DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. The Preliminary Amendments filed on August 11, 2023, March 3, 2003 and August 11, 2025, have been received and entered.
3. Applicant's election without traverse of Group I (with species), on August 11, 2025, is acknowledged.
Claim Disposition
4. Claims 2, 4-5, 8-9, 12-14, 16-18, 20, 22-24, 26-36, 39, 41-46, 48-50, 52-54, 56-65, 67-94, 96-102, 104, 106-109, 112-127 and 129-138. Claims 1, 3, 6-7, 10-11, 15, 19, 21, 25, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-11, 128 and 139-146 are pending. Claims 1, 3, 6-7, 10-11, 15, 19, 21, 25, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 128 and 139-140 are under examination. Claims 141-146 are withdrawn from consideration pursuant to 37 CFR 1.12(b), as being drawn to a non-elected invention, there being no allowable generic or linking claim. The claims are only being considered to the extent that they pertain to the elected subject matter.
Information Disclosure Statement
5. The Information Disclosure Statements filed on August 11, 2023, September 23, 2024 and August 11, 2025 have been considered by the examiner. A copy of the PTO-Form 1449 is attached.
Drawing
6. The drawings filed on March 3, 2023, have been accepted by the examiner.
Specification Objection
7. The specification is objected to for the following informalities:
The title of the invention is not descriptive. A new title is required that is clearly indicative of the invention to which the claims are directed. The following is suggested: "A methylotrophic host cell and synthetic expression systems".
The specification is also objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code. See MPEP § 608.01. See page 76 for example. It is suggested that http:// is deleted.
The specification is objected to because organism names are not all italicized (see page 33, line 10 for ‘Kluyveromyces’.
Appropriate correction is required.
Claim Objection
8. Claims 1, 3, 6-7, 10-11, 15, 19, 21, 25, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 128 and 139-140 are objected to for the following informalities:
For clarity and precision of claim language it is suggested that claim 1 is insert ‘and’ to link the wherein clauses (i.e, “…..wherein the DBD and TAD are not native to the methylotrophic host cell, and wherein the input promoter…..”. The dependent claims hereto are also included. See also claim 110 with similar language.
For clarity it is suggested that claim 19 is amended to read, “…..promoter is a polynucleotide having at least 90%.....or at least 99% sequence identity to a nucleic acid sequence [[of any one of ]] set forth in SEQ ID NOs: 16-25”. See also claims 37 and 128 with similar language.
For clarity it is suggested that claim 38 is amended to read, “….nucleic acid sequence [[of any one of]] set forth in SEQ ID NOs: 26-40 or SEQ ID NOs:182-185”. See also claim 55 with similar language.
Claims 21, 47, 51, 139 and 140 are objected to because the acronyms are not spelled out.
For clarity it is suggested that claim 105 is amended to read, “a bioproduct produced in a control host cell”.
For clarity and precision of claim language it is suggested that claim 110 is amended to read, “…..wherein the synthetic expression system [[provides for production of]] produces a bioproduct….. level of [[the]] a bioproduct produced in a control….”.
For clarity it is suggested that claim 111 is amended to read, “….host cell of [[according to]] claim 1.”.
For clarity it is suggested that claim 128 is amended to read, “…..at least 99% sequence identity to …..”.
For clarity it is suggested that claim 139 is amended to read, “…..wherein the….expression system….into…..genome…..host cell [[at a single copy]] at….locus”.
For clarity it is suggested that claim 140 is amended to read, “…..wherein……. terminator [[serves as]] is a ……”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
9. Claims 1, 3, 6-7, 10-11, 15, 19, 21, 25, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 128 and 139-140 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AlA), 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.
The claimed invention is directed to “a methylotrophic host cell comprising a synthetic expression system that comprises a first transcriptional unit comprising an input promoter…. and a polynucleotide encoding at least one component of a synthetic transcription factor…….and a second transcriptional unit comprising a synthetic output promoter operably liked to a gene of interest…..”.The invention is also directed to a synthetic expression system. The claimed invention is not adequately described in claims 1, 110, 128 and dependents thereto because of the large genus of host, genes, promoters and expression products. Claims 1 and 110 recites ‘a methylotrophic host cell which is very variable and encompasses a microorganism typically a bacterium or a yeast that has the natural or engineered ability to use reduced C1 compounds like methanol and methane as the sole carbon source and energy for growth. It is noted that claim 95 recites ‘Pichia pastoris’, however, the independent claims are not limited to that organism and is overly broad. The claims also recite polynucleotide encoding at least one component of a synthetic transcription factor, promoters, gene of interest that encodes protein, domains, tags and percent language without the corresponding structures or accompanied by functional language. The claimed invention encompasses any genes, any promoters and any expression products without demonstration of possession of the large variable genus in the claims (see claims 1, 66, 110 and 128 for example). The invention as set forth in for example, claim 128 is devoid of any functional limitation. The claimed invention does not correlate structure with function and is not commensurate in scope with the disclosure in the specification.
