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 Amendment filed on April 7, 2026, has been received and entered.
Claim Disposition
3. Claims 2, 4-5, 8-9, 7-10, 12-14, 16-18, 20, 22-36, 39, 41-46, 48-50, 52-54, 56-65, 67-94, 96-102, 104, 106-109, 112-127, 129-138 and 141-146. Claims 1, 3, 6, 11, 15, 19, 21, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 128, 139-140 and 147-154 are pending. Claims 1, 3, 6, 11, 15, 19, 21, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 139-140 and 153 are under examination. Claims 128,147-152 and 154 are withdrawn from consideration pursuant to 37 CFR 1.12(b), as being drawn to a non-elected invention, there being no allowable generic or linking claim. Claim 128 as amended is no longer directed to subject matter pertaining to the elected invention, therefore, withdrawn. The claims are only being considered to the extent that they pertain to the elected subject matter (election of SEQ ID NOs:16, 29, 44, 59, 88, 92, 114, 131, 103, 114 and 163).
Information Disclosure Statement
4. The Information Disclosure Statement filed on April 7, 2026, has been considered by the examiner. A copy of the PTO-Form 1449 is attached. Note that some references have been lined through due to improper citation of the date.
Specification Objection
5. The specification remains objected to for the following informalities:
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
6. Claims 1, 3, 6, 11, 15, 19, 21, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 139-140 and 153 are objected to for the following informalities:
For clarity and precision of claim language it is suggested that claim 1 is amended to read, “A methylotrophic host cell comprising: [[a synthetic expression system that comprises]]
a first transcriptional unit having:[[comprising]]
[[an]] a synthetic input promoter [[comprising]] with an upstream activating sequence……..a second transcriptional unit having:[[comprising]] a synthetic output promoter….. wherein the synthetic transcription factor of (ii) is an activator of……”. The dependent claims hereto are also included. Claim 1 recites “a methylotrophic host cell comprising a synthetic expression system…” which means the entire system is ‘synthetic’ thus appears redundant to recite ‘synthetic transcription factor’, ‘not native to the methylotrophic host cell’ and ‘synthetic output promoter’ because the preamble recites “synthetic expression system’. See also claim 110 with similar language.
For clarity it is suggested that claim 11 is amended to delete the broad and narrow ranges, for example “an amino acid and methionine” and “a vitamin and thiamine”.
For clarity it is suggested that claim 47 is amended to read, “…..the core promoter element ……and… the upstream activating sequence………[[or a combination thereof]].
Claim 51 is objected to for the recitation of non-elected subject matter (see also claims 19, 21, 37-38, 47, 55, 110 and 153).
For clarity it is suggested that claim 110 is amended to recite, “….wherein the synthetic output promoter,……. and wherein the synthetic transcription factor……”.
For clarity it is suggested that claim 153 is amended to read, “(b)……wherein the second….. and wherein the synthetic…..”.
For clarity and precision of claim language it is suggested that claim 153 is amended to read, “….a first transcriptional unit comprising [[a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence set forth in SEQ ID NOs:71-85, wherein the first transcriptional unit comprises:]]
an input promoter……”.
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.
7. Claims 1, 3, 6, 11, 15, 19, 21, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 139-140 and 153 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 nucleic acid sequence encoding 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 in a methylotrophic yeast cell, a polynucleotide and a Pichia pastoris cell with and undefined ‘gene of interest’ (see claims 110 and 153). The claimed invention is not adequately described in claim 1 (any methylotrophic host cell with no structural limitations for the expression products), 110 (any gene of interest), and dependents thereto because of the large genus of host, nucleic acid sequences, 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 and 153 recites ‘Pichia pastoris’, however, the other independent claims are not limited to that organism and is overly broad. The claims also recite nucleic acid sequence encoding 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 claims do not consistently recite limitations that are crucial to inform the ordinary skilled worker what is inventive. 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 and 110 (any yeast), for example). The gene of interest encodes a secretion tag and is recited as having an mRNA expression that when cultured in production phase is at least 100% (claim 103) or 200% (claim 105) higher than its counter-part but the gene of interest is undisclosed and the bioproduct it encodes. The invention 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.
8. Claims 1, 3, 6, 11, 15, 19, 21, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 139-140 and 153 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, 11, 15, 19, 21, 37-38, 40, 47, 51, 55, 66, 95, 103, 105, 110-111, 139-140 and 153 and dependent claims hereto lacks clarity as to whether the second transcriptional unit has the nucleic acid sequence that encodes a synthetic transcription factor or a separate gene from the first transcriptional unit.
Claim 1 and the dependent claims hereto are indefinite for the recitation of ‘depletion or limitation of a nutrient’ because the input promoter drives expression and is induced in the host cell in response to the depletion or limitation of the nutrient that is not defined in the claim. The metes and bounds of the claim language is not clear. Clarification if needed.
Claim 11 is indefinite for the recitation of the “the promoter is responsive to nutrient limitation or depletion” as dependent from claim 1 because for example, hydrogen peroxide, steroid, among others are not construed in the art as a ‘nutrient’.
Claim 47 is indefinite for the recitation of “…core promoter element; UAS or a combination thereof”, because claim 40 from which it depends recites ‘UAS and core promoter”.
Claim 103 lacks clear antecedent basis for mRNA, because the gene of interest is not described in the claim and not all gene has mRNA.
Claim 153 is indefinite for the recitation of “ a nucleic acid sequence at least 90% identical to SEQ ID NOs:71-85 and a nucleic acid sequence at least 90% identical to SEQ ID NOs:41-55” because there is no nexus between the two structures. Is the first nucleic acid the ‘gene of interest’, how is related to the first or second transcriptional unit.
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.
9. 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.
10. Claim(s) 1, 3, 6, 15, 40, 66, 95, 103, 105, 111 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.
Response to Arguments
11. Applicant’s comments have been considered in full. Withdrawn objections/rejections will not be discussed herein as applicant’s comments are moot. Note that the rejections of record under 112 first and second paragraphs remain for the reasons stated above and listed herein.
Applicant traverses the rejection under 112 first paragraph and state that the claims have been amended. However, note that the amendments were either not sufficient to obviate this ground of rejection or the amendments led to new issues being raised. The claimed invention remains overly broad with the recitation of any methylotrophic host cell with a synthetic expression system in claim 1 and any gene of interest (see claims 1, 110 and 153 for example). Claim 1 does not provide structures or the host cell, it is noted that new claim 153 provides structure and the specific organism, except for the gene of interest. Thus the rejection remains. Note that new rejections have been instituted under 112, 2nd for the reasons stated above based on amendments made.
Applicant traversed the art rejection, however, the arguments are not persuasive. The 103 rejection remains over claim 1 which has no structural limitation and broadly recites depletion or limitation of any nutrient with no and cells experience limitation or depletion of nutrients on a regular basis thus renders this limitation as obvious. The rejection also addresses the UAS of the claimed invention, thus obvious. Applicant’s representative is urged to contact the examiner to reduce the remaining issues.
Conclusion
12. 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.
13. Applicant’s amendment necessitated the new/modified ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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
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