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 .
This is the First Office Action of US 18/281,117 filed on 09/08/2023 which is a 371 of PCT/US2022/019962 filed on 03/11/2022 which claims US priority benefit of US Provisionals 63/221,041 filed on 07/13/2021 and 63/159,843 filed on 03/11/2021.
Election/Restrictions
Applicant's election with traverse of Group III, claims 16 and 21, drawn to a polypeptide comprising a pre-protein signal peptide and a pro-protein signal peptide, in the reply filed on March 23, 2026 is acknowledged.
Applicant's election of the species A) SEQ ID NO:14 (from those listed in claim 9) and B) SEQ ID NO: 22 (from those listed in claim 13) in the reply filed on March 23, 2026 is acknowledged.
Applicant's election of the species C) Saccharomyces; D) SEQ ID NO:1 & SEQ ID NO:20; E) SEQ ID NO:4 & 20; F) SEQ ID NO:14 & 22; G) SEQ ID NO:31 & 34; and H) SEQ ID NO:70 & 73, in the reply filed on March 23, 2026 is acknowledged.
The traversal is on the ground(s) that the applicants argue that the Office describes the discovery of proinsulin and the effect of the discovery on the field of protein-precursor processing but that Philipson does not reference signal peptides of any kind, let alone pre or pro signal peptides.
This traverse is not found persuasive because the Philipson et al article recites the proinsulin. Group III recites a polypeptide product comprising a pre-protein signal peptide, or a pro-protein signal peptide, and a payload which may be insulin. Group I recites a pre-protein signal peptide product and Group II recites a pro-protein signal peptide product. The applicants argue that the single inventive concept of the six groups is the use of novel synthetic signal peptides to direct the secretion of heterologous payload proteins in yeast. The applicants argue that the special technical feature common to all groups is the novel synthetic signal peptide sequences.
First, the applicants’ argument is unpersuasive because the determination whether a group of inventions is so linked as to form a single general inventive concept shall be made without regard to whether the inventions are claimed in separate claims or as alternatives within a single claim. See 37 CFR 1.475(e). As the applicant argues, the individual SEQ ID Nos listed as alternatives in the claims are distinct sequences. Since no technical features are shared among the signal peptide sequences, the groups lack unity a priori.
Second, the applicants’ argument is unpersuasive because as provided in 37 CFR 1.475 (b), a national stage application containing claims to different categories of invention will be considered to have unity of invention if the claims are drawn only to one of the following combinations of categories: (1) A product and a process specially adapted for the manufacture of said product; or (2) A product and a process of use of said product; or (3) A product, a process specially adapted for the manufacture of the said product, and a use of the said product; or (4) A process and an apparatus or means specifically designed for carrying out the said process; or (5) A product, a process specially adapted for the manufacture of the said product, and an apparatus or means specifically designed for carrying out the said process. As noted in the restriction requirement mailed 01/22/2026 the present claims recite several distinct product groups and thus lack unity because they do not meet the criteria of only one of the different combination categories (1) –(5) listed just above.
Lastly, the applicants’ argument are not persuasive because the argument appears to recite methods as the unifying feature whereas Groups I-IV are drawn to distinct products. Further, whereas Groups I and II only requires a pre-protein signal peptide listed in claim 9 or a pro-protein signal listed in claim 13, Group III only lists these features in the alternative but it does require a payload protein, which includes insulin. Thus, the special technical feature may be considered to be a signal peptide sequence. Contrary to the applicants’ argument, a signal peptide was known in the prior art as disclosed in the Philipson et al article recites the concept of a preproinsulin. The preproinsulin of Philipson et al contains a nascent signal peptide. (See page 940, right col.)
The requirement is still deemed proper and is therefore made FINAL.
Claims 9-11, 13-15, 22-30, and 39-41 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention Group, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on March 23, 2026.
Rejoinder of an additional species A and species B
The Examiner notes that the elected species of SEQ ID NO: 14 and 22 are free of the prior art. However, note that prior art has been applied regarding SEQ ID Nos 14 and 22 because the present claim language does not require a sequence identical to either of SEQ ID NO:14 or 22.
In the interest of compact prosecution, the examiner is REJOINING an additional species A) being SEQ ID NO: 2 and species B) being SEQ ID NO: 17.
Claim status
Claims 1-8, 12, 17-20, 31-38, and 42-59 are cancelled.
Claims 9-11, 13-16, 21-30, and 39-41 are pending.
