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 .
Applicants filed a Preliminary Amendment May 10, 2022, in which Applicants canceled claims 1-2 and 43-56. Applicants amended claims 23 and 35. Claims 23-42 are pending in this application, and are under examination.
Information Disclosure Statement
The Information Disclosure Statement filed May 28, 2022 has been considered.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code at paragraph [0025]. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of the terms ILLUMINA® at paragraphs[0025], [0035] and [0041], TRUSEQ® at paragraphs [0025] and [0035], AGILENT® at paragraphs [0025] and [0035], BIOANALYZER® at paragraph [0025], HISEQ® at paragraphs [0025] and [0035], IMAGEQUANT® at paragraph [0033], TRITON® at paragraph [0034], BIOCOMP® at paragraph [0034], BRANDEL® at paragraph [0034], GENELUTE™ at paragraph [0034], BIO-SPIN® at paragraph [0034], and PHUSION® at paragraph [0034], which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms 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.
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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
Claims 23-42 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 of U.S. Patent No. 10,883,109.
Although the claims at issue are not identical, they are not patentably distinct from each other because ‘109 patent claims a method of modulating expression of a recombinant protein in a host cell by identifying optimal and non-optimal codons in a wild-type cDNA that encodes the protein and preparing a synthetic cDNA sequence where optimal codons are replaced by non-optimal codons or non-optimal codons are replaced by optimal codons, transfecting a host cell with the synthetic cDNA, and expressing the protein. The ‘109 patent claims a list of optimal and non-optimal codons. The ‘109 patent claims that the synthetic cDNA has at least 70% optimal codons. The ‘109 patent claims that the cell is a yeast cell or a mammalian cell.
The instant application claims a method of preparing a synthetic nucleic acid by determining optimal and non-optimal codons for expression in a eukaryotic cell, which may be a yeast cell, a CHO cell, or a plant cell. The instant application synthetic nucleic acid that encodes a protein, the nucleic acid having at least one optimal or non-optimal codon replaced by either a non-optimal or optimal codon, such that the protein is the same as the protein encoded by the wild-type nucleic acid. The instant application claims at least about a 10%, a 50%, or a 75% difference in the level of expression, depending on whether non-optimal or optimal codons were used as replacements. The instant application claims a list of optimal codons and non-optimal codons. The instant application claims that the nucleic acid can have less than about 40% optimal codons. The instant application also claims that the nucleic acid sequence can have more than 70% optimal codons. The instant application claims that the cell can be a Chinese Hamster Ovary (CHO) cell. The instant application further claims a method of producing a recombinant protein in a eukaryotic host cell.
Therefore, the claims are not deemed to be patentably distinct.
Claims 23-42 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. 11,236,345.
Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘345 patent claims a synthetic nucleic acid that encodes a protein, the nucleic acid having at least one optimal or non-optimal codon replaced by either a non-optimal or optimal codon, such that the protein is the same as the protein encoded by the wild-type nucleic acid. The ‘345 patent claims at least about a 10%, a 50%, or a 75% difference in the level of expression, depending on whether non-optimal or optimal codons were used as replacements. The ‘345 patent claims a list of optimal codons and non-optimal codons. The ‘345 patent claims that the nucleic acid can have less than about 40% optimal codons. The ‘345 patent also claims that the nucleic acid sequence can have more than 70% optimal codons. The ‘345 patent claims that the cell can be a Chinese Hamster Ovary (CHO) cell. The ‘345 patent further claims a method of modulating expression of a protein in a mammalian host cell.
The instant application claims a method of preparing a synthetic nucleic acid by determining optimal and non-optimal codons for expression in a eukaryotic cell, which may be a yeast cell, a CHO cell, or a plant cell. The instant application synthetic nucleic acid that encodes a protein, the nucleic acid having at least one optimal or non-optimal codon replaced by either a non-optimal or optimal codon, such that the protein is the same as the protein encoded by the wild-type nucleic acid. The instant application claims at least about a 10%, a 50%, or a 75% difference in the level of expression, depending on whether non-optimal or optimal codons were used as replacements. The instant application claims a list of optimal codons and non-optimal codons. The instant application claims that the nucleic acid can have less than about 40% optimal codons. The instant application also claims that the nucleic acid sequence can have more than 70% optimal codons. The instant application claims that the cell can be a Chinese Hamster Ovary (CHO) cell. The instant application further claims a method of producing a recombinant protein in a eukaryotic host cell.
The instant case is analogous to Sun Pharmaceutical Industries, Ltd. v. Eli Lilly and Company (Fed. Cir. July 28, 2010), where the courts ruled that obviousness-type double patenting exist between previously-disclosed, but newly-claimed utility. Therefore, the instant claims are not patentably distinct from the issued claims.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Sinclair et al. (26 Protein Expression and Purification 96-105 (2002), and cited in the Information Disclosure Statement filed May 28, 2022) disclose that the codon optimization increases protein activity 10.6 and 7.5 fold (i.e., a difference of at least 75%) (abstract). Sinclair further discloses that either optimal or non-optimal codons can be used (page 102, Table 4). Sinclair further discloses preferred codon substitutions for the yeasts Pichia pastoris and Saccharomyces cerevisiae, which include the claimed codon usage (Table 2). Sinclair discloses that the RNA can be in vitro transcribed (page 101, paragraph bridging columns 1 and 2). Sinclair discloses that codon bias and choice can affect mRNA stability (page 103, paragraph bridging columns 1 and 2). However, while Sinclair discloses codon optimization of proteins for expression in mammalian cells, Sinclair does not disclose or suggest a method of preparing a synthetic nucleic acid by either replacing optimal codons with non-optimal codons or replacing non-optimal codons with optimal codons in order to modulate expression levels by either increasing or decreasing expression.
Koresawa et al. (127 Journal of Biochemistry 367-372 (2000), and cited in the Information Disclosure Statement filed May 28, 2022) disclose nucleic acids encoding Cre recombinase (a bacteriophage protein) that are codon optimized for expression in mammalian cells, such as Chinese hamster ovary (CHO) cells (abstract). Koresawa discloses determination of preferred codons for mammalian cells, construction of an expression vector, transformation of the CHO cells, and expression of the recombinant protein (abstract and pages 367-368). Koresawa discloses a codon-usage table for expression of proteins in CHO cells (Table I). However, while Koresawa discloses codon optimization of proteins for expression in mammalian cells, Koresawa does not disclose or suggest a method of preparing a synthetic nucleic acid by either replacing optimal codons with non-optimal codons or replacing non-optimal codons with optimal codons in order to modulate expression levels by either increasing or decreasing expression.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NANCY J LEITH whose telephone number is (313)446-4874. The examiner can normally be reached Monday - Thursday 8:00 AM - 6:30 PM.
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NANCY J. LEITH
Primary Examiner
Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636