DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of DLLF-Fc as the target protein in the reply filed on 06/08/2026 is acknowledged.
Priority
This application is a continuation of, and claims priority under 35 U.S.C. § 120 to, International Application No. PCT/JP2022/044832, filed December 6th, 2021, and claims priority therethrough under 35 U.S.C. §119 (a)-(d) to Patent Application No. JN2021-197463, filed December 6th, 2022. As such, the effective filing date of Claims 1-2 and 4-29 is December 6th, 2021.
Status of the Claims
Amendments dated 06/08/2026 have been entered.
Claim 3 has been cancelled by Applicant.
Claims 28-29 are newly added.
Claims 1-2 and 4-29 are pending.
Claims 19-22 are withdrawn from consideration as being directed to a non-elected invention.
Claims 1-2, 4-18, and 23-29 are examined herein.
Information Disclosure Statement
The Information Disclosure Statements filed on 06/05/2026 and 12/10/2025 are in compliance with the provisions of 37 CFR 1.97 and have been considered in full. Signed copies of the lists of references cited from the IDS are included with this Office Action.
Specification
The disclosure is objected to because of the following informalities:
The use of the term Protein G Sepharose™ 4 Fast Flow on pg. 56, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Appropriate correction is required.
Claim Objections
Claims 1-2, 4-18, and 23-29 are objected to because of the following informalities:
Claim 1 recite the terms “ERp27” and “TMX1” which are not defined acronyms. As Claim 1 comprises the first recitations of “ERp27” and “TMX1” in the claim set, Applicant is advised to clearly define the full names of the acronyms.
Claim 1, line 3 should be amended to recite “…the plant has been modified [[so as]] to express…”
Claim 4, part (b) should be amended to recite “a protein comprising the[[an]] amino acid sequence…”
Claim 4, part (c) should be amended to recite “…the amino acid sequence of [[shown as]] SEQ ID NO: 21…”
Claim 5, part (b) should be amended to recite “a protein comprising the[[an]] amino acid sequence…”
Claim 5, part (c) should be amended to recite “…the amino acid sequence of [[shown as]] SEQ ID NO: 23…”
Claim 13 recites the term “HA” tag wherein the “HA” is not a defined acronym. As Claim 13 comprises the first recitation of “HA” in the claim set, Applicant is advised to clearly define the full name of the acronym.
The term “or” at the end of Claim 14, part (b) should be amended to recite “and” for proper Markush formatting.
Claim 14, part (b) should be amended to recite “a protein comprising the[[an]] amino acid sequence…”
Claim 14 part (c) should be amended to recite “…the amino acid sequence of [[shown as]] SEQ ID NO: 17…”
Claim 23 recites the term “DLL4-Fc” is not a defined acronym. As Claim 23 comprises the first recitation of “DLL4-Fc” in the claim set, Applicant is advised to clearly define the full name of the acronym.
The term “or” at the end of Claim 27, part (b) should be amended to recite “and” for proper Markush formatting.
Claim 27, part (b) should be amended to recite “a protein comprising the[[an]] amino acid sequence…”
All dependent claims thereof are included in these objections for the same reasons as given above.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
Indefiniteness
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.
Claims 7, 14, and 28-29 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.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, Claim 7 recites the broad recitation “tobacco”, and the claim also recites " which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 14 recites a peptide “comprising a substitution, deletion, insertion, and/or addition of 1-5 amino acid residues which renders the claim indefinite. Because instant SEQ ID NO: 17 only comprises 9 amino acids residues and SEQ ID NO: 18 only comprises 7 amino acids residues, it is not clear what would be considered a sequence in relation to SEQ ID NOS: 17-18, when up to 5 amino acid residues could be modified or deleted. Additionally, Claim 14, part (b) and part (c) refer to the sequence variants of SEQ ID NOs: 17-19 as having a “function to increase production of the target protein by the plant when added to the target protein. HA tags are known in the art to allow for the purification of target proteins. It is unclear to one of ordinary skill in the art how the recited HA tag variants should increase ethe production of a target protein in a plant when added to the target protein. As such, one of ordinary skill in the art would not be reasonably apprised of the metes and bounds of the claimed invention.