Claims 9-11, 13-15, 22-30, and 39-41 are withdrawn.
Claims 16 and 21 are under examination.
Information Disclosure Statement
The IDS statements filed on 09/08/2023 and 03/01/2024 have been considered by the examiner.
Drawings
The drawings are objected to because Figure 33 has illegible text. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 16 and 21 are objected to because of the following informalities:
For improved clarity, the limitation in claim 16 which recites: “X1 is the pre-protein signal peptide of claim 9” should be amended to include the limitation of claim 9 into claim 16 instead of reciting “of claim 9”. (For example, such amendment is presently correctly made regarding instant claim 16 regarding the listing of peptide SEQ ID Nos of claim 13.)
Claim 21 appears to have a typographical error in the phrase: …plant growth stimulator, or fertilizer), a vaccine…. 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.
Claims 16 and 21 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.
Claims are drawn to a polypeptide comprising a formula of (Xi)n-(Yi)m-Zi wherein: Zi is a payload protein and Xi is the pre-protein signal peptide comprising an amino acid sequence having at least 90% identity to the elected species of:
SEQ ID NO: 14: Met Lys Phe Lys Leu Thr Leu Leu Ala Ala Leu Leu Ala Leu Ala Ala Leu Val Leu Ala Ala Ser (22 aa);
and Yi is a pro-protein signal peptide comprising an amino acid sequence having at least 90% identity to the elected species of:
SEQ ID NO: 22: Glu Pro Trp Ser Thr Leu Thr Val Thr Arg Ser Thr Tyr Asp Glu Ile
Thr Asp Thr Asp Tyr Asn Ser Thr Gly Ile Ala Val Asn Pro Tyr Thr Val Ser Ala Ser Arg His Lys Arg Asp Val (42 aa).
The specification states that the performance of an N-terminal signal peptide “varies greatly depending on the payload protein” (See para 0004). Claims encompass compositions with the intended use of treating a disease in a subject. Claims require the critically essential element of a functional, therapeutic polypeptide that is effective in treating a disease including an infection, an autoimmune disease, diabetes, and Celiac disease. See instant claim 41. The method of treating is by transfecting a yeast with a nucleic acid encoding the therapeutic polypeptide, inducing secretion of the payload protein by the engineered yeast, and administering to the subject a therapeutically effective amount of such yeast. See instant claim 22.
The specification shows possession of the signal peptides consisting of the SEQ ID Nos listed in claims 9 and 16. However, as presently written in the claims, these signal peptides read on variants of these SEQ ID Nos. It is considered that one of ordinary skill in the art would not be able to envision whether a given species of variant of SEQ ID NO as encompassed by the claims would possess the required properties required of the therapeutic polypeptide encompassed by claims 16 and 21 for effective treating in a patient. In addition, the specification provides generic amino acid sequences showing how to make many signal peptide variants. For example, see paragraphs 0119-0188 and Tables 5-16. However, the specification does not contain a representative set of variants of these signal peptides, having these required properties of the claims.
Further, the applicants do not show possession of the genus of payload protein as the Z1 portion of the claimed polypeptides having the required properties for use in treating a disease linked to any of the variant signal peptide combinations. Base claim 16 recites a generic payload protein and claim 21 lists specific types of payload proteins including an antiviral, insulin, an incretin, an enzyme, an enzyme inhibitor, a hormone, a cytokine, an antibody, an antimicrobial peptide, a mucosal protein, pesticide, bactericide herbicide, fungicide, nematicide, miticide, plant growth regulator, plant growth stimulator, or fertilizer, a vaccine, a diagnostic protein, a feed conversion enzyme, a flavoring, and a nutritional protein. The specification does describe some specific amino acid SEQ ID NO structures for specific payload proteins. For example, see para 206 (SEQ ID NO:60). In para 0253, the control pre-protein signal peptide is shown as glucoamylaseprotein, as represented by SEQ ID NO: 77.
Further, the specification does not disclose a payload protein example of a fertilizer protein as presently claimed in claim 21.
In para 0529, Example 17, the specification shows exemplary pre-peptide, pro-peptide, and payload protein combinations. See Tables 18-19. The specification shows one example is Example 5: “Effect of Synthetic Signal Peptide on Secretion of Invertase”
However, the specification does not show a representative set of examples of such combinations useful for treating the diseases listed in instant claim 41 so that one of ordinary skill in the art would be able to envision whether a given combination of pre-peptide, pro-peptide, and payload protein encompassed by the vast number of embodiments encompassed by the claims would possess the property of treating a disease.
