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 .
Priority
The instant application claims priority to prior-filed United States Provisional Patent Application Nos. 62/847,914 (filed 05/14/2019) and 62/938,786 (filed 11/21/2019); and is a continuation of PCT/US2020/032988 (filed 05/14/2020) and application number 17/082,955 (filed 10/28/2020); and is a divisional of application number 17/677,473.
Status of Application/Claims
The preliminary amendment, filed 05/11/2023, is acknowledged. Claims 1-74 are canceled. Claims 75-87 are new. Claims 75-87 are currently pending and are examined on the merits herein.
Information Disclosure Statements
The four separate information disclosure statements (IDSs) submitted on 02/13/2024 listed foreign and non-patent literature documents, but no pdfs were provided. Thus, these references were not considered by the examiner. The U.S. Patent and U.S. Patent Application Publication documents, which were listed on two of the IDS documents, were considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Figures 36-54, and 63A contain amino acid sequences with no associated SEQ ID NOs.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The use of the terms Clonetech, Novagen, Stratagene, Invitrogen, Life Technologies, Kodak, Pharmingen, Sigma, Sigma-Aldrich, Promega, Beckman-Coulter, Millipore Guava EasyCyte, Merck, Millipore, GraphPad Prism, R&D Systems, Bio-techne, Pharsight, and InvivoGen, which are trade names or marks used in commerce, have been noted in this application. The terms should be in all caps wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
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.
Claim Objections
Claim 78 is objected to because of the following informalities: Claim 78 recites “…activity to another to another amino acid…” which should be corrected to ““…activity to another amino acid…”. Appropriate correction is required.
Claims 80 and 83 are objected to because of the following informalities: Claims 80 and 83 recite “…one or more nucleic acids further encode…” which should be corrected to ““…one or more nucleic acids further encode(s)…”. Appropriate correction is required.
Claims 81 and 82 are objected to because of the following informalities: Claims 81 and 82 recite “…blocking moiety comprises…” which should be corrected to ““…blocking moiety comprising…”. 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.
Claims 76-77, 81, and 84 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.
Claim 76 recites “…or a combination thereof.” It is unclear whether this phrase refers only to “an antibody or an antigen-binding portion thereof” or if the phrase refers to any of the preceding “cytokine, chemokine, growth factor, a soluble receptor, antigen-binding polypeptide, an antibody or antigen-binding portion”.
Claim 77 recites the limitations “ P1 " and “ P1’ ” in line 3. There is insufficient antecedent basis for these limitations in the claim. Thus, the claim is rendered indefinite.
Claim 81 recites “…or a fragment thereof.” It is unclear whether this phrase refers to the Fc alone, or all three steric blocking moieties. Thus, the claim is rendered indefinite.
Claim 84 recites “…comprises at least one of an extracellular domain, a transmembrane domain, and an intracellular domain.” It is not clear if the claim requires only one of the three listed limitations or if the claim requires one of each of the three limitations. For further examination, the claim is interpreted to mean that only one of the listed limitations is required. In other words, the claim is interpreted to mean “…comprises at least one of an extracellular domain, a transmembrane domain, and/or an intracellular domain”.
Claim Rejections - 35 USC § 112(a)
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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 75-87 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. THIS IS A WRITTEN DESCRIPTION REJECTION.
Instant claims 76-87 are dependent on instant claim 75, which is directed to a recombinant pro-protein comprising a cleavable moiety that is a substrate for a protease, wherein the cleavable moiety comprises the amino acid sequence of SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO: 381 or an amino acid sequence at least at least 85% identical to the amino acid sequence of SEQ ID NO: 198; SEQ ID NO: 199, SEQ ID NO: 381; and, a polypeptide with biological activity.
The claims recite a cleavable moiety that need only comprise at least 85% sequence identity with an amino acid sequence of SEQ ID NO:198, 199, or 381. The claims recite that the cleavable moiety is a substrate for a protease. The claims recite that the pro-protein comprises a polypeptide with biological activity.
The specification teaches that linker-3 (i.e., SEQ ID NO:198), which is comprised within exemplary peptides of species ALU30-1 and ALU30-5 through ALU30-16; thus, cleavable moiety species comprising the sequence for SEQ ID NO: 198 at 100% identity are supported by a representative number of species in the disclosure (see disclosure Figures 5, 36, 41-42, 44, 46, 48, 51-54, and 63A). Instant SEQ ID NO: 198 is an amino acid sequence of 8 amino acids in length. A sequence comprising at least 85% identity to SEQ ID NO: 198 would allow for a single mutation at any one of these 8 positions as the claim does not specify which position can be variable or if substitution of a specific amino acid residue is required. Thus, “cleavable moieties” comprising less than 100% identity to an amino acid sequence of SEQ ID NO: 198 are not supported by the disclosure.
