DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s response and amendments received June 8, 2026 are acknowledged.
Claims 1-17, 20-27, and 32-52 have been canceled.
Claim 18 has been amended.
Claims 53-62 have been added.
Claims are pending in the instant application.
Applicant’s election without traverse of the invention of group II, directed toward methods of suppressing splice variants in the reply filed on June 8, 2026 is acknowledged.
Information Disclosure Statement
The IDS forms received 10/24/2023 and 6/8/2026 are acknowledged and the references cited therein have been considered.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
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 18, 19, 28-31, and 53-62 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Applicant has broadly claimed methods of reducing the expression and secretion of splice variant isoforms. Such methods involve the process steps of transfecting mammalian cells, culturing said cells, and recovering the expressed protein from the cell culture medium, all of which is standard and routine in the art with regard to recombinant protein production methods. However, the nucleic acid used for transfection is recited as comprising a “first polynucleotide” and a “second polynucleotide” wherein both the first and second are in the same reading frame (and thus necessarily on a single long piece of nucleic acid rather than for example two separate nucleic acid molecules with one having the “first” and the other having the “second” sequence), with the “first” comprising a signal peptide that must use the GGG codon to encode all glycine residues that are within 6 residues form the C terminal end of signal peptide (i.e. the residue immediately N terminal to the cut and the 5 preceding residues, also known in the art as P6-P1 as per Figure 2 of Owji et al., see entire document)) while the second encodes “a recombinant protein” that can be anything in the broadest claims (such as independent claim 18) with dependent claims indicating it is an antibody (claims 55 and 58) of defined sequence (claim 56).
To support such claims, applicant discloses that during production of the bispecific T cell engager (BiTE) specific for CD3 and PMSA in CHO cells as disclosed in US 2017/0218079, in addition to the predicted bispecific antibody construct applicant also recovered low molecular weight species that was non-functional in binding assays (example 2) due to a large portion of the anti-PMSA scFv sequence being spliced out (example 3, see graphically in Figure 8). In an attempt to eliminate production of the low molecular weight species, applicant made two changes in the nucleic acid sequence which did not alter the translated polypeptide sequence, namely 1) using GGG rather than GGT to encode glycine in signal peptide to remove a suspected strong splice donor site and 2) using TCC rather than TCA to encode serine in the PMSA scFv to weaken a suspected splice acceptor site (see most particularly paragraph [0122] of the instant specification). These changes were demonstrated to reduce, but not eliminate, the synthesis of undesirable low molecular weight species (see particularly paragraph [0123] and Figure 10). While applicant provides only one working example wherein both putative splice donor and splice acceptor sites were simultaneously mutated in a specific bispecific antibody construct, applicant asserts that replacing GGT codons with GGG in signal peptides is a universal fix to avoid alternative splicing (see most particularly the end of paragraph [0122]). It should be noted that applicant’s own data demonstrates a reduction of low molecular weight species rather than elimination as is reasonably implied by applicant’s use of the term “avoid” (see also Figure 10).
Splicing of messenger RNA is a complex phenomenon, with not all consensus sites being used when present (see for example Miki et al.) and splicing events occurring even when such consensus sites are not present, say due to gene mutations (see for example Oh et al.). Such complexity appears to expand exponentially when non-canonical splicing pathways, such as cryptic sites, are also considered (see for example Sibley et al. and Zheng et al.). Indeed, the specification teaches that it is not possible to predict alternative splicing events simply by sequence gazing (see paragraph [0120], particularly the last sentence and the references cited therein). Despite such complexity, applicant has claimed methods asserted to be universally applicable to all recombinant proteins which have a signal peptide which comprises a glycine within 6 residues from the start of the mature protein. It should be noted that a vast array of signal peptides are in use in the art for the production of recombinant proteins (see for example Owji et al., particularly Table 1) with the art recognizing that the yield of recombinantly produced antibodies can be increased by optimization of signal peptides used for expression, with different signal peptides being optimal for different antibodies (i.e. there is no one sequence optimal for all antibodies, see for example You et al. and Haryadi et al.). It is important to point out that while many signal peptides originally isolated from antibody heavy and light chain genes comprise a glycine within the last 6 residues of the signal peptide, such a feature is not universal as many antibody signal peptides do not contain a glycine residue in the required location (see for example Table 1 of Haryadi et al.) and non-antibody signal peptides are widely used for the expression of all possible recombinant polypeptides (see Table 1 of Owji et al. and the NovoPro website printout). Thus applicant is asserting they have found a generic solution to a problem which is not universally present.