Further, the state of the art provides evidence that even a single amino acid change to a therapeutic peptide may significantly change the functional properties of the peptide. For example, Sengupta et al discloses that site-specific amino acid substitution in dodecameric peptides determine the function of the peptide in cancer cells (See Sengupta et al, Nucleic Acids Res 2018 Nov 2 Vol 46 No. 19 pages 9932-9950).
The Court of Appeals for the Federal Circuit has recently held that a "written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as be structure, formula [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." University of California v. Eli Lilly and Co., 1997 U.S. App. LEXlS 18221, at *23, quoting Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) (bracketed material in original).
To fully describe a genus of genetic material, which is a chemical compound, applicants must (1) fully describe at least one species of the claimed genus sufficient to represent said genus whereby a skilled artisan, in view of the prior art, could predict the structure of other species encompassed by the claimed genus and (2) identify the common characteristics of the claimed molecules, e.g., structure, physical and/or chemical characteristics, functional characteristics when coupled with a known or disclosed correlation between function and structure, or a combination of these.
The specification does not provide sufficient descriptive support for the myriad of embodiments embraced by the claims. When there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. Given this lack of description of representative species encompassed by the genus of the claim, the specification does not sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that applicants were in possession of the entire scope of the claimed invention.
For inventions in an unpredictable art, adequate written description of a genus, which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See, e.g., Eli Lilly. Description of a representative number of species does not require the description to be of such specificity that it would provide individual support for each species that the genus embraces. If a representative number of adequately described species are not disclosed for a genus, the claim to that genus must be rejected as lacking adequate written description under 35 U.S.C. 112, first paragraph. In the instant case, the unpredictability of the art is evidenced by the cited reference(s), above. Adequate written description requires more than a mere statement that a compound is part of the invention and reference to a potential method of isolating a compound. The compound itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim 16 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kittleson et al (WO2018132821-A2 published July 19, 2018) as evidenced by attached SCVUi/STIC SEQ ID NO result for instant SEQ ID No 2.
Kittleson et al disclose the alpha mating factor precursor protein signal peptide, reference SEQ ID NO: 46 which has an amino acid precursor protein sequence which is 100% identical to the instant SEQ ID NO: 2 (MRFPSIFTAVLFAASSALA). (See ref Example 7; page 65). Kittleson et al disclose that this signal peptide is attached to the payload protein resilin on the N-terminal end of the payload protein. (See FIG3; para 0053). Thus, Kittleson et al anticipates claim 16.
Claim 16 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Stevens (WO2019222633-A1 published November 21, 2019) as evidenced by attached SCVUi/STIC results for SEQ ID NO 2 and SEQ ID NO 17 for Stevens.
Stevens disclose the Saccharomyces cerevisiae MF alpha 1 variant signal peptide, ref SEQ 90 which is 100% identical to the instant SEQ ID NO: 2 (See ref Example 7; page 42). See para 0020 which states:
[0020] In some embodiments, the recombinant protein comprises a secretion signal peptide. In some embodiments, the secretion signal peptide is selected from the group consisting of: a PEP4 signal sequence, a CPY +4 signal sequence, a DAP2 signal sequence, and a MFal signal sequence. In some embodiments, the secretion signal peptide is selected from the group consisting of: SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, and SEQ ID NO: 90.
Stevens disclose the Saccharomyces cerevisiae MF alpha 1 propeptide sequence, ref SEQ 106 which is 100% identical to the instant SEQ ID NO: 17 (See ref Example 7). (See Stevens Table 7A). Stevens disclose that the signal peptide is attached to the N-terminus of the payload protein which is a silk protein. (FIG5). Thus, Stevens anticipates claim 16.
Claims 16 and 21 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Seidel III et al AU 2018327224 A1 published 2020-04-23
Claim interpretation: During examination, claims must be given their broadest reasonable interpretation in light of specification. The claimed formula recites that n is 0-1 and m is 0-1, and n and m cannot concurrently be 0. Thus, as presently written, the claimed formula requires either Xi or Yi connected on the amino terminus of the payload protein Zi. For example, the claimed formula requires either an Xi-payload protein or a Yi-payload protein. Also, the elements of Xi and Yi are defined in the claim as an amino acid sequence having at least 90% identity to the elected species of SEQ ID NO:14 (Xi) or SEQ ID NO:22 (Yi).
