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 .
Claim Status
Claims 1-2, 4, 7, 15-18, 21-25, 28-31 and 33 are pending.
Claims 1-2, 4, 7, 15-18, 21-25, 28-31 and 33 are examined on the merits.
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 1-2, 7, 15, 17, 21-24, 28-31 and 33 are rejected under 35 U.S.C. 103 as being unpatentable over Zetsche, cell 163.3 (2015): 759-771 in view of -----Hudson, Soybean-molecular aspects of breeding. InTech Open: InTech (2011): 19-42 and Endo, Scientific reports 6.1 (2016): 38169.
Claim 1 is drawn to a recombinant nucleic acid comprising a sequence with at least 99% identity to SEQ ID No: 47. The instant specification clarifies on page 36 in paragraph 00087 that Francisella novicida CPF1 (FnCpf1) sequences were codon optimized through algorithmic methods partly based on plant codon optimized to design seven FnCpf1 CO (Codon optimized) sequences where are described in Table 10. Table 10 on page 37 of the specification describes the sequence of SEQ ID NO: 47 as a codon optimized FnCPF1 optimized for soybean (Glycine max) using a codon frequency table for soybean plants. On the next page in paragraph 00091, the specification clarifies the starting material for generating the optimized protein was the human codon-optimized Cpf1 sequence described by Zetsche in 2015 (Specification, page 38, 00091).
Therefore, claim 1 is drawn to a sequence having at least 99% sequence identity to a CPF1 protein which was optimized for expression in soybean plants through the use of a codon frequency table.
With respect to claim 1, Zetsche teaches FnCPF1 (Zetsche, Page 760, Figure 1). Zetsche teaches that the FnCPF1 protein was optimized for optimal expression and nuclear targeting in human cells (Zetsche, Page 764, Column 1, Last Paragraph). Zetsche also teaches human codon optimized FnCpf1 sequences in the supplemental information (Zetsche Supplemental Information, Page 1). Finally,
With respect to claim 1, Zetsche does not teach a codon optimized FnCPF1 protein for expression and targeting in soybean.
With respect to claim 1, Endo teaches FnCPF1 (Endo, Page 1, Abstract). Endo teaches that the FnCPF1 protein was optimized for effective translation in A. thaliana and rice (Endo, Page 2, Penultimate Paragraph). Further, Endo teaches that the codon-optimized FnCpf1 was placed under the control of the ubiquitin promoter from maize (Endo, Page 2, Penultimate Paragraph) and used to induce targeted mutations in the phytoene desaturase and STENOFOLIA genes in Nicotiana tabacum (Endo, Page 2, Last Paragraph- Page 3, Third Paragraph) and OsDrooping leaf and OsAcetolactone synthase in rice (Endo, Page 3, First Paragraph-Page 4, Last Paragraph).
With respect to claim 1, Hudson teaches molecular optimization of synthetic genes for expression in soybean plants by eliminating the use of low frequency codons and replacing them with preferred codons (Hudson, Page 21, Second Paragraph – Page 22, Second Paragraph). Further, Hudson provides an example of a codon bias table for soybean seeds which was produced by analyzing the codons in a selection of soybean proteins (Hudson, Page 22, Figure 1).
Given the teachings of Zetsche and Endo, which describe codon optimization of FnCpf1 genes for expression in three different organisms and the teachings of Hudson which are drawn to codon optimization of sequences for translation in soybean plants, it would have been obvious to use the codon optimization techniques in order to codon optimize the FnCpf1 sequence of Zetsche for translation in plants as taught by Endo and specifically to use the methods of Hudson in order to optimize the sequences for translation in soybean plants. This would have been obvious because it is combining prior art elements according to known methods to yield predictable results.
This is the case because FnCpf1 proteins are a known prior art element, plant optimized FnCpf1 sequences are a known prior art element and codon optimization of exogenous polypeptides for expression in soybean plants is another known prior art element. In the description of codon optimization for soybean expression, Hudson describes a known method of codon optimization which is highly predictable and Endo provides evidence for the predictability of optimizing FnCpf1 sequences for translation in plant cells. Given these teachings there would be a high level of predictability in combining the teachings of Zetsche, Endo and Hudson to produce a FnCPF1 protein that was codon optimized for soybean.