The specification fails to provide a representative number of species for the claimed genus to show that applicant was in possession of the claimed genus. A representative number of species means that the species, which are adequately described, are representative of the entire genus.
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, disclosure of drawings, or by disclosure of relevant identifying characteristics, for example, 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. Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991), states that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed" (See page 1117). The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed" (See Vas-Cath at page 1116). The skilled artisan cannot envision the detailed chemical structure of the encompassed genus of products or diseases or conditions, and therefore, conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method of isolating it. The compound itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993).
Therefore, for all these reasons the specification lacks adequate written description, and one of skill in the art cannot reasonably conclude that the applicant had possession of the claimed invention at the time the instant application was filed.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
10. Claims 1, 3, 6-7, 10-11, 15, 19, 21, 25, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 128 and 139-140 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1, 3, 6-7, 10-11, 15, 19, 21, 25, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 128 and 139-140 and dependent claims hereto lacks clear antecedent basis for the recitation of “the gene of interest is expressed in the absence of exogenously provided methanol” because the claim does not mention exogenously providing methanol.
Claim 10 is indefinite for the recitation of the “the promoter is responsive to nutrient addition, limitation or depletion” because it is unclear if ‘responsive’ is positive or negative and there are no indicia as to what ‘response’ is received and if the resulting effect is desirable. See also claim 11 with similar language.
Claim 11 lacks clarity for the recitation of “…the regulatable input promoter is responsive to thiamine depletion…..; or is increased by the presence of exogenously provided formic acid”, because it is not that the regulation of the promoter is the addition of formic acid, depletion of thiamine etc. Also there are no indicia in the claim limitation of how much increase and the increase is clearly defined (is it an increase responsiveness of the promoter, an increase in promoter copies or an increase in a desired resulting effect?) and what effect occurs from the thiamine depletion and how does it response to that condition?
Claim 47 is indefinite for the recitation of percent language without a reference structure (i.e. at least 94% identical to the sequence set forth in SEQ ID NO:X). The reference to for example, P(AOX1) does not provide a discrete nucleic acid structure for comparison.
Claim 51 lacks clear antecedent basis for the recitation of the UAS having ‘one or more copies (for bmO, phlO, tetO and vanO)’, when claim 40 from which it depends recites “an upstream activating sequence (UAS)’, there is no implied multiple sequences.
Claim 103 lacks clear antecedent basis for the recitation of “the quantity of transcripts”, “the production phase” and “the growth phase”.
Claim 105 lacks clear antecedent basis for, “the biproduct produced in a control….”. See also claim 110 with similar language.
Claim 128 is indefinite because the ordinary skilled worker cannot determine the metes and bounds of the claim, since it recites an expression system that is synthetic and that has a polynucleotide with at least 90% identity to a nucleic acid in another structure such as SEQ ID NO:1 and there is no nexus made between the expression system and the nucleic acid, no activity is aligned with it as well.
Claim 140 lacks clear antecedent basis for, “the native AOX1”.
Clarification is needed.
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.
11. 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.
12. Claim(s) 1, 3, 6-7, 10-11, 15, 19, 21, 25, 38, 40, 47, 51, 66, 95, 103, 105, 110-111, 128 and 139-140 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mojzita et al. (US 2018/0371468 A1, 2018, of record in the application) in view of Lu et al. (WO 2018/013551 A1 2018, of record in the application) and Ahmad et al. Applied Microbiol. Biotech., 2014 of record in the application) and Suppmann et al. (US 2004/0259197, 2004, of record in the application).
The claimed invention is directed to a methylotrophic host cell with a synthetic expression system. The general knowledge in the art is that Pichia pastoris is great for heterologous protein production, which is a methylotrophic host cell. Ahmad et al. discloses that P. pastoris is an established protein expression host mainly applied for the production of biopharmaceuticals.
Mojzita et al. discloses a methylotrophic host cell (P. kudriavzevii) comprising a synthetic expression that comprises a first transcriptional unit comprising an input promoter comprising a core promoter element driving the expression of a synthetic transcription factor comprising a BM3R1-NLS DNA-binding domain and a VP16 activation domain. The expression system further comprises a second transcriptional unit comprising a synthetic output promoter (having an upstream activating sequence and a core promoter element) that is activated by the synthetic transcription factor and is operably linked to a gene of interest (mCherry). The system can express the gene of interest in the absence of exogenously provided methanol (see Example 4; Fig. 1 and Fig. 4). The NLS is an SV40 nuclear localization signal (see par. [0159]). In addition, synthetic expression systems are disclosed, including a system expressed in a Pichia pastoris host cell wherein the gene of interest encodes a protein comprising a secretion signal (see para. [0187] and Fig. 9C). The host cells express the encoded gene of interest at a level that is at least 600% higher than the level of the gene of interest in a control host cell, wherein the control host cell does not comprise the synthetic expression system and so does not express the gene of interest. Claims 1 and 110 differ from the primary reference in that the input promoter comprises an upstream activating sequence (UAS). The present specification suggests that the UAS of the input promoter is an optional element that is not essential to the working of the invention (page 13, lines 16-17; Fig 1A), and it is not clear if any of the exemplified embodiments actually utilize an input promoter comprising a UAS. The use of upstream activating sequences in promoters of expression systems is routine in the art for the purpose of enhancing the expression of a gene or regulating the expression of a gene through the use of an inducible element, thus, claims 1 and 110 are obvious. The claimed invention is also directed to a host cell comprising the synthetic expression system wherein the quantity of transcripts of a gene of interest produced in production phase is at least 100% higher than in the growth phase. The primary reference does not explicitly disclose this feature, however, it is a well-known goal of microbial expression systems to have elevated expression of a desired product in the production phase. This feature is easily achieved by method that are common and general knowledge in the art, such as the use of an inducible input promoter, therefore obvious.
