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 .
DETAILED ACTION
Applicant’s submission filed on 11/15/2024 is duly acknowledged.
Claims 4 and 5 have been canceled by applicant’s current claim amendments.
Claims 1-3 and 6-18, as currently amended/presented are pending in this application, and have been examined on their merits in this action hereinafter.
Priority
This application is a DIV of 17/458,929 (filed on 08/27/2021, now US PAT 12163122), which claims domestic benefit from US provision applications PRO 63/072,745 (filed on 08/31/2020) and PRO 63/072,740 (filed on 08/31/2020).
Objection to Specification
Instant claim 15 recites the following subject matter:
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Specification is objected because the instant disclosure of record does not provide proper antecedent basis for the limitations “contacting said amino acids to 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate” per se. The subject matter of the claim 15 appears to refer to the undisclosed components of a commercial kit (“AccQ-Tag reagent kit” from Waters, Milford, MA) described by applicants in paragraph [00232] of instant specification. However, such limitations have not been described in order to provide appropriate basis for the claim. Appropriate correction and/or explanation is required.
NOTE: 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.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
1. Claims 1-3 and 6-18 (as currently amended/presented) are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al (2016; cited as NPL in applicant’s IDS dated 11/08/2024) taken with Solacroup et al (2020; US 10,526,631 B1; cited as USPAT on applicant’s IDS 11/08/2024) and Armenta et al (2010; NPL cited as ref. [U] on PTO 892 form).
Claims 1-3 and 14-18 as presented are reproduced herein as follows:
“1. (Currently Amended) A method for detecting asparagine sequence variants in a recombinant protein of interest expressed from CHO
(a) propagating or maintaining CHO
(b) expressing a recombinant protein of interest from the CHO
(c) measuring a concentration of asparagine or one or more asparagine-related amino acids in the cell culture or cell culture medium; and
(d) correlating the measured concentration of asparagine or one or more asparagine-related amino acids to the presence of asparagine sequence variants in the expressed recombinant protein of interest.”
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See also limitations of claims 2 and 6-13 as recited by applicants.
Zhang et al (2016), while studying the optimization of the total amounts and the ratio of two vital amino acids (glutamine and asparagine; i.e. result-effective variables recognized in the art for expressing/producing recombinant proteins in mammalian cells, such as CHO cells, or variants thereof) in feed medium to increase chimeric antibody production in fed-batch cell culture using Chinese Hamster ovary cell (CHO-DHFR cells, a variant of CHO cells; see Title, Abstract, Background on page 2 left column, and section “Methods”, in particular), disclose the method for propagating or culturing mammalian CHO-DHFR cells expressing a human chimeric anti-CD20 antibody in a defined cell culture medium (DMEM/Ham’s F-12, 1:1; see “Methods” section “Cell line and cell culture” on page 2, right column), wherein the fed-batch cell culture was performed using 4 mM asparagine (ASN), followed by supplementation with 3% (v/v) feed media with different concentrations of ASN and glutamine (GLN) per day for 12 days (see page 2, left column, last paragraph, and entire disclosure in “Methods”; it is noted that said supplementation of feed media in a FB-H condition with ASN/GLN high ratio of 2:1 with 120 mM ASN and 60 mM GLN corresponds to 3.6 mM ASN supplementation in the fed-batch cell culture medium); wherein positive effects of ASN/GLN ratio studied in terms of cell viability, cell growth, antibody production and titer were demonstrated by Zhang et al (see results on page 7, Figure 3, in particular); wherein they showed that the maximum viable cell density (VCD) was increased by 18% compared to the FB-L (low ASN/GLN ratio or 1:2) and FB-N (no ASN and GLN supplementation) conditions, and the antibody production and titer was increased by 33.5 and 79.3% compared to lower ASN conditions (see Results, discussion at page 5, left column); and wherein the generated waste by-product lactate of FB-H was about 19.1% lower than that of FB-L during the stationary phase, and it was higher than the FB-N (see figure 3e, for instance), whereas the levels of ammonia and alanine were not found to be lower than no-supplementation control, FB-N (see page 5, right column, and Figure 3f, 3g, for instance). In addition, Zhang et al disclose the method steps involving analytical measurements and specific metabolic rates for the cultured cells after extraction, as well as cultured medium (see page 2, section “Extraction of intracellular metabolites”, for instance), wherein they measure the concentrations of amino acids using reversed phase HPLC (1525 Binary HPLC pump, 717plus Autosampler, 2487 Dual λ absorbance detector, Nova-Pak C18 column, Waters) after chemical derivatization with a commercial ACCQ-Tag kit from Waters (see section “Analytical measurements and specific metabolic rates”, in particular).
