DETAILED ACTION
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/23/2025 has been entered.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
The following amendments, additions, and cancelations as submitted on 12/23/2025 are acknowledged:
Claims 2, 7, 11-13 are cancelled.
New claim 14 is added.
Claims 1, and 3-6 8-10, and 14 are pending.
Claims 1 and 6 are amended.
Claims 6, 8-10 are withdrawn.
Claims 1, and 3-5, and 14 are being examined.
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 .
Priority
Acknowledgment is made of a claim for foreign priority under 35 U.S.C. 119(a)-(d). Applicants claim to foreign priority for No.JP2020-011149 filed on 01/27/2020 is acknowledged.
Information Disclosure Statement
The information disclosure statements filed on 08/19/2022, 08/19/2022, 03/15/2024, 03/15/2024, 02/18/2025, 06/30/2025, and 12/23/2025 have been received and the references therein have been considered.
Drawings
The drawing submitted on 07/12/2022 have been reviewed and are accepted by the examiner for examination purposes.
Claim Objections
Claim 13 was previously objected to because of the following informalities: Claim 13 recited “The method according to claim 4, wherein the extracellular protease is encoded by epr, wprA, mpr, nprB, bpr, vpr, aprE, aprE and aprX”. As shown, the limitation of “aprE” was recited twice. Claim 13 has since been canceled, rendering the previous objection moot. Accordingly, the previous objection to claim 13 is withdrawn.
Claim 1 is objected to due to the recitation of “encoded by wprA and bpr…encoded by epr, mpr….and aprX…. encoded by epr….and aprX”. To be consistent with commonly used claim language, the term should be amended to recite “encoded by the wprA and bpr genes…encoded by the epr, mpr….and aprX genes…. encoded by the epr….and aprX genes”. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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.
Claim 13 was previously 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. In view of the cancellation of claim 13, this rejection is hereby withdrawn.
Claim 3 is indefinite in the recitation of “consists of an amino acid sequence of SEQ ID NO: 2…. or 138” for the following reasons. The term “an amino acid sequence of SEQ ID NO: 2…. or 138” can be interpreted as “a fragment of the amino acid sequence of SEQ ID NO: 2…or 138”. Therefore, it is unclear if the variable domain is required to “consist of the amino acid sequence of SEQ ID NO: 2…or 138”, or if the variable domain is required to “consist of a fragment of the amino acid sequence of SEQ ID NO: 2…or 138”. For examination purposes, it will be assumed that the claim recites “consists of the amino acid sequence of SEQ ID NO: 2 …or 138”. Correction is required.
Claim 4 is indefinite in the recitation of “wherein the Bacillus bacterium is Bacillus subtilis or a mutant strain thereof” for the following reasons. It is unclear as to which organisms are encompassed by the term “a mutant of a Bacillus subtilis”. One cannot determine which genus/species are deemed mutants of a Bacillus subtilis. For examination purposes, no patentable weight will be given to the term “mutant strain thereof”. Correction is required.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
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, 3-5, 14 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This rejection is necessitated by the introduction of new matter.
As set forth in MPEP 2163 (I)(B), new or amended claims which introduce elements or limitations that are not supported by the as-filed disclosure violate the written description requirement. See, e.g., In re Lukach, 442 F.2d 967, 169 USPQ 795 (CCPA 1971) (subgenus range was not supported by generic disclosure and specific example within the subgenus range); In re Smith, 458 F.2d 1389, 1395, 173 USPQ 679, 683 (CCPA 1972) (an adequate description of a genus may not support claims to a subgenus or species within the genus). Claims 1, 3-5, 14 are now directed to a method for producing a variable domain of a heavy chain of a heavy chain antibody, wherein said method requires culturing a Bacillus cell that is deficient in one or both of the extracellular proteases encoded by the wprA and bpr genes and not deficient in any extracellular protease encoded by epr, mpr, nprB, nprE, vpr, aprE, and aprX genes. While the specification discloses a method for producing a variable domain of a heavy chain of a heavy chain antibody, wherein said method requires culturing a Bacillus cell that is deficient in at least one extracellular