DETAILED ACTION
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 02 March 2026 has been entered.
Status of Application
The amendments and response filed 02 March 2026 are acknowledged and have been considered in their entireties. Claim 7 is cancelled, thus, claims 1-6 and 8-19 remain pending; Claims 1-2 and 15-19 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected subject matter, there being no allowable generic or linking claim. Thus, claims 3-6 and 8-14 are subject to examination on the merits.
The species election has now been extended to instant SEQ ID NO: 3 (e.g. Nucleobindin-2).
Applicant’s representative reached out to discuss the potential deletion of the elected species of SEQ ID NO: 2 and encoding nucleic acid SEQ ID NO: 12 from the claims on 28 January 2026 and if this was permissible and the amendments entered. The Examiner indicated this would be acceptable; but that new search and consideration would be required.
Withdrawal of Previous Objections/Rejections
The rejection of claim(s) 3-5, 7-10 and 12-14 under 35 U.S.C. 103 as being unpatentable over Andersen et al. (EP 3323826 – cited on IDS of 30 June 2023) in view of UniProt G3GTT2 submission 2011 (See Supplemental Content, 20241215_202215_us-17-781-873a-2.rup file, Result #1 and attached/cited UniProt file) is withdrawn in view of the deletion of SEQ ID NO: 2, encoded by SEQ ID NO: 12, from the claims.
New Objection/Rejections
Specification
Compliance with Sequence Rules
The sequence listing, filed in computer readable form (.txt) on 28 November 2022, has been received and entered. This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 C.F.R. § 1.821(a)(1) and (a)(2) ST.25. However, this application fails to fully comply with the requirements of 37 C.F.R. § 1.821 through 1.825 ST.25.
The following parts of the specification contain sequences that contain four or more specifically defined amino acids or ten or more specifically defined nucleotides without any corresponding SEQ ID NO: and/or no reference to any SEQ ID NO:.
Table 4 of the specification discloses 10 protein sequences, 10 signal peptides and 10 nucleotide sequences encoding the signal peptides, each of which require a sequence identifier.
* If the noted sequences are in the sequence listing as filed, Applicants must amend the specification to identify the sequences appropriately by SEQ ID NO:. If the noted sequences are not in the sequence listing as filed, Applicants must provide (1) an updated copy of the sequence listing containing the requisite sequences in computer readable form (.txt), (2) an amendment directing its entry into the specification, (3) a statement that no new matter has been added and (4) an amendment to the specification to identify the identified sequences by SEQ ID NO: and, if necessary, (5) an updated incorporation by reference statement with the new date of creation, sequence file name and size. – See also MPEP 2422.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 3-5, 8-10 and 12-14 are rejected under 35 U.S.C. 103 as being unpatentable over Andersen et al. (EP 3323826 – cited on IDS of 30 June 2023) in view of UniProt G3IF52 submission 2011 (See Supplemental Content, 20241215_202215_us-17-781-873a-3.rup file, Result #1 and attached/cited UniProt file) and von Heijne (JMB, 1984 – cited herein) and Perlman & Halvorson (JMB, 1983 - cited herein).
Andersen et al. teach Chinese hamster ovary (CHO) cells are currently the expression system of choice for production of therapeutic proteins, mainly because they are able to produce proteins that require complex folding, post-translational modifications such as glycoforms that are compatible with and bioactive in humans. It is further taught that while some signal peptides can be used interchangeably between species to some degree, the production of therapeutic proteins such as interleukin-2, growth factors, IgG’s have shown limited yield in CHO cells and this has been attributed to insufficient secretion efficiency. Thus, it is stated: “Accordingly, there exists a need for signal peptides that can enhance the secretion efficiency and yield of recombinant proteins expressed in CHO cells.” – See paragraphs 0003-0006. It is further stated: “The invention is further based on evidence that native CHO cell secretion signal peptides can outperform the standard signal peptides currently used in biopharmaceutical production by enhancing the secretion efficiency and yield of recombinant proteins expressed in CHO cells.” – See paragraph 0029. Andersen et al. thus have attempted to identity native CHO secretion/signal peptides via in silico methods utilizing the signal peptide prediction program SignalP 4.1 (See Examples 1-2), where they identified 13 different CHO signal/secretion peptides and experimentally compare these again commonly used human secretion peptides. Seven of these were identified as having significantly better secretion activity when attached to an IgG antibody as compared commonly used CHO secretion peptides from human or that are synthetic and produced in an expression cassette for testing (See Example 3), wherein many of the native CHO signal sequences (SP1-5, 7 and 11) consistently outperformed the human IFNγ, and the two commonly utilized synthetic peptides - Section 3.7 and See Figures 4a, b and c. Finally, Andersen et al. teach in paragraph 0005, usually the cleavage sites of any signal peptide has to have small and natural residues at the -3 and -1 positions from the cleavage site for correct cleavage.