However, Zhang et al do not explicitly disclose the method for detecting asparagine sequence variants in the recombinant antibody expressed in CHO cells in culture, comprising the steps of -1) “correlating the measured concentration of asparagine or one or more asparagine-related amino acids to the presence of asparagine sequence variants in the expressed recombinant protein” (see step (d) in instant claim 1); wherein the “measured concentration of asparagine or the one or more asparagine-related amino acids is inversely correlated to the presence of asparagine sequence variants” (see instant claim 2); and 3) wherein the step of measuring comprises collecting cell culture media, derivatizing said amino acids, and separating and quantifying said derivatized amino acids using liquid chromatography-mass spectrometry analysis. (see limitations of instant claims 14-18).
Solacroup et al (2020) discloses a method of reducing serine for asparagine misincorporation in a recombinant antibody protein produced by a culture of cells (such as CHO host cells) by supplementing the fed-batch cell culture medium with asparagine (ASN) and iron on selected days (see Title, Abstract, and claims 1, 5-7, 9-11, 16, and 18, in particular); wherein they exemplify the culture of CHO-2 cells expressing adalimumab, a human antibody targeting TNF-alpha (see Examples 2-3, column 18-20, in particular) that were supplemented with ASN using multiphase supplementation strategies, wherein supplementation between 10-18 mM ASN at the beginning of the culture (day 0) was followed by reduced amounts of between 2 and 8 mM at several days of the culture, including the bolus feeds on selected days of fed-batch cell culture (see disclosure of feeding strategies on column 18-20, examples 2-3); wherein one of the strategies for example, “Strategy 3b” employs supplementation of 12.5 mM ASN at day 0 followed by 6.9 mM ASN at day 5 and 1.7 mM ASN supplementation at days 7 and 10, which provided the best results, at least in terms of reducing serine misincorporation, i.e. reduced ASN sequence variants; wherein they also disclose that addition of iron helped increase maximum cell density without affecting the rate of misincorporation of ASN to serine (see Example 3, for instance). They disclose the fact that the “misincorporation can be determined by various methods known in the art, such as: intact measurement, peptide mapping analysis, or mass spectroscopy sequencing” (see column 1, lines 24-27), and provide such quantitative and comparative analyses of ASN-SER misincorporation of the sequence variants in the recombinantly produced protein using mass spectrometry, ESI-MS (see column 6, lines 3-4, and Figure 1, and Example1, in particular).
Although, the details of chemical derivatization of amino acids from extracted samples of cells or culture media has not been explicitly disclosed by the cited prior art references of Zhang et al when taken with Solacroup et al as discussed above, such measurements and/or quantitative comparison of amino acid derivatives would have been obvious and fully contemplated by an artisan of ordinary skill in the art because Armenta et al (2010) already disclosed a sensitive and rapid method for amino acid quantitation using AccQ•Tag UPLC-ESI-MS/MS with multiple reaction monitoring, the same reagents and technique used by the applicants (see instant SPEC, [0232]), which utilizes 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate to chemically transform primary and secondary amines into highly stable fluorescent derivatives (see Armenta et al, page 3, 2nd paragraph; and page 5, section “Method Development”, for instance), has been used in the prior art for the advantages of faster analysis.