The specification provides only one exemplary peptide comprising the claimed amino acid sequence of SEQ ID NO: 199, which is species ALU30-18. Instant SEQ ID NO: 199 varies from instant SEQ ID NO: 198 by one amino acid and comprises a K>F substitution in the fourth position. Thus, SEQ ID NO: 199 falls within the scope of 85% sequence identity to SEQ ID NO: 198. Thus, the disclosure provides only a single example of an “at least 85% identity” (i.e., EQ ID NO: 199) of the claimed cleavable moieties. Thus, while the disclosure supports pro-proteins comprising the cleavable moiety of SEQ ID NO: 199 at 100% identity, the disclosure does not provide support for a representative number of species to support the full scope of the genus of cleavable moieties of 85% identity to SEQ ID NO: 198 as claimed.
The specification does not teach a single exemplary peptide comprising the claimed SEQ ID NO: 381. Comparison of instant amino acid SEQ ID NO: 381 to instant SEQ ID NO: 198 shows that SEQ ID NO: 381 comprises the following two mutations: S>F in the sixth position and F>P in the seventh position. Comparison of instant amino acid SEQ ID NO: 381 to instant SEQ ID NO: 199 shows that SEQ ID NO: 381 comprises two mutations: F>K in the fourth position and S>F in the sixth position. Thus, SEQ ID NO: 381 is not supported by the disclosure and comprises two mutations (i.e., harbors less than 85% identity) compared to SEQ ID NO: 198 and SEQ ID NO: 199. Therefore, pro-proteins comprising a cleavable moiety comprising SEQ ID NO: 381 are not supported by the disclosure.
Thus, a large genus of polypeptides is encompassed by the claims, whereas only species comprising SEQ ID NO: 198 at 100% identity and the species ALU30-18 comprising SEQ ID NO: 199 at 100% identity are sufficiently supported by the specification.
To provide evidence of possession of a claimed genus, the specification and prior art must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of making the claimed product, or any combination thereof. In this case, the only factor present in the claim is a partial structure of the genus in the form of a recitation of percent identity. Accordingly, in the absence of sufficient recitation of distinguishing identifying characteristics, the specification does not provide adequate written description of the claimed genus.
The instant specification states SEQ ID NO: 198 of amino acid sequence ALFKSSFP is cleaved by cathepsin L (CTSL1) and that SEQ ID NOs: 199 and 381 are functional variants (p.29, [0137]; p31, [0146]). The art teaches that protease substrate specificity is dictated by amino acid sequence.
Biniossek, et al., Proteomic identification of protease cleavage sites characterizes prime and non-prime specificity of cysteine cathepsins B, L, and S. J. Proteome Res. (2011), 10, p.5363-5373 (herein referred to as Biniossek), for example, teaches that cathepsin L specificity is dominated by the canonical preference for aromatic residues in P2 with limited contribution of prime-site selectivity determinants (abstract; p.5368, para.4). Thus, the “cleavable moieties” of having less than 100% identity to instant SEQ ID NOs: 198, 199, and 381 that harbor amino acid variations to any other amino acid at position 2, as currently recited by the instant claims, are not supported by specification or by the prior art.
The problem of predicting protein structure from sequence data and in turn utilizing predicted structural determinations to ascertain functional aspects of the protein is extremely complex. While it is known that many amino acid substitutions are generally possible in any given protein the positions within the protein's sequence where such amino acid substitutions can be made with a reasonable expectation of success are limited. Certain positions in the sequence are critical to the protein's structure/function relationship, e.g. such as various sites or regions directly involved in protease recognition and cleavage. (see Tokuriki et al. Stability effects of mutations and protein evolvability. Curr. Opin. Struc. Biol. (2009), 19, p.596-604 and Biniossek).
Bhattacharya, et al. Impact of genetic variation on three-dimensional structure and function of proteins. PLOS ONE (2017), 12:3, p. 1-22 teaches that the range of possible effects of even single nucleotide variations at the protein level are significantly greater than currently assumed by existing software prediction methods, and that correct prediction of consequences remains a significant challenge (p. 18). Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111 (Fed. Cir. 1991), clearly states that “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.” (See page 1117.) The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed.” (See Vas-Cath at page 1116).
With the exception of a peptide comprising an amino acid sequence 100% identical to the amino acid of SEQ ID NO: 198 or 199, the skilled artisan cannot envision the detailed chemical structure of the encompassed polypeptides required by the claims, and therefore conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method of isolating it. The compound itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016 (Fed. Cir. 1991).
One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481 at 1483 (BPAI 1993). In Fiddes, claims directed to mammalian FGF’s were found to be unpatentable due to lack of written description for that broad class. The specification provided only the bovine sequence.
Therefore, only pro-proteins comprising a cleavable moiety that is a substrate for a protease and a polypeptide wherein the cleavable moiety comprises the amino acid sequence of SEQ ID NO: 198 at 100% identity or SEQ ID NOs 199 at 100% identity, meet the full breadth of the claims in order to meet the written description provision of 35 U.S.C. §112, first paragraph. Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. §112 is severable from its enablement provision (see page 1115).
Allowable Subject Matter
Instant SEQ ID NOs: 198 and 199 are novel in the context of recombinant pro-protein design. While SEQ ID NOs: 198 and 199 are present in the prior art as fragments from plant peptides, the use of these amino acid sequences as protease cleavable moieties is novel.