Claim 28 recites “SEQ ID NO: 21 with a shortened N-terminus” which renders the claim indefinite. It is unclear, based off this recitation, if SEQ ID NO: 21 already comprises what the Applicant considers to be a “shortened” N-terminus or if the claim is reciting that the N-terminus of SEQ ID NO: 21 is required to be shorter than it is in the current sequence listing. It is unclear what basis of comparison needs to be made to determine if the instant SEQ ID NO. is “shortened” (i.e., shortened relative to what?). As such, one of ordinary skill in the art would not be reasonably apprised of the metes and bounds of the claimed invention.
Claim 29 recites “SEQ ID NO: 23 with a shortened N-terminus” which renders the claim indefinite. It is unclear, based off this recitation, if SEQ ID NO: 23 already comprises what the Applicant considers to be a “shortened” N-terminus or if the claim is reciting that the N-terminus of SEQ ID NO: 23 is required to be shorter than it is in the current sequence listing. It is unclear what basis of comparison needs to be made to determine if the instant SEQ ID NO. is “shortened” (i.e., shortened relative to what?). As such, one of ordinary skill in the art would not be reasonably apprised of the metes and bounds of the claimed invention.
Claim Rejections - 35 USC § 112
Written Description
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 1-2, 4-18 and 23-29 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The Federal Circuit has clarified the application of the written description requirement to inventions in the field of biotechnology. The court stated that "[a] description of a genus of cDNAs may be achieved by means of a recitation of a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or of a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus." University of California v. Eli Lilly and Co., 119 F. 3d 1559; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997).
Claims 1-2, 4-18, and 23-29 are broadly directed to a method for producing a target protein comprising: expressing a gene encoding the target protein in a plant, wherein the plant has been modified to express ERp27 and/or TMX1. The method encompasses a broad genus of any plant from any diverse source known in the art.
Applicant describes ERp27 and TMX1 as human protein disulfide isomerase genes, wherein the function of ERp27 is unknown and TMX1 may have activities for catalyzing reactions that form, cleave, and rearrange disulfide bonds of proteins (pg. 1, paragraph 0006; emphasis added by Examiner). Applicant discloses SEQ ID NO: 21, encoding a human ERp27 protein and SEQ ID NO: 23 encoding a human TMX1 protein (paragraph 0013; paragraph 0217; paragraph 0219). Additionally, based on Applicant disclosure, included in the scope of the invention are variants of ERp27 (i.e., a protein comprising an amino acid sequence of SEQ ID NO: 21, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, and functions to increase production of the target protein by the plant when expressed in the plant; and a protein comprising an amino acid sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 21, and functions to increase production of the target protein by the plant when expressed in the plant; Claim 4) and variants of TMX1 (i.e., a protein comprising an amino acid sequence of SEQ ID NO: 23, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, and functions to increase production of the target protein by the plant when expressed in the plant; and a protein comprising an amino acid sequence having at least 80% identity to the amino acid sequence shown as SEQ ID NO: 23, and functions to increase production of the target protein by the plant when expressed in the plant; Claim 5).
However, Applicant has not described any amino acid sequence having any degree of variance relative to human ERp27 and human TMX1. Applicant has not described the core structure or the critical amino acid residues for ERp27 and TMX1 that are required for any function, much less functioning to increase production of the Applicant’s target protein by the plant when expressed in any plant known in the art. Applicant has not described which amino acid residues of human ERp27 and human TXM1 can be modified (by any degree) while still retaining any function (Note, the function of ERp27 is disclosed as “unknown” by Applicant), much less functioning to increase production of Applicant’s target protein when expressed in any plant known in the art.
The state of the art regarding human ERp27 proteins discloses that little is known about the precise role and function of ERP27, wherein the ERP27 gene has been mapped to Chr 12p12.3 of the human genome and encodes the 273 amino acids long protein. The ERP27 protein contains a cleavable NH2-terminal signal sequence, leaving the mature protein to be 248aa, beginning at Glu-26. The state of the prior art discloses that no knockout studies have been conducted, and future studies are needed to fully understand the function and role of ERP27 (See, Galligan and Petersen (2012); pg. 4, paragraph bridging left and right column; IDS Document).