Thus, given the detailed disclosure from Solacroup et al for multiphase ASN supplementation strategies including bolus feeding of ASN in fed-batch cell culture of CHO cells producing recombinant antibody protein, wherein the strategy of supplementing higher amount of ASN followed by lower amount of ASN to the cell culture medium (on selected days starting from day 0) has already been disclosed to reduce ASN depletion as well as its misincorporation into serine (in other words, reducing the ASN sequence variants in the Ab produced), it would have been obvious to a person of ordinary skill in the art to employ and/or optimize such feeding strategies in order to avoid ASN depletion and reduce ASN variants in the resulting polypeptides produced from CHO cells, as already demonstrated by Solacroup et al as discussed above. The specific amounts and/or ranges of ASN supplement (in the form of continuous or as bolus feeds), selected days of feeding (and/or feeding intervals; see instant claim 3) the fed-batch cell culture, and/or its discontinuation after a selected regimen or day, would have been obvious to an artisan in the art given the combined disclosure from Zhang et al taken with the results and motivation provided by Solacroup et al, as discussed above, unless evidence provided on record to the contrary. Since, instant claim 1, as presented, is not limited to any specific culture condition(s), amino acids, nutrients or levels thereof, and any specific sampling or technique for measuring and correlating the amino acid sequence variants (that were already disclosed by the same comparative analysis in protein produced by CHO cells; see Solacroup et al), such adjustments and selection for days of feeding (intervals thereof) and/or amount ranges for ASN supplements, as well as specific chemical derivatization of extracted samples (of cell culture and/or spent media, for instance taken at different time points of culturing cells) before analysis using AccQ•Tag UPLC-ESI-MS/MS (as disclosed by Armenta et al, above for the benefit of faster analysis of biological samples, albeit using malaria samples) would have been obvious and/or fully contemplated by an artisan of ordinary skill in the art, unless evidence/data provided on record to the contrary (which is currently lacking on record for the entire scope of the invention, as claimed). It is noted that applicants have not shown on the record any criticality based on the particular samples or the technique for measuring and/or comparative analysis of the derivatized amino acids, in particular relevant to any specific asparagine sequence variants per se, and therefore, the invention as generically claimed fails to distinguish itself over the combined teachings and/or suggestion from the cited prior art references as discussed above. It is also noted to applicants that the scope of the showing must be commensurate with the scope of claims to consider evidence probative of unexpected results, for example. In re Dill, 202 USPQ 805 (CCPA, 1979), In re Lindner 173 USPQ 356 (CCPA 1972), In re Hyson, 172 USPQ 399 (CCPA 1972), In re Boesch, 205 USPQ 215, (CCPA 1980), In re Grasselli, 218 USPQ 769 (Fed. Cir. 1983), In re Clemens, 206 USPQ 289 (CCPA 1980). It should be clear that the probative value of the evidence/data provided by applicants on record is not commensurate in scope with the degree of protection sought by the claim (see instant claim 1, in particular).
Thus, the claim as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the invention as currently claimed.
As per MPEP 2111.01, during examination, the claims must be interpreted as broadly as their terms reasonably allow. In re American Academy of Science Tech Center, F.3d, 2004 WL 1067528 (Fed. Cir. May 13, 2004)(The USPTO uses a different standard for construing claims than that used by district courts; during examination the USPTO must give claims their broadest reasonable interpretation.). This means that the words of the claim must be given their plain meaning unless applicant has provided a clear definition in the specification. In re Zletz, 893 F.2d 319, 321, 13 USPQ2d 1320, 1322 (Fed. Cir. 1989).
Conclusion
NO claims are currently allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SATYENDRA K. SINGH whose telephone number is (571)272-8790. The examiner can normally be reached M-F 8:00- 5:00.
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SATYENDRA K. SINGH
Primary Examiner
Art Unit 1657
/SATYENDRA K SINGH/Primary Examiner, Art Unit 1657
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