While they do identify seven to 13 CHO secretion/signal peptides (termed SP1-7, SEQ ID NOs: 2, 4, 6, 8, 10, 14 and 22), they do not, however, teach any additional CHO derived signal peptides such as SEQ ID NO: 3 and encoded by SEQ ID NO: 13, which is derived from Nucleobindin-2. Nor do the specifically teach the signal sequence results in cleavage between the signal peptide and the target protein wherein no extra amino acids exist at the N-terminus of the mature target protein.
The UniProt G3IF52 submission in 2011 reveals the known CHO protein of nucleobin-2 possesses a 24 amino acid signal/secretion sequence which has 100% sequence identity to instant SEQ ID NO: 3 – See Supplemental Content, 20241215_202215_us-17-781-873a-3.rup file, Result #1. The signal sequence specifically is identified as: Met Arg Trp Lys Ile Ile Gln Leu Gln Tyr Cys Phe Leu Leu Val Pro Cys Met Leu Thr Ala Leu Glu Ala. (The bold positions are the -3 and -1 positions).
Von Heijne teach signal peptides and their correct processing are guided by a universal rule, namely, the signal peptide and cleavage site must fulfill the “ -3, -1 rule” where the -1 position of the signal peptide (i.e., the last residue before the start of the mature target protein) must be occupied by A/S/G/C/T/Q amino acid residues and must not have aromatic (F/H/W), charged (D/Q/K/R), or large polar residues (N/Q) in position -3, and, no P residues from position -3 to +1. It is stated, a similar universal rule was established by Perlman & Halvorson – See pp. 243-244.
Perlman & Halvorson teach the signal peptide and cleavage site (recognized by signal peptidases) adhere to the A-X-B rule, wherein said A-X-B amino acids are adjacent to the N-terminal first amino acid of the mature target protein. Position A consists of A/G/S residues or the larger aliphatic amino acids L/V/I, and position B is occupied by A/G/S.
Therefore it would have been obvious to create an expression cassette comprising a native known CHO signal peptide as publicly available and taught as the nucleobindin-2 signal sequence of UniProt G3IF52, which is 24 amino acids in length and possesses a L at -3/A position and A at -1/B position as taught by von Heijne/ Perlman & Halvorson, and to operably link it to a protein of interest/target protein, such as an antibody, enzyme, etc. in the expression cassette/gene taught for expression in CHO host cells as taught by Andersen et al. because Andersen et al. teach that utilizing native signal/secretion sequences results in better secretion efficiency (See Example 3). One skilled in the art would be motivated to utilize any known secretion/signal sequence in the expression cassettes/vectors/CHO host cells because Andersen et al. teach utilizing secretion/signal sequences from non-native CHO proteins results in insufficient secretion efficiency (See paragraph 0006 and Example 3). Furthermore, given said signal sequence possesses the correct amino acids in the -3 and -1, and/or A-X-B positions (e.g. Leu and Ala), as identified by Andersen et al. and specifically taught by von Heijne/ Perlman & Halvorson in combination with the UniProt G3IF52 Nucleobin-2 signal sequence, it would also be obvious to use such a signal sequence, and one skilled in the art particularly would be motivated to utilize this CHO identified signal sequence because it, according to the well known rules for correct cleavage of signal peptides, will result in mature proteins having been correctly cleaved, e.g. not having any extra additional amino acids at the N-terminus of the mature protein. One skilled in the art would have a reasonable expectation of success in substituting any of the secretion signal sequences of Andersen et al. with any known and publicly available CHO secretion signal/secretion sequence such as Nucleobindin-2 UniProt G3IF52 sequence having 100% identity to instant SEQ ID NO: 3 and encoded by SEQ ID NO: 13 because this is a simple substitution to make for one skilled in the art given the specific and exact details as described in the Examples of Andersen et al. and given the publicly available information in the UniProt G3IF52 database. Additional expectation of success comes from von Heijne/ Perlman & Halvorson and the fact that said identified signal sequence has the correct amino acids in the -3 and -1/A-X-B positions, namely, Met Arg Trp Lys Ile Ile Gln Leu Gln Tyr Cys Phe Leu Leu Val Pro Cys Met Leu Thr Ala Leu Glu Ala so as to ensure correct cleave resulting in no additional amino acids at the N-terminus of the mature target protein.
Applicant’s Response and Examiner’s Rebuttal:
Applicant’s traverse the rejection of record and state a case of prima facie obviousness has not been established. Said rejection has been withdrawn in view of the deletion of SEQ ID NO: 2 from the claim(s). However, said arguments will be addressed as they pertain to the instant rejection.