The invention also encompasses limitations such as the specific type of input promoter, output promoter, DNA binding domain or gene of interest, or the incorporation of a self-cleaving peptide. Each of these features/elements is common general knowledge in the art and is a technical equivalent that are described in the primary reference, thus obvious. Further, the synthetic expression systems each comprising an input promoter, a nucleic acid encoding a synthetic transcription factor, a transcription terminator, a spacer, and an output promoter, DNA-binding domain or gene of interest, or the incorporation of a self-cleaving peptide, are also elements that are common general knowledge in the art and is a technical equivalent of that described in primary reference, and so is also obvious.
The invention is further directed to synthetic expression systems, each comprising an input promoter, a nucleic acid encoding a synthetic transcription factor, a transcription terminator, a spacer, an output promoter. The primary reference discloses nucleic acids comprising each of these classes of elements (see Fig 4) that differ from the present claims in the substitution of specific sequences with technical equivalents that are common general knowledge in the art, thus rendering the claimed synthetic expression system and transcription factor as obvious.
Lu et al. discloses a methylotrophic host cell (Komagataella phaffi/Pichia pastoris) comprising a synthetic expression system that comprises a first transcriptional unit comprising an input promoter comprising a core promoter driving the expression of a synthetic transcription factor. The transcription factor comprises a zinc finger DNA binding domain, a beta-estradiol binding domain and a VP64 activation domain. The expression system comprises a second transcriptional unit comprising a promoter that is activated by the synthetic transcription factor and drives expression of a gene of interest that encodes GFP or rHGH (page 9 lines1-24;Fig. 1B).The host cell expresses the gene of interest in the presence of glycerol and beta-estradiol, but in the absence of methanol (Fig. 4A). Culturing of the cell demonstrates that expression of the gene of interest (rHGH) in the production phase (52-72h) is at least 100% higher than in the growth phase 90-24h) (Table 4, page 56; Fig 5C). The protein encoded by the gene of interest comprises a secretion signal (page 75, line 22-page 76, line 5). The exemplified embodiments differ from independent claims of the invention because the input promoter does not comprise a UAS, however, this feature is not the crux of the invention as mentioned pertaining to the primary reference, and would be construed as general teaching in the art.
Moreover, Suppmann et al. teaches a methylotrophic yeast used as a heterologous host organism. Suppmann et al. teaches a multiple integration element comprising a homing endonuclease site, the AOX1 promoter, a secretion signal, a selection marker gene, a DNA sequence encoding a detection and/or purification polypeptide, as well as a terminator. The reference also teaches sequences that are 96% identical with instant SEQ ID NOs:16 and 29 among others (see Abstract, Fig 3 and 10).
Therefore, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to arrive at the claimed invention as a whole because the combined teaching of the references renders the claimed invention as obvious. The art is replete with references teaching about this area and the advantages of culturing the claimed microorganism such as Ahmad et al. Ahmad et al. discloses that P. pastoris is a good host cell and has established protein expression host mainly applied for the production of biopharmaceuticals. There is motivation to combine the teaching of the references because they are analogous art. Moreover, the Supreme Court pointed out in KSR, “a patent composed of several elements is not proved obvious merely by demonstrating that each of its elements was, independently, known in the prior art.” KSR, 127 S. Ct. at 1741. The Court thus reasoned that the analysis under 35 U.S.C. 103 "need not seek out precise teachings directed to the specific subject matter of the challenged claim, for a court can take account of the “inferences and creative steps that a person of ordinary skill in the art would employ.” Id. at 1741. The Court further advised that “[a] person of ordinary skill is…a person of ordinary creativity, not an automation.” Id. at 1742. Therefore, the claimed invention was obvious to make and use at the time the invention was made and was prima facie obvious.
Conclusion
13. No claims are presently allowable, however, full length sequences set forth in SEQ ID NOs:44, 59, 1, 2, 88 and 103 are free of the art.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to HOPE A ROBINSON whose telephone number is (571) 272-0957. The examiner can normally be reached 9-5pm on Monday to Friday.
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/HOPE A ROBINSON/Primary Examiner, Art Unit 1652