The state of the art regarding human TMX1 proteins discloses that TMX1 is located at Chr 14q22.1 of the human genome and encodes the 280 amino acids long TMX1 protein. TMX1 contains an NH2-terminal signal sequence of 26 amino acids, one a-type TRX domain with active site Cys-Pro-Ala-Cys, one transmembrane domain (amino acid positions 183 to 203), and lacks an ER-retention sequence. The state of the art teaches that mature TMX1 proteins possesses the ability to both oxidize and reduce disulfide bonds, although chaperone-like activity has yet to be investigated (See, Gilligan and Petersen (2012); pg. 11; right column, first paragraph; IDS Document).
In light of the instant claims, while ERp27 and TMX1 are known in the prior art to be singular, specific genes from the human genome, it appears that Applicant is expanding the genus of ERp27 and TMX1 proteins recited in the claims to include variations of both genes that are not described in the instant specification or in the prior art. Based on the disclosure of the instant specification and the state of the prior art, Applicant has not described any sequence variants of ERp27 and TMX1, and how one of ordinary skill in the art would be able to modify ERp27 and TMX1 proteins derived from the human genome and still retain a functional protein, much less the function of increasing production of the target protein by the plant when expressed in any plant known in the art. Applicant does not appear to be in possession of which modification can be made to ERp27 and TMX1 proteins and still have functional proteins in a plant.
Applicant describes one Erp27 protein and one TMX1 protein that provided increases production of Applicant’s target protein by a Nicotiana benthamiana plant when expressed in the plant, denoted as SEQ ID NO: 21 (Examples 1 and 2) and SEQ ID NO: 23 (Example 1), respectively. It should be noted that Applicant does not describe or provide any working examples of the co-expression of SEQ ID NO: 21 and SEQ ID NO: 23 with a target protein in a singular plant, as recited in the instant claims.
With the exception of the full-length sequence of SEQ ID NO: 21 expressed in a plant and the full-length sequence of SEQ ID NO: 23 expressed in a plant, Applicant has not described any other variations of ERp27 and TMX1 suitable for the practice of the invention.
Additionally, Applicant has not described a protein comprising an amino acid sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 21, that has any function, much less functioning to increase production of the target protein by the plant when expressed in the plant. Applicant has not described a protein comprising an amino acid sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 23, that has any function, much less functioning to increase production of the target protein by the plant when expressed in the plant.
Amino acid sequences having at least 80% sequence identity to the 273 amino acids long SEQ ID NO: 21 encompass polypeptides with 55 unspecified amino acid additions, deletions, and substitutions relative to SEQ ID NO: 21. Polypeptides with 55 amino acid substitutions relative to SEQ ID NO: 21 encompass approximately 1955(2.23e58) unique polypeptides. The instant specification fails to provide guidance for which amino acids of SEQ ID NO: 21 can be altered or duplicated, and to which amino acids, as well as failing to provide guidance for which amino acids must not be changed, to maintain any function, should a function exist for Erp27, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The specification fails to provide guidance for which amino acids can be deleted and which region of the sequence can tolerate additions and still have any function, should a function exist for Erp27, much less the function of increasing the Applicant’s target protein by the plant when expressed in the plant. The specification does not provide adequate guidance with respect to the structure/function relationship of the claimed genera of polypeptides that perform any function, should a function exist for Erp27, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The same logic extends to an amino acid sequence of SEQ ID NO: 21, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, encompasses approximately 1930(8.77e39) unique polypeptides.
Applicant has only provided one polypeptide out of the myriad of polypeptides encompassed by the vast genus Applicant currently claims. As such, there is substantial variation within the genus of amino acid sequences having at least 80% identity to instant SEQ ID NO: 21, or an amino acid sequence of SEQ ID NO: 21, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, and Applicant has only provided one example species from this vast genus. While it is known in the art that computer programs can predict the proteins discussed above, the prior art teaches that protein-based predictors are still limited in their predictive ability to model mutations that do not negatively affect protein structure and function because of the unbalance and intrinsic variability of the thermodynamic data and their prediction performance [See Liu et al. (2022); pg. 7, left column, last paragraph; IDS Document]. Although the Applicant would be able to predict the amino acid sequence variants discussed above, it is uncertain if these predicted proteins would have any function, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. Therefore, the mere fact that the Applicant discloses SEQ ID NO: 21 is insufficient to
adequately describe a representative number of species of the vast and highly diverse genus of
sequence variants.
