter which could also be performed to render “completely deficient” production of the transcription factor.
As such, the Applicant was not in possession of modifications in the gene that would render “completely deficient” production of the transcription factor, as such modifications are not limited to complete gene deletion but can instead include targeted deletions of critical regions of a gene’s promoter, where Pu teaches that the identification of such critical regions requires stepwise empirical analysis.
Response to Arguments
The Applicant’s remarks filed 2/18/2026 have been considered but are not persuasive. The Applicant argues that the amendment of claims 1 and 12 obviates the 112(a) rejection, as a practitioner would conclude that the Applicant demonstrated possession of the genus of modifications which render “95%” deficiency for the production of the transcription factor. As discussed above, what the Applicant has actually reduced to practice and demonstrated was a complete deletion of the recited transcription factors (i.e., 100% deficient). The state of the art teaches that transcriptional apparatus such as transcription factors are coordinated with specific nucleic acid motifs within promoters, where fine-tuning such promoters and their respective motifs in order to achieve “95%” reduction in the efficiency of transcription of a given product would require empirical and experimental evaluation which was not performed by the Applicant. For instance, the Applicant has not identified critical regions within the promoters of the recited transcription factor genes which could be mutated/modified in order to achieve the recited functionality of “95%” deficient production of the recited transcription factors. Thus, the amendments do not obviate the 112(a) rejection.
Furthermore, the 112(a) rejection includes a rejection of the genus of “filamentous fungal cell” which was neither addressed in the amendments to the claims nor the arguments. As such, the rejection of the claims based on the recitation of the unpredictable genus of “filamentous fungal cell” coupled with the functional requirements of the claims is sustained.
Regarding the new claims 28-29, these claims recite that the modification renders completely deficient production of the one or more transcription factors. The Applicant further quotes page 11 of the previous non-final action which states “It is acknowledged that the Applicant was in possession of complete deletions/complete deficiencies in the recited transcription factors.” The Office reiterates, and clarifies, that indeed the Applicant showed possession of complete deletions which render complete deficiencies of the production of the transcription factors. However, it is further clarified here and in the 112(a) rejection that because other mutational approaches aside from “complete deletions” exist in order to render mutants with complete deficiencies of transcription factor production. For instance, mutations in the critical and essential regions of the promoter, which are required for transcription factor binding to carry out “regulatory function” (per Pu, see 112(a) rejection) is an embodiment of modification presently encompassed by the claim language of claims 28-29. However, the Applicant has not performed sufficient characterization to identify such critical regions of the promoter which would yield complete deficiency of the expression of the transcription factor, as Pu teaches that such promoters must be characterized empirically. As such, while the Applicant has shown possession of complete deletions to yield complete deficiency of transcription factor expression, they did not show possession of the entirety of the genus of modifications which would yield complete deficiency which would reasonably include embodiments where critical mutations of the promoter are deleted and not the entire gene.
The Applicant argues that a practitioner would reasonably expect based on the Applicant’s specification that reducing the claimed transcription factor to 95% deficiency would have the same effect obtained by the Applicant. However, the present issue is not whether or not the effect (e.g., such as level of protein production, which is not recited in the claim) would be different. Instead, the present issue is whether or not the specification describes such a cell or reasonably shows possession of a 95% percent reduction in the production of the transcription factor, where the Applicant does not appear to have demonstrated or shown possession of such a scope of modifications in the specification (see 112(a) rejection, above).
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DOUGLAS CHARLES RYAN whose telephone number is (571)272-8406. The examiner can normally be reached M-F 8AM - 5PM.
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/D.C.R./Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
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