[AltContent: textbox (Instant SEQ ID NO: 198 vs. La Rosa SEQ ID NO: 183375
[img-media_image1.png])] The closest prior art is provided by amino acid residues 175-182 of US20040031072A1 – La Rosa, et al. SEQ ID NO: 183375 which encodes for a small portion of a full-length protein from Glycine max (soybean) for improvement of plant properties and is unrelated to the instant application (see alignment below).
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.
Copending Application 17/082,955
Claims 75-87 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 75-97 of copending Application No. 17/082,955 (herein referred to as App ‘955); in further view of University of Waikato. The genetic code. Science Learning Hub Pokapu Akoranga Putaiao (2014), internet, p.1 (herein referred to as UW): and, further in view of Hong, et al., Viral vectors for gene transfer. Current protocols in mouse biology (2018), 8:4, p.e58 (herein referred to as Hong).
App ‘955 teaches a polypeptide comprising a separation moiety of instant SEQ ID NO: 198 (same as App ‘955 SEQ ID NO: 198) or a functional variant thereof that is SEQ ID NO: 199 or 381 (i.e., instant SEQ ID NOs: 199 or 381; App ‘955 claim 95); instant claims 75 and 77); and, wherein the cleavable moiety links two protein domains of interest (App ‘599 claim 75; instant claims 75 and 78) wherein one of the domains is a polypeptide with biological activity (App ‘955 claim 87; instant claims 75 and 79); and, a recombinant pro-protein comprising a cleavable moiety that is a substrate for a protease wherein the cleavable moiety is SEQ ID NO: 198 (i.e., instant SEQ ID NO: 198. Thus, App ‘955 teaches cleavable moieties wherein the amino acid at P1 is lysine/K and the amino acid at P1’ is serine/S (App ‘955 claim 76, 87, and 95; instant claims 75 and 77). App ‘955 teaches that the polypeptide and pro-protein comprise a cytokine, chemokine, growth factor, soluble receptor, or combination thereof (App ‘955 claims 79 88; instant claim 76). App ‘955 teaches a fusion protein (i.e., pro-protein) that encodes a blocking moiety that is a steric blocking moiety or a specific blocking moiety App ‘955 claim 92; instant claim 80); wherein the blocking moiety comprises a steric blocking moiety comprising human serum albumin (HSA; App ‘955 claim 93; instant claim 81); wherein cleavage by the protease produces a polypeptide with biological activity that is not attenuated (App ‘955 claims 76 and 87; instant claim 79). App ‘955 teaches that the specific blocking moiety comprises an antibody or antigen-binding fragment thereof (App ‘955 claims 82, 91, and 92; instant claim 82). App ‘955 teaches that the polypeptide comprises a half-life extension domain (App ‘955 claim 83; instant claim 83); that the polypeptide with biological activity comprises at least one of an extracellular domain, transmembrane domain, or intracellular domain (App ‘955 claims 80 and 89; instant claim 84); that the polypeptide with biological activity comprises a cell surface receptor, a chimeric antigen receptor (CAR), or a T Cell Receptor (TCR) subunit (App ‘955 claims 81 and 90; instant claim 85).
App ‘955 does not teach a nucleic acid composition comprising nucleic acids that encode the pro-protein polypeptides (instant claims 75); a vector comprising the nucleic acid composition (instant claim 86); or, that the vector is a viral vector (instant claim 87).
UW teaches the genetic code for amino acids that correspond to nucleic acid codons.
It would have been prima facie obvious for one of ordinary skill in the art to combine the teachings of App ‘955 with the teachings of UW by performing a reverse translation of the amino acid polypeptide sequences taught by App ‘955 by using the genetic code taught by UW, in order to arrive at the instantly claimed invention, because the combination of prior art elements results in the predictable result of obtaining nucleic acids encoding the polypeptides (taught by UW) for the cleavable moiety of App ‘955 SEQ ID NOs: 198, 199, or 381 and a polypeptide with biological activity to result in the instantly claimed pro-protein. One of ordinary skill in the art would have a reasonable expectation of success because UW teaches codons for expression of amino acids.
It would have also been obvious to further combine the teachings of App ‘955 and UW with the teachings of Hong by using a viral vector to express the nucleic acids encoding the polypeptides of the cleavable moiety and peptide with biological activity, to arrive at the instantly claimed invention, because the combination of prior art elements results in the predictable result of producing the claimed pro-protein by reverse translating the amino acid sequence (taught by UW) and expressing the nucleic acid using viral vector protein expression (taught by Hong) to produce the polypeptide of App ‘955.
This is a provisional nonstatutory double patenting rejection.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jami M Gurley whose telephone number is (571)272-0117. The examiner can normally be reached Monday - Friday, 8am - 4pm.
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/JAMI MICHELLE GURLEY/Examiner, Art Unit 1647
/JOANNE HAMA/Supervisory Patent Examiner, Art Unit 1647