The instant specification discloses SEQ ID NO: 21 (paragraph 0013; paragraph 0217; paragraph 0219), but does not discloses any other polypeptides with at least 80% identity relative to instant SEQ ID NO: 21, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NO: 21. The other polypeptides disclosed by the instant specification appear to have less than 23.6% sequence identity relative to instant SEQ ID NO: 21 (See in file wrapper 20260810_144608_us-18-734-393a-21.rapbm).
The prior art teaches that even minor changes in a polypeptides sequence can change or eliminate activity. Guo et al. (2004) describes that while proteins are fairly tolerant to mutations resulting in single amino acid changes, increasing the number of substitutions additively increases the probability that the protein will be inactivated (pg. 9209, right column, paragraph 2).
Thus, the structural features that distinguish polypeptides with at least 80% identity relative to instant SEQ ID NO: 21, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NO: 21 that have any function from other polypeptides with at least 80% identity relative to instant SEQ ID NO: 21, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SE Q ID NO: 21 that do not have a function.
Amino acid sequences having at least 80% sequence identity to the 280 amino acids long SEQ ID NO: 23 encompass polypeptides with 56 unspecified amino acid additions, deletions, and substitutions relative to SEQ ID NO: 23. Polypeptides with 56 amino acid substitutions relative to SEQ ID NO: 23 encompass approximately 1956(4.21e59) unique polypeptides. The instant specification fails to provide guidance for which amino acids of SEQ ID NO: 23 can be altered or duplicated, and to which amino acids, as well as failing to provide guidance for which amino acids must not be changed, to maintain any function, should a function exist for TMX1, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The specification fails to provide guidance for which amino acids can be deleted and which region of the sequence can tolerate additions and still have any function, should a function exist for TMX1, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The specification does not provide adequate guidance with respect to the structure/function relationship of the claimed genera of polypeptides that perform any function, should a function exist for TMX1, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The same logic extends to an amino acid sequence of SEQ ID NO: 23, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, encompasses approximately 1930(8.77e39) unique polypeptides.
Applicant has only provided one polypeptide out of the myriad of polypeptides encompassed by the vast genus Applicant currently claims. As such, there is substantial variation within the genus of amino acid sequences having at least 80% identity to instant SEQ ID NO: 23, or an amino acid sequence of SEQ ID NO: 23, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, and Applicant has only provided one example species from this vast genus. While it is known in the art that computer programs can predict the proteins discussed above, the prior art teaches that protein-based predictors are still limited in their predictive ability to model mutations that do not negatively affect protein structure and function because of the unbalance and intrinsic variability of the thermodynamic data and their prediction performance [See Liu et al. (2022); pg. 7, left column, last paragraph; IDS Document]. Although the Applicant would be able to predict the amino acid sequence variants discussed above, it is uncertain if these predicted proteins would have any function, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. Therefore, the mere fact that the Applicant discloses SEQ ID NO: 23 is insufficient to
adequately describe a representative number of species of the vast and highly diverse genus of
sequence variants.
The instant specification discloses SEQ ID NO: 23 (paragraph 0013; paragraph 0217; paragraph 0219), but does not discloses any other polypeptides with at least 80% identity relative to instant SEQ ID NO: 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NO: 23. The other polypeptides disclosed by the instant specification appear to have less than 12.5% sequence identity relative to instant SEQ ID NO: 23 (See in file wrapper 20260810_144608_us-18-734-393a-23.rapbm).
The prior art teaches that even minor changes in a polypeptides sequence can change or eliminate activity. Guo et al. (2004) describes that while proteins are fairly tolerant to mutations resulting in single amino acid changes, increasing the number of substitutions additively increases the probability that the protein will be inactivated (pg. 9209, right column, paragraph 2).
Thus, the structural features that distinguish polypeptides with at least 80% identity relative to instant SEQ ID NO: 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NO: 23 that have any function from other polypeptides with at least 80% identity relative to instant SEQ ID NO: 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NO: 23 that do not have a function.
One of ordinary skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the genus in view of the disclosed species. Since the disclosure fails to describe the common attributes that identify members of the genus, and because the genus is both vast and highly diverse, SEQ ID NOs: 21 and 23 are insufficient to describe the claimed genera.
The number of species described by Applicant are insufficient to describe the recited genus by virtue of example, given the vast size of the recited genus and the lack of written description in the instant specification with regard to the structural and functional characteristics of the claimed compositions.