Therefore all soybean codon optimized FnCPF1 genes including those having at least 99% sequence identity to instant SEQ ID NO: 47 are obvious.
The ordinary artisan would have been motivated to combine these teachings because it would allow for a FnCPF1 protein which was expressed more highly and was therefore more efficient at editing the genome of soybeans. This would have been motivating because of the agronomic and economic significance of soybean and therefore more efficiently editing the genes in this plant to produce higher quality plants would have been motivating.
As such claim 1 is rejected as obvious under Zetsche in view of Endo and Hudson.
With respect to claim 2, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 1, see above.
Further, Zetsche teaches that the codon optimized FnCPF1 proteins were fused to a nuclear localization signal (Zetsche, Page 764, Column 1, Last Paragraph).
With respect to claim 7, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 1, see above.
Further, Hudson teaches soybean cells comprising a heterologous codon optimized protein as well as the specific subcellular localization of those proteins (Hudson, Page 24, First Paragraph).
With respect to claim 15, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 1, see above.
Further, Zetsche teaches cells comprising the FnCPF1 protein and a guide RNA which comprises a crRNA and a spacer (Zetsche, Page 764, Paragraph spanning Columns 1-2; Zetsche, Page 759, Paragraph Spanning Columns 1-2).
With respect to claim 17, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 1 including the use of codon optimized FnCpf1 and a gRNA to edit target genes in rice and Arabidopsis thaliana plant cells, see above.
With respect to claim 21, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 17 taught above, see above.
Further, Hudson teaches codon optimization and transformation of soybean plants (Hudson, Pages 21-23, Section 3; Hudson, Page 30, Second to Last Paragraph).
With respect to claim 22, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 17, see above.
Further, Zetsche discloses designing DNA inserts which would be able to integrate into the target site in the correct orientation due to the sticky ends produced by the Cpf1 enzyme’s mechanism of action (Zetsche, Page 765, Column 2).
With respect to claim 23, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 22 taught above, see above.
With respect to claim 24, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 1, see above.
With respect to claim 28, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 24 taught above, see above.
Further, Hudson teaches codon optimization and transformation of soybean plants (Hudson, Pages 21-23, Section 3; Hudson, Page 30, Second to Last Paragraph).
With respect to claim 29, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 24 taught above, see above.
Further, Zetsche discloses designing DNA inserts which would be able to integrate into the target site in the correct orientation due to the sticky ends produced by the Cpf1 enzyme’s mechanism of action (Zetsche, Page 765, Column 2).
With respect to claim 30, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 29 taught above, see above.
With respect to claim 31, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 1, see above.
With respect to claim 33, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 31 taught above, see above.
With respect to claims 2, 7, 15, 17, 21-24, 28-31 and 33, Zetsche Endo and Hudson do not explicitly teach transforming cells with donor DNA, identifying cells comprising the donor DNA or creating kits for modifying a target sequence.
At the time of filing it would have been obvious to the ordinary artisan to modify the recombinant nucleic acids and methods of Zetsche in view of Endo and Hudson to include a donor DNA which was transformed into the target cell, to check transformed cells for integrated donor DNA and to package the gene editing system into a kit.
This would have been obvious to because Zetsche teaches designing donor DNA which Zetsche calls “DNA inserts” and teaches the benefits of the use of the Cpf1 nuclease when integrating “DNA inserts” into a target site. Given this teaching it would have been obvious to the ordinary artisan to transform target cells with the DNA for the “DNA insert” and further given that the goal is to insert this DNA into a target site it would have been obvious to check transformed cells for the presence of this donor in the genomic DNA.
The ordinary artisan would have been motivated to make this modification in order to take advantage of the sticky ends left in genomic target sites after cleavage with Cpf1 enzymes which allow for predictable orientation of donor DNA. This facilitates the efficient integration of a specific sequence which could be a gene, a marker or any other modification into the target genome rather than an unspecific edit at a target site as occurs during gene editing approaches that do not use a donor DNA template to make a DNA insert.