protease encoded by the epr, wprA, mpr, nprB, bpr, nprE, vpr, aprE, or aprX gene, the Examiner is unable to locate adequate support for a Bacillus cell that is deficient in an extraceullar protease encoded by the wprA and/or bpr genes but not deficient in any extracellular protease encoded by the epr, mpr, nprB, nprE, vpr, aprE, and aprX genes. There is no indication in the specification that a subgenus of extracellular proteases that excludes the extracellular protease encoded by the epr, mpr, nprB, nprE, vpr, aprE, and aprX genes is a preferred embodiment of the invention. Thus, there is no indication that a method for producing a variable domain of a heavy chain of a heavy chain antibody, wherein said method requires culturing a Bacillus cell that is deficient in one or both of the extracellular proteases encoded by the wprA and bpr genes and not deficient in any extracellular protease encoded by epr, mpr, nprB, nprE, vpr, aprE, and aprX genes, was within the scope of the invention as conceived by Applicant at the time of the invention. Accordingly, Applicant is required to cancel the new matter in the response to this Office Action.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1, 3-5 were previously rejected under 35 U.S.C. 103 as being unpatentable over unpatentable over Wu (cited in IDS filed 08/19/2022) in view of Kirchhofer (cited in IDS filed 08/19/2022). Applicant argues that the teachings of Wu in view of Kirchhofer do not give one of ordinary skill in the art a reason or motivation to combine the references with a reasonable expectation of success because Wu requires chaperones for the production of MH-1 SCA at a high yield. Applicant’s arguments are found persuasive. This rejection is hereby withdrawn and a new rejection follows.
Claims 1, 3-5 are rejected under 35 U.S.C. 103 as being unpatentable over Wu et al. (Biotechnology 11.1 (1993): 71-76 published 01/01/1993; hereinafter “Wu1”), in view of Kirchhofer (cited in IDS filed 08/19/2022), in further view of Krishnappa (Applied and environmental microbiology 80.4 (2014): 1463-1468)
Wu1 teaches a method for producing a functional antidigoxin SCA (single-chain antibody consisting of VL -linker-Vu) and the individual variable domains of light (VJ) and heavy (VH) chains (Page 71; abstract). Wu1 teaches the use of B. subtilis WB600, an engineered, six-extracellular protease-deficient strain (Page 72; Table 1). Wu1 teaches that the six-extracellular protease-deficient strain is deficient in the following extracellular protease genotypes: NprA, NprB, Apr, Epr, Mpr, and Bpr (Wu, table 1). Wu1 teaches the use of B. subtilis WB600 is vital for the production of antidigoxin SCA in high quality and quantity (5 mg/ liter in a shake ftask culture) (Page 71; abstract) (Page 73-74; Discussion).
Wu1 does not teach production of a variable domain of a heavy chain of a heavy-chain antibody and does not teach Bacillus bacterium being deficient in all the extracellular proteases encoded by epr, wprA, mpr, nprBl, bpr, nprE, vpr, aprE, and aprX. Wu1 does not teach production of a variable domain of a heavy chain of a heavy-chain antibody consisting of an amino acid sequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110,112,114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, or 138 or an amino acid sequence having an identity of at least 85% to any of these sequences.
Kirchhofer teaches the amino acid sequence a nanobody, which is a single-domain polypeptide derived from the variable heavy chain (VHH) of the heavy chain-only antibodies of camelids (Kirchhofer, pg. 133, [3]). Kirchhofer teaches that nanobodies (i.e., the 3G9A nanobody) are potent alternatives to conventional antibodies, with enhanced stability and reduced size but similar antigen-binding characteristics (Kirchhofer, pg. 133, [3]). The amino acid sequence was deposited under accession number 3G9A in the Protein Data Bank. The amino acid sequence of 3G9A was found to be a 100% identity match to instant SEQ ID NO: 2. The sequence alignment is shown below.
PNG
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554
774
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Greyscale
PNG
media_image2.png
477
967
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Greyscale
Krishnappa teaches that B. subtilis produces at least eight extracellular proteases known as AprE, Bpr, Epr, Mpr, NprB, NprE, Vpr, and WprA (page 1463 [3]). Krishnappa teaches that B. subtilis extracellular proteases have a high propensity for degrading secreted proteins which leads to commercial loss (page 1463 [3]).