Hence, Applicant has not, in fact, described the claimed methods within the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention.
Scope of Enablement
Claims 1-2, 4-18 and 23-29 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method for producing a target protein comprising:, does not reasonably provide enablement for protein variations of human ERp27 and/or human TXM1 and the method being performed in any plant from any diverse source known in the art. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
The Federal Circuit in In re Wands lists eight considerations for determining whether or not undue experimentation would be necessary to practice an invention. In re Wands, 858 F2d 731, 8 USPQ2d 1400, 1406 (Fed. Cir. 1988). These factors are: the quantity of experimentation necessary, the amount of direction or guidance presented, the presence or absence of working examples of the invention, the nature of the invention, the state of the prior art, the relative skill of those in the art, the predictability or unpredictability of the art, and the breadth of the claims. Id.
Claims 1-2, 4-18, and 23-29 are broadly directed to a method for producing a target protein comprising: expressing a gene encoding the target protein in a plant, wherein the plant has been modified to express ERp27 and/or TMX1. The method encompasses a broad genus of any plant from any diverse source known in the art.
Applicant teaches that ERp27 and TMX1 as human protein disulfide isomerase genes, wherein the function of ERp27 is unknown and TMX1 may have activities for catalyzing reactions that form, cleave, and rearrange disulfide bonds of proteins (pg. 1, paragraph 0006; emphasis added by Examiner). Applicant discloses SEQ ID NO: 21, encoding a human ERp27 protein and SEQ ID NO: 23 encoding a human TMX1 protein (paragraph 0013; paragraph 0217; paragraph 0219). Additionally, based on Applicant disclosure, included in the scope of the invention are variants of ERp27 (i.e., a protein comprising an amino acid sequence of SEQ ID NO: 21, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, and functions to increase production of the target protein by the plant when expressed in the plant; and a protein comprising an amino acid sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 21, and functions to increase production of the target protein by the plant when expressed in the plant; Claim 4) and variants of TMX1 (i.e., a protein comprising an amino acid sequence of SEQ ID NO: 23, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, and functions to increase production of the target protein by the plant when expressed in the plant; and a protein comprising an amino acid sequence having at least 80% identity to the amino acid sequence shown as SEQ ID NO: 23, and functions to increase production of the target protein by the plant when expressed in the plant; Claim 5).
However, Applicant has not taught any amino acid sequence having any degree of variance relative to human ERp27 and human TMX1. Applicant has not described the core structure or the critical amino acid residues for ERp27 and TMX1 that are required for any function, much less functioning to increase production of the Applicant’s target protein by the plant when expressed in any plant known in the art. Applicant has not taught which amino acid residues of human ERp27 and human TXM1 can be modified (by any degree) while still retaining any function (Note, the function of ERp27 is disclosed as “unknown” by Applicant), much less functioning to increase production of Applicant’s target protein when expressed in any plant known in the art.
The state of the art regarding human ERp27 proteins teaches that little is known about the precise role and function of ERP27, wherein the ERP27 gene has been mapped to Chr 12p12.3 of the human genome and encodes the 273 amino acids long protein. The ERP27 protein contains a cleavable NH2-terminal signal sequence, leaving the mature protein to be 248aa, beginning at Glu-26. The state of the prior art discloses that no knockout studies have been conducted, and future studies are needed to fully understand the function and role of ERP27 (See, Galligan and Petersen (2012); pg. 4, paragraph bridging left and right column; IDS Document).
The state of the art regarding human TMX1 proteins teaches that TMX1 is located at Chr 14q22.1 of the human genome and encodes the 280 amino acids long TMX1 protein. TMX1 contains an NH2-terminal signal sequence of 26 amino acids, one a-type TRX domain with active site Cys-Pro-Ala-Cys, one transmembrane domain (amino acid positions 183 to 203), and lacks an ER-retention sequence. The state of the art teaches that mature TMX1 proteins possesses the ability to both oxidize and reduce disulfide bonds, although chaperone-like activity has yet to be investigated (See, Gilligan and Petersen (2012); pg. 11; right column, first paragraph; IDS Document).