Regarding claim 16, Seidel III et al shows a series of constructs comprising a human β2Μ polypeptide sequence. The constructs comprise from N-terminus to C-terminus: the leader sequence MSRSVALAVLALLSLSGLEA, an optional linker and sulfatase site and another independently selected linker as described in Examples 1 and 2. (See para 0017 FIG. HA to FIG. HE)
Regarding claim 21, Seidel et al teach a payload including a chemotherapeutic agent or enzyme (See para 0046 & “Payloads” listed in para 00445.
[00445] In an embodiment, the payload is selected from biologically active agents or drugs selected independently from the group consisting of: therapeutic agents (e.g., drugs or prodrugs) , chemotherapeutic agents, cytotoxic agents, antibiotics, antivirals, cell cycle synchronizing agents, ligands for cell surface receptor(s), immunomodulatory agents (e.g., immunosuppressants such as cyclosporine), pro-apoptotic agents, anti-angiogenic agents, cytokines, chemokines, growth factors, proteins or polypeptides, antibodies or antigen binding fragments thereof, enzymes, proenzymes, hormones and combinations thereof.
Thus, Seidel et al anticipates claims 16 and 21 as presently written.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 16 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 2-3, 5, 8, 12-14, 16, 20-21, 24-25, 28-29, 32, 36-37, 40-41, and 45 of copending Application No. 18/864,992 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because the copending claims anticipate or are essentially the same as the present claims.
Regarding instant claim 16, copending claim 5 recites a recombinant polypeptide comprising a formula X1-Z1 wherein: X1 is the pre-protein signal peptide comprising an amino acid sequence having at least 90% identity to the amino acid sequence of copending SEQ ID NO 1-4, and Z1 is a payload protein. Note that copending SEQ ID NO:1 is MKKLLALGLLALGLLLSSSAQAAD which reads on an amino acid sequence having 90% identity to the amino acid sequence of instant SEQ ID NO:14: Met Lys Phe Lys Leu Thr Leu Leu Ala Ala Leu Leu Ala Leu Ala Ala Leu Val Leu Ala Ala Ser (22 aa);
Regarding instant claim 21, copending claim 8 depends from copending claim 5 and recites that the Z1 may be an antiviral, insulin, an incretin, an enzyme, a cytokine, an antibody, and a hormone.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 16 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3-5, 7-10, 12-13, 15, 18-27, 29-30, 39, and 42 of copending Application No. 18/281,388 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because the copending claims anticipate or are essentially the same as the present claims.
Regarding instant claim 16, copending claim 5 recites a recombinant polypeptide comprising a formula X1-Z1 wherein: X1 is the pre-protein signal peptide comprising an amino acid sequence having at least 90% identity to the amino acid sequence of copending SEQ ID NO 1, 3, 11, or 13, and Z1 is a payload protein. Note that copending SEQ ID NO:1 is Met Lys Lys Thr Leu Leu Leu Leu Leu Val Leu Leu Ala Ser Leu Leu
Val Leu Ala Ala Cys Gly Ser Ala Ser Ala which reads on an amino acid sequence having 90% identity to the amino acid sequence of instant SEQ ID NO:14: Met Lys Phe Lys Leu Thr Leu Leu Ala Ala Leu Leu Ala Leu Ala Ala Leu Val Leu Ala Ala Ser (22 aa);
Regarding instant claim 21, copending claim 8 depends from copending claim 5 and recites that the Z1 may be an antiviral, insulin, an incretin, an enzyme, a cytokine, an antibody, and a hormone.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is allowed.
Related prior art which may be applied in a future office action if appropriate:
Silverman et al WO 2011123830 A2 published 2011-10-06;
Graves et al US 20250242012 A1 filed on 2021-02-25 (published 2025-07-31);
Furukawa et al in “Mutational analysis of the C-terminal signal peptide of bovine liver 5’-nucleotidase for GPI anchoring: a study on the significance of the hydrophilic spacer region” (Biochimica et Biophysica Acta 1997 Vol 1328, pages 185-196).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHERINE S HIBBERT whose telephone number is (571)270-3053. The examiner can normally be reached M-F 8:00-5:00.
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CATHERINE S. HIBBERT
Primary Examiner
Art Unit 1658
/CATHERINE S HIBBERT/Primary Examiner, Art Unit 1658
Prosecution Insights