Claims 1, 3-5 are directed in part to a method for producing a variable domain of a heavy chain of a heavy- chain antibody, comprising culturing a Bacillus subtilis into which a gene that encodes a variable domain of a heavy chain of a heavy-chain antibody is introduced, wherein the Bacillus subtilis is (i) deficient in one or both extracellular proteases encoded by wprA and bpr and not deficient in any extracellular protease encoded by epr, mpr, nprBl, nprE, vpr, aprE, and aprX, or (ii) deficient in all of the extracellular proteases encoded by epr, wprA, mpr, nprBl, bpr, nprE, vpr, aprE, and aprX, wherein the variable domain of heavy chain of heavy-chain antibody consists of an amino acid sequence of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, or 138 or an amino acid sequence having an identity of at least 85%o to any of these sequences.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to produce the 3G9A nanobody taught by Kirchhofer by modifying the method taught Wu1 and use Bacillus subtilis deficient in extracellular proteases as suggested by Wu1 and Krishnappa. A person of ordinary skill in the art is motivated to produce the nanobody of Kirchhofer using the method of Wu1 for producing nanobodies that have enhanced stability and to avoid the degradation of the nanobody due to the action of extracellular proteases, thus increasing yield. Also, a person of ordinary skill in the art is motivated to further inactivate additional proteases, such as those of Krishnappa not inactivated in the Bacillus cell of Wu 1 for the benefit of further minimizing the degradation of the nanobody. Therefore, it would have been obvious to one of ordinary skill in the art to use the method and Bacillus subtilis cell taught by Wu1, for the production of the 3G9A nanobody taught by Kirchhofer. Furthermore, the applicant discloses that Bacillus subtilis, secretes extracellular proteases, such as AprE, Epr, WprA, Mpr, NprB, Bpr, NprE, Vpr, and AprX which the applicant expresses are known as factors that reduce the productivity of a target protein in heterologous protein production using Bacillus bacteria. Additionally, Krishnappa states that it is known in the art that the recited extracellular proteases have a high propensity for degrading heterologous secreted proteins in Bacillus subtilis. Therefore, it would have also been obvious to one of ordinary skill in the art to try the method taught by Wu1 on Bacillus subtilis with different combinations of extracellular protease deficiencies to improve protein production. One of ordinary skill in the art has a reasonable expectation of success at arriving to producing the 3G9A nanobody taught by Kirchhofer by modifying the method taught Wu1 and use Bacillus subtilis deficient in extracellular proteases as suggested by Wu1 and Krishnappa because all that is required is substituting the SCA fragment taught in Wu1 with the 3G9A nanobody taught by Kirchhofer in extracellular protease deficient Bacillus subtilis. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Wu1 et al. (Biotechnology 11.1 (1993): 71-76 published 01/01/1993), Kirchhofer (cited in IDS filed 08/19/2022), and Krishnappa (Applied and environmental microbiology 80.4 (2014): 1463-1468), in further view of Overkamp (cited in IDS filed 12/23/2025)
The teachings of Wu, Kirchhofer, and Krishnappa are described above
Wu1 suggest the production of Bacillus subtilis antibodies that can be grown in production quantities in large fermenters, wherein said antibodies can be grown in a day and the culture medium is relatively cheap. (Page 75 [1]). Wu1 does not teach the use of SigF deficient Bacillus subtilis.
Overkamp teaches that sigF in Bacillus subtilis promotes sporulation (Page 1; abstract). Overkamp teaches that sporulation is undesirable in certain circumstances, such as with industrial fermentations, evolution experiments and particular chemostat experiments and the use of sporulation deficient strains can be a solution (Page 2 [2]). Overkamp teaches a method of sigF disruption (Page 2 [6]; Material and Methods) (Page 3, Table 1; Material and Methods).
Claim 14 are directed in part to claim 4, wherein the Bacillus subtilis is deficient in a sigma factor gene, wherein the sigma factor gene is a sigF gene.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to produce a heavy chain antibody taught by Kirchhofer by modifying the method taught Wu1 and use Bacillus subtilis deficient in a sigma facto gene, as taught by Overkempt, and extracellular proteases, as suggested by Wu1 and Krishnappa. A person of ordinary skill in the art is motivated to modify the method taught Wu1 and use Bacillus subtilis deficient in a sigma factor gene, as taught by Overkempt, and extracellular proteases as suggested by Wu1 and Krishnappa to achieve a high antibody yield on an industrial level. Therefore, it would have been obvious to one of ordinary skill in the art to combine the recited teachings, for the production of a heavy chain antibody. One of ordinary skill in the art has a reasonable expectation of success at arriving to producing antibodies at a high yield in Bacillus subtilis because all that is required is using the sigF deficient Bacillus subtilis taught in overkamp in a modified method taught in Wu1 wherein various extracellular proteases are depleted to produce the heavy antibody taught by Kirchhofer. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
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 1, 3-5, 11-13 were previously provisionally rejected on the ground of non-statutory obviousness type double patenting as allegedly being unpatentable over claim 15 of U.S. Patent Application No. 18/033,639 (the '639 application) in view of Wu and further in view of Kirchhofer. Office Action, pp. 9-15. Additionally, claims 1, and 11-13 were provisionally rejected on the ground of non- statutory obviousness type double patenting as allegedly being unpatentable over claim 15 of U.S.