In light of the instant claims, while ERp27 and TMX1 are known in the prior art to be singular, specific genes from the human genome, it appears that Applicant is expanding the genus of ERp27 and TMX1 proteins recited in the claims to include variations of both genes that are not taught in the instant specification or in the prior art. Based on the disclosure of the instant specification and the state of the prior art, Applicant has not taught any sequence variants of ERp27 and TMX1, and how one of ordinary skill in the art would be able to modify ERp27 and TMX1 proteins derived from the human genome and still retain a functional protein, much less the function of increasing production of the target protein by the plant when expressed in any plant known in the art. Applicant does not appear teach which modifications can be made to ERp27 and TMX1 proteins and still have functional proteins in a plant, without undue experimentation. Applicant does not appear to teach any method of how to use a modified ERp27 and/or TMX1 protein that elicits any function, without undue experimentation.
Applicant teaches one Erp27 protein and one TMX1 protein that provided increases production of Applicant’s target protein by a Nicotiana benthamiana plant when expressed in the plant, denoted as SEQ ID NO: 21 (Examples 1 and 2) and SEQ ID NO: 23 (Example 1), respectively. It should be noted that Applicant does not teach or provide any working examples of the co-expression of SEQ ID NO: 21 and SEQ ID NO: 23 with a target protein in a singular plant, as recited in the instant claims.
With the exception of the full-length sequence of SEQ ID NO: 21 expressed in a plant and the full-length sequence of SEQ ID NO: 23 expressed in a plant, Applicant has not taught any other variations of ERp27 and TMX1 suitable for the practice of the invention.
As such, undue trial and error experimentation would be required by one of ordinary skill in the art to make or use the claimed genera of Erp27 and/or TMX1 proteins that would still retain any function, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant.
Additionally, Applicant does not teach any proteins comprising an amino acid sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 21, that have any function, much less functioning to increase production of the target protein by the plant when expressed in the plant. Applicant does not teach any proteins comprising an amino acid sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 23, that have any function, much less functioning to increase production of the target protein by the plant when expressed in the plant.
Amino acid sequences having at least 80% sequence identity to the 273 amino acids long SEQ ID NO: 21 encompass polypeptides with 55 unspecified amino acid additions, deletions, and substitutions relative to SEQ ID NO: 21. Polypeptides with 55 amino acid substitutions relative to SEQ ID NO: 21 encompass approximately 1955(2.23e58) unique polypeptides. The instant specification fails to provide guidance for which amino acids of SEQ ID NO: 21 can be altered or duplicated, and to which amino acids, as well as failing to provide guidance for which amino acids must not be changed, to maintain any function, should a function exist for Erp27, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The specification fails to provide guidance for which amino acids can be deleted and which region of the sequence can tolerate additions and still have any function, should a function exist for Erp27, much less the function of increasing the Applicant’s target protein by the plant when expressed in the plant. The specification does not provide adequate guidance with respect to the structure/function relationship of the claimed genera of polypeptides that perform any function, should a function exist for Erp27, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The same logic extends to an amino acid sequence of SEQ ID NO: 21, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, encompasses approximately 1930(8.77e39) unique polypeptides.
The instant specification discloses SEQ ID NO: 21 (paragraph 0013; paragraph 0217; paragraph 0219), but does not discloses any other polypeptides with at least 80% identity relative to instant SEQ ID NO: 21, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NO: 21. The other polypeptides disclosed by the instant specification appear to have less than 23.6% sequence identity relative to instant SEQ ID NO: 21 (See in file wrapper 20260810_144608_us-18-734-393a-21.rapbm).
Amino acid sequences having at least 80% sequence identity to the 280 amino acids long SEQ ID NO: 23 encompass polypeptides with 56 unspecified amino acid additions, deletions, and substitutions relative to SEQ ID NO: 23. Polypeptides with 56 amino acid substitutions relative to SEQ ID NO: 23 encompass approximately 1956(4.21e59) unique polypeptides. The instant specification fails to provide guidance for which amino acids of SEQ ID NO: 23 can be altered or duplicated, and to which amino acids, as well as failing to provide guidance for which amino acids must not be changed, to maintain any function, should a function exist for TMX1, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The specification fails to provide guidance for which amino acids can be deleted and which region of the sequence can tolerate additions and still have any function, should a function exist for TMX1, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The specification does not provide adequate guidance with respect to the structure/function relationship of the claimed genera of polypeptides that perform any function, should a function exist for TMX1, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant. The same logic extends to an amino acid sequence of SEQ ID NO: 23, but which includes substitution, deletion, insertion, and/or addition of 1 to 30 amino acid residues, encompasses approximately 1930(8.77e39) unique polypeptides.