With respect to creating a kit comprising the genome editing components, this would have been obvious because Zetsche in view of Endo and Hudson teach the codon optimized Cpf1 enzyme and a guide RNA which complements a target site. These are the only components required by the kit and as such it would have been obvious to the ordinary artisan at the time of filing upon viewing the teachings of Zetsche to group these two components together to make a kit. The motivation for this would be the easy access, storage and organization gained by grouping these two elements together.
As such claims 2, 7, 15, 17, 21-24, 28-31 and 33 are rejected as obvious over Zetsche in view of Endo and Hudson.
Claims 4, 18 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Zetsche in view of -----Endo, Hudson and Geldner, The Plant Journal 59.1 (2009): 169-178.
Claims 4, 18 and 25 are drawn to recombinant nucleic acids and methods of their use where the recombinant nucleic acids are linked to a promoter having a sequence of SEQ ID NO: 7, 22, 27 are 32. The specification provides clarity, stating that these sequences are ubiquitin promoters (Specification, Page 25, Paragraph 00084; Specification, Page 32, Paragraph 00075; Specification, Page 32, Paragraph 00077; Specification, Page 32, Paragraph 0078).
With respect to claim 4, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 2, see above.
With respect to claim 18, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 18, see above.
With respect to claim 25, Zetsche in view of Endo and Hudson collectively teach all of the limitations of claim 25, see above.
With respect to claims 4, 18 and 25, Zetsche, Endo and Hudson do not explicitly teach the use of a ubiquitin promoter including those of SEQ ID NOs: 7, 22, 27 and 32.
With respect to claims 4, 18 and 25, Geldner teaches constructs for the transformation into any genetic background or species of plants that allow for optimal levels of expression of genes of interest that avoid the silencing common with the use of other promoters that cause intolerable levels of overexpression in plants (Geldner, Page 169, Abstract; Geldner, Page 169, Column 2, Only Paragraph- Page 170, Column 1, First Paragraph). Importantly Geldner teaches the use of the Arabidopsis thaliana ubiquitin promoter (UBQ10) which leads to ubiquitous expression at moderate levels which minimizes overexpression artifacts and avoids numerous problems associated with the widely used viral 35S promoter (Geldner, Page 170, Column 1, First Complete Paragraph; Geldner, Supplemental Figure 1). The alignment provided in Figure 1 below shows that the desirable UBQ10 promoter taught by Geldner is 100% identical to the sequence of instant SEQ ID NO: 32.
PNG
media_image1.png
1010
698
media_image1.png
Greyscale
Figure 1: Alignment between the cloning vector pNIGEL13 of Geldner and the sequence of Instant SEQ ID NO: 32.
At the time of filing it would have been obvious to use the ubiquitin promoter of Geldner to drive expression of the codon optimized Cpf1 gene of Zetsche in view of Endo and Hudson. This would have been obvious because the Cpf1 gene of Zetsche in view of Endo and Hudson encodes a gene editing protein optimized for editing plants and driving ubiquitous expression at moderate levels which minimizes overexpression artifacts and avoids numerous problems associated with the widely used viral 35S promoter or other constitutive promoters would allow for efficient editing of the target nucleic acids in plants and Geldner teaches a promoter having those characteristics.
The motivation to combine these elements is that optimal expression of the gene editing protein leads to greater occurrence of edits and allows for the more efficient identification and isolation of plants comprising the specific targeted modification. Therefore, the ordinary artisan upon seeing the teachings of the references would have found it obvious and motivating to use the ubiquitin promoter of Geldner to drive optimal expression of the protein of Zetsche in view of Endo and Hudson in transgenic plants in order to efficiently edit those plants.
Therefore, claims 4, 18 and 25 are rejected as obvious under Zetsche in view of Endo, Hudson and Geldner.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Zetsche, in view of Endo, -----Hudson and Rech, Nature protocols 3.3 (2008): 410-418.
With respect to claim 16, Zetsche in view of Hudson collectively teach all of the limitations of claim 15, see above.
With respect to claim 16, Zetsche, Endo and Hudson do not explicitly teach the composition on a particle suitable for biolistic delivery to a plant cell.
With respect to claim 16, Rech teaches that biolistics allows for the high-frequency recovery of transgenic soybean plants through the use of microparticle-coated DNA bombardment of apical meristems