Applicant argues that the amendment of claim 1 renders previous rejection moot. Applicant also argues that it would not have been obvious to one of ordinary skill in the art to modify the teachings of the '639 application with the teachings of Wu and Kirchhofer because one would have no reason or motivation to combine the references with a reasonable expectation of success due to the '639 application teaching that a preferred host cell is Bacillus subtilis strain Dpr9, which is deficient in extracellular proteases but does not overexpress intracellular chaperones. Due to the requirement of chaperones in Wu, applicant’s arguments are found persuasive, and the rejection is withdrawn. Claims 11-13, has since been canceled, rendering the previous rejection moot. Accordingly, the previous rejection of claims 11-13 are withdrawn.
Claims 1, 4-5, and 14 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 15 of copending application No. 18/033639. In instant case, claims 1, 4-5, and 14 encompass a method for producing a variable domain of a heavy chain of a heavy- chain antibody, comprising culturing a Bacillus subtilis, or a mutant strain thereof, into which a gene that encodes a variable domain of a heavy chain of a heavy-chain antibody is introduced, wherein the Bacillus bacterium is (i) deficient in one or both extracellular proteases encoded by wprA and bpr and not deficient in any extracellular protease encoded by epr, mpr, nprBl, nprE, vpr, aprE, and aprX, or (ii) deficient in all of the extracellular proteases encoded by epr, wprA, mpr, nprBl, bpr, nprE, vpr, aprE, and aprX, wherein the Bacillus subtilis deficient in an extracellular protease is a Bacillus subtilis in which the gene that encodes the extracellular protease is deleted or inactivated, wherein the Bacillus subtilis is deficient in a sigma factor gene, wherein the sigma factor gene is a sigF gene.
Claim 15 of application No. 18/033639 recites “A method for producing a protein of interest, comprising: culturing the recombinant Bacillus bacterium according to claim 14; and collecting the protein of interest secreted extracellularly”. Claim 14 of application No. 18/033639 recites “a recombinant Bacillus bacterium comprising the nucleic acid construct according to claim 1”. Claim 1 of application No. 18/033639 recites “A nucleic acid construct for expression and extracellular secretion of a protein of interest, comprising: a polynucleotide encoding the protein of interest and a polynucleotide linked upstream of the polynucleotide and encoding a modified signal peptide, wherein the modified signal peptide includes amino acid residues of X1X2X3X4X5X6 at positions 1 to 6 as counted from the C-terminus, where X1 is G, P, or A; X2 is G, S, or A; and X3 is P, S, or A, provided that X1X2X3 is not GGP; X4 is A; X5 is S, H, or F; and X6 is A and is located at the C-terminus of the modified signal peptide”. The disclosure of application No. 18/033639 states that a preferred host cell is Bacillus subtilis strain Dpr9, which is deficient in extracellular proteases epr, wprA, mpr, nprB, bpr, nprE, vpr, aprE, and aprX and deficient in sigF (application No. 18/033639, [0070]). Additionally, the specification of copending application No. 18/033639 discloses a VHH antibody, which is a heavy chain antibody that comprises a variable domain of a heavy chain, as a preferred embodiment of the genus of antibody related molecules made by the method of claim 15 (application No. 18/033639, [006]). Therefore, the invention of claims 1, 4-5 and 14 are deemed an obvious variation of claim 15 of copending application 18/033639 in view of the preferred embodiments disclosed. Accordingly, claims 1, 4, 5, and 14 are provisionally rejected on the ground of nonstatutory double patenting.
Conclusion
No claims are allowed.
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/S.L.S./Examiner, Art Unit 1652
/ROBERT B MONDESI/Supervisory Patent Examiner, Art Unit 1652
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