The instant specification discloses SEQ ID NO: 23 (paragraph 0013; paragraph 0217; paragraph 0219), but does not discloses any other polypeptides with at least 80% identity relative to instant SEQ ID NO: 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NO: 23. The other polypeptides disclosed by the instant specification appear to have less than 12.5% sequence identity relative to instant SEQ ID NO: 23 (See in file wrapper 20260810_144608_us-18-734-393a-23.rapbm).
Undue experimentation would be required by one of ordinary skill in the art to make or use all the polypeptides with at least 80% identity relative to instant SEQ ID NOs: 21 and 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NOs: 21 and 23 that would still retain any function, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant.
The specification does not provide any teachings, working examples, or prophetic examples of making or using the claimed polypeptides with at least 80% identity relative to instant SEQ ID NO: 21 and/or SEQ ID NO: 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NO: 21 and/or SEQ ID NO: 23, other than the full length SEQ ID NO: 21 and the full length SEQ ID NO: 23. While it is known in the art that computer programs can predict the proteins discussed above, the prior art teaches that protein-based predictors are still limited in their predictive ability to model mutations that do not negatively affect protein structure and function because of the unbalance and intrinsic variability of the thermodynamic data and their prediction performance [See Liu et al. (2022); pg. 7, left column, last paragraph; IDS Document]. Although Applicant would be able to predict amino acid sequence variants of SEQ ID NOs: 21 and 23, it is not clear that Applicant would be able to make these modifications in the claimed sequence variants wherein the predicted proteins would have any function, much less the function of increasing production of Applicant’s target protein by the plant, when expressed in the plant. At the most basal level, this would require one of ordinary skill in the art to identify all proteins from any diverse source in the art that have the claimed sequence variance relative to SEQ ID NO: 21 that have any function known in the art, which at the time the application was filed, is currently unknown or undescribed in regard to ERp27 proteins. Additionally, this would require one of ordinary skill in the art to identify all proteins from any diverse source in the art that have the claimed sequence variance relative to SEQ ID NO: 23 that have any function known in the art. This would also require one of ordinary skill in the art to design expression cassettes that can be transformed into any plant known in the art wherein the claimed sequence variants have the capacity to increase the production of Applicant’s target protein. Accordingly Applicant has no demonstrated that all proteins with at least 80% identity relative to instant SEQ ID NOs: 21 and 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NOs: 21 and 23 would be able to perform any function, much less be able to increase production of Applicant’s target protein by the plant when expressed in the plant—and without a function, the claimed genus does not have an obvious use. Therefore, the mere fact that Applicant teaches SEQ ID NO: 21 and 23 is insufficient to adequately enable the making or use of the claimed genus of polypeptides across the entire scope of the claims.
Thus, from the teachings of the instant specification, it would appear that one of ordinary skill in the art would need to make the claimed polypeptides by making random amino acid deletions, substitutions, and additions which would be unpredictable.
Making additions, deletions and substitutions relative to SEQ ID NO: 21 and 23 while retaining any function, known or unknown, is unpredictable. The amino acid, which is the primary structure of the polypeptide, is the basis for the spatial structure of the polypeptide, which in turn directly determines its function. Small changes in the amino acid sequences produced by SEQ ID NOs: 21 and 23 may lead to large changes in spatial structure, in turn altering the function of the polypeptide. Such differences in sequence structure will result in changes or even loss of function in certain nucleic acids/polypeptide molecules. While it is known that many amino acid substitutions, additions or deletions are generally possible in any given protein, the positions within the protein’s sequence where such amino acid changes can be made with a reasonable expectation of success (without altering protein function) are limited. Certain positions in the sequence are critical to the protein’s structure/function relationship, for example various sites or regions directly involved in binding, activity, and in providing the correct three-dimensional spatial orientation of binding and active sites. These regions can tolerate only relatively conservative substitutions or no substitutions at all. See Keskin et al., 2004, Protein Science 13: 1043-1055), who teach that proteins with similar structures may have different functions (Abstract; pages 1043-1044). See also Guo et al., 2004, Proceedings of the National Academy of Sciences USA 101: 9205-9210), who teach that there is a probability factor of 34% that a random amino acid replacement in a given protein will lead to its inactivation (Abstract; page 9206; Table 1). In the instant case, such a probability factor will be much higher as the claims encompass more than a single amino acid change in the proteins encoded by SEQ ID NOs: 21 and 23. Furthermore, Thornton et al. (2000) (Nature Structural Biology, structural genomic supplement, November 2000: 991-994;), teach that structural data may carry information about the biochemical function of a protein, while its biological role in the cell or organism is much more complex and additional experimentation is needed to elucidate actual biological function (page 992, left column, paragraph 2).