As has already been discussed, applicant provides data concerning aberrant alternative splicing for only one bispecific antibody construct, and the solution utilized in the working example is more extensive than that which has been claimed in independent claim 18. Specifically, claim 18 simply requires the glycine to be encoded by GGG in the absence of any consideration of surrounding sequence to reasonably check for the presence of a splice donor site (which in the absence of any additional limitations on the sequence of the signal peptide are not reasonably present) and does not require alteration of a splice acceptor site as was done as part of the working example. Based upon the data presently of record there is no indication that making one change without the other is necessarily sufficient, or that the solution designed by applicant is widely applicable to other recombinant polypeptide production methods, including antibodies. Indeed, there are many reasons why undesirable low molecular weight species are observed when purifying recombinantly produced antibodies, such as spontaneous hydrolysis of peptide bonds and enzymatic clipping by host enzymes (Delmar et al., see entire document, particularly the first paragraph of the introduction). Low molecular weight species can also occur due to aberrant splicing at the mRNA level, with Delmar et al. reporting two such variants in which the heavy chain is aberrantly spliced, neither of which, based upon their reported data, appear to have any involvement with the encoding sequence for the signal peptide (ibid., see particularly Figure 3). Similarly, Spahr et al. also disclose alternative splice variants of an antibody expressed in CHO cells which also appear unrelated to the signal peptide (see entire document). Given that alternative splice variant isoforms of recombinant polypeptides can be made in many diverse ways, applicant’s claimed solution to the alternative splicing problem which recites only mutating an encoding glycine in the signal peptide does not appear to be universally applicable as the signal peptide sequence is not universally involved.
Therefore, in view of the breadth of the claimed inventions, the disclosure of the instant specification and the working examples contained therein, and the teachings of the art, artisans would not reasonably be able to practice the full extent of the claimed invention without performing additional unpredictable trial and error basic research and experimentation for the reasons discussed above.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 18, 58, and 60-62 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bond et al. (WO 2017/072310).
Bond et al. disclose the synthesis and testing of various antibody expression constructs wherein different signal peptides were paced upstream of antibody sequences in an effort to inhibit the production of improperly processed N termini of antibody products. Notably, as part of such efforts a V-kappa-1 leader peptide was placed upstream of the VL sequence of the MEDI8490 antibody which was then transfected into CHO cells followed by recovery and testing of the antibody product recovered from the cell culture medium (see entire document, notably working examples 1-8, most particularly example 6). It should be noted that the human Vkappa1 leader is a “first polynucleotide” in the same open reading frame as the VL of the MEDI8490 antibody (i.e. the “second polynucleotide”), that such a construct was transfected into a mammalian cell, that said cells were cultured to produce antibody, and the antibody was harvested from the cell culture media. Further, the polypeptide sequence of the Vkappa1 leader is MDMRVPAQLLGLLLLWLPGAKC (disclosed by Bond et al. as SEQ ID NO:4 in Table 5) which is encoded by a polynucleotide wherein the glycine at the P4 position is encoded by GGG, and the polynucleotide immediately preceding the GGG codon is a C (SEQ ID NO:20 of Bond et al., i.e. ATG GAC ATG AGG GTG CCC GCC CAG CTG CTG GGC CTG CTG CTG CTG TGG CTG CCC GGG GCC AAG TGC (emphasis added by the examiner) as per Table 5). Thus Bond et al. practiced all of the physical and observable process steps presently recited in the independent claim.
It is noted that Bond et al. do not discuss alternative mRNA splice variants, or provide comparisons to constructs wherein the glycine at the P4 position is encoded by a GGT rather than GGG. However, as written the wherein clause of the independent claim sets forth what artisans would expect to observe if a comparison was made to a different construct. As written the claim does not require artisans to make and test two different constructs, and thus the wherein clause is most properly interpreted to be a statement of intended results. See also MPEP 2111.04.
Therefore, the prior art anticipates that which is presently claimed.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 29-31 are rejected under 35 U.S.C. 103 as being unpatentable over Bond et al. (WO 2017/072310) in view of Oguchi et al.
The teachings of Bond et al. have been discussed above and differ from the presently claimed invention in that they do not disclose the pH of the tissue culture medium used for recombinant antibody production in CHO cells in their working examples.
Oguchi et al. disclose that a pH of 6.8 resulted in a larger yield of recombinant antibody produces from CHO cells as compared to pH 7.0 (see entire document, particularly Table 1).
Therefore, artisans would have been motivated to practice the methods of Bond et al using a media pH of 6.8 because as taught by Oguchi et al. that pH provided the advantage of increased yield of recombinantly produced antibodies from CHO cells.
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Michael Szperka whose telephone number is (571)272-2934. The examiner can normally be reached Monday-Friday 8:30-5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Misook Yu can be reached at 571-272-0839. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Michael Szperka
Primary Examiner
Art Unit 1641
/MICHAEL SZPERKA/Primary Examiner, Art Unit 1641
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