It is argued that a person of ordinary skill in the art would not be motived to utilize the secretory factor of SEQ ID NO: 3 in an expression cassette for expressing a target protein (nor SEQ ID NO: 1 or 5) because Andersen does not disclose SEQ ID NO: 3 (or SEQ ID NOs: 1 or 5) and because not all peptides function as secretory factors. It is suggested because of this, it would not have been predictable to create an expression cassette comprising SEQ ID NO: 3 (or SEQ ID NOs: 1 or 5) and thus it would not be obvious to a skilled artisan that any of these sequences function as protein secretory factors (See Remarks, p. 8-9). This is also argued on p. 10, 2nd paragraph, that as shown in Figure 4, Example 4, instant SEQ ID NO: 3 and 5 function so as not to mis-cleave target proteins thus leaving said target proteins with no additional amino acids at the mature N-terminus of the target protein.
The Examiner acknowledges this argument but counters that the UniProt submission does in fact directly disclose instant SEQ ID NO: 3 as a signal/secretion sequence and as such, one skilled in the art would have no reason to assume otherwise. In addition, regarding predictability, given Andersen et al. (paragraph 0005) and von Heijne/ Perlman & Halvorson teach the universal rules for most signal peptides, e.g. the -3, -1 rule, and the signal peptide of Nucleobindin-2 adhere precisely to this rule, there is a reasonable expectation that predictably, said signal sequence would work as expected and cleave between the -1 and +1 (e.g. first amino acid of the mature target protein), thus not adding any additional amino acids to the mature target protein. Furthermore, one skilled in the art would have little to no unpredictability of simply making an expression cassette, this is well within the skill and knowledge of those skilled in the art.
Applicant’s further suggest that because some of the secretory signals tested in instant Example 2, data shown in Figure 2, that sequences like Nid, Sulf, Pro and Lip exhibited lower levels of secretion, that one skilled in the art would not readily recognize that a specific protein functions as a protein secretory factory unless it has been specifically tested/disclosed (See Remarks, p. 10, 3rd paragraph).
The Examiner acknowledges this argument but counters that while the secretory factors Nid, Sulf, Pro and Lip may not have had the levels of secretion as other secretion factors tested, they still in fact did function as secretory factors, at least Sulf and Pro, given the results as demonstrated in Figure 2. The fact is out of the 11 in silico identified secretion factors tested, nine of them functioned as expected as secretion factors. This suggests that there is a reasonable expectation that if a peptide is identified as a secretion factor even in silico, it likely will have to least some level of this function. Applicant’s seem to be of the opinion that the requirement for obviousness lies with absolute predictability of success. However, this is not the standard, as noted, only a reasonable expectation of success is required (See MPEP 2143.02).
It is additionally argued that neither Andersen nor none of the other references teach making an expression cassette for recombinant target protein production to improve efficiency or quality. (See Remarks, p. 9, 2nd paragraph).
However, this is not accurate as Andersen specifically teaches in Figure 3 the configuration of the expression cassettes utilized in the overall expression vector which comprises signal peptide fused to the N-terminus of the protein of interest.
With regard to Applicant’s assertions on p. 11, 1st paragraph of the Remarks of unexpected results because SEQ ID NO: 3 and 5 have significantly better secretion levels compared to a conventional secretion factor like the human secretion factor SP7.2 (SEQ ID NO: 33). However, this is not necessarily unexpected or surprising given Andersen et al. specifically state that based on their evidence, native CHO cell secretion signal peptides can outperform the standard signal peptides which are not CHO cell derived currently used in biopharmaceutical production by enhancing the secretion efficiency and yield of recombinant proteins expressed in CHO cells (See paragraph 0029). As such, using a CHO secretion/signal peptide such as SEQ ID NO: 3 compared to a non-CHO secretion/signal sequence according to the prior art, would lead to an expectation of superior results. It is noted, SP7.2 (SEQ ID NO: 33), is not from CHO cells, but rather is from human and/or macaque (they are identical – See Supplemental Content, 20251024_093206_us-17-781-873a-33.rup, Results #1-4).
With regard to Applicant’s remarks about no mis-cleavage as presented in Example 4 and Figure 5 for SEQ ID NO: 2, 3 and 5 (See p. 11, 2nd paragraph of Remarks), the Examiner does not find this convincing for the same reasons identified above, e.g. utilizing non-CHO cell secretion/signal sequences as compared to those derived from CHO cells.
For these reasons the rejection of record is maintained.
Conclusion
No claim is allowed; claims 6 and 11 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SUZANNE M NOAKES whose telephone number is (571)272-2924. The examiner can normally be reached M-F (7-4).
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/SUZANNE M NOAKES/Primary Examiner, Art Unit 1656 04 March 2026