Therefore, the specification fails to overcome the unpredictability in the art of making amino acid substitutions in polypeptides with at least 80% identity relative to instant SEQ ID NOs: 21 and 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NOs: 21 and 23 that would still retain any function, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant, as it does not provide any working examples of plants that have been transformed with the claimed sequences variants of SEQ ID NOs: 21 and 23.
Undue experimentation would be required by one of ordinary skill in the art to use and evaluate polypeptides with at least 80% identity relative to instant SEQ ID NOs: 21 and 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NOs: 21 and 23 and to determine whether the broadly claimed genus of all possible claimed polypeptides would have any function in a plant, much less the function of increasing production of Applicant’s target protein by the plant when expressed in the plant.
In the absence of guidance from wither the instant disclosure or the art, and the unpredictability discussed above, it would require undue trial and error experimentation for a skilled artisan to use the broadly claimed genus of amino acid sequences comprising polypeptides with at least 80% identity relative to instant SEQ ID NOs: 21 and 23, or any other polypeptides having substitutions, deletions, insertions, and/or additions of 1 to 30 amino acid residues relative to instant SEQ ID NOs: 21 and 23, with no reasonable expectation of success. For this reason, the specification does not teach a person with skill in the art how to make and use the subject matter within the full scope of the claims.
Closest Prior Art
Claims 1-2, 4-18 and 23-29 appear to be free of the prior art. The closest prior art can be found in Myers et al. (WO 2018/220595 A1, published 12/06/2018) which teaches a method of increasing the expression and/or promoting the correct folding of a heterologous polypeptide of interest in a plant cell, the method comprising: providing a first nucleic acid encoding a mammalian chaperone protein; providing a second nucleic acid encoding a heterologous polypeptide of interest; cloning the first and second nucleic acids into at least one expression vector adapted to express a polypeptide in a plant cell; transforming or infiltrating a plant cell with the at least one expression vector of step (iii); co-expressing the heterologous polypeptide of interest and the polypeptide encoding the mammalian chaperone protein in the plant cell; and recovering the polypeptide of interest from the plant cell (Claim 1), wherein the mammalian chaperone protein is at least one human chaperone protein such as ERp57 (Claim 2), wherein the expression of the heterologous polypeptide of interest in the plant cell is increased relative to a control plant cell which has only been transformed with the heterologous polypeptide of interest (Claim 5), wherein the co-expression of the heterologous polypeptide of interest and the chaperone protein in the plant cell leads to an at least 1.17-fold increase in the expression of the heterologous polypeptide of interest (Claim 6). However, the disclosure of Myers et al. does not teach or suggest ERp27 and/or TMX1 as chaperone proteins that could be used in the method of the invention. Based on the disclosure of Myers et al., a person of ordinary skill in the art would have considered using plants or plant cells as a suitable host for the biofactory of human proteins, specifically because the effect of Erp57 (a PDI protein) overexpression producing a protein of interest in a plant cell was documented in the results of Myers et al. However, when looking at the vast genus of PDI proteins known in the art (See Gilligan and Petersen (2012); IDS Document), there is no motivation or rationale for using human ERp27 and human TMX1 as chaperone proteins for the production of other human proteins in a host plant or host plant cell as taught by Myers et al., with a reasonable expectation of success, because ERp27 and TMX1 have different structures than ERp57; therefore, ERp27 and TMX1 would not be obvious candidates for substitution in the methods taught by Myers et al.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KELSEY L. MCWILLIAMS whose telephone number is (703)756-4704. The examiner can normally be reached M-F 08:00-17:30.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, AMJAD ABRAHAM can be reached at (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KELSEY L MCWILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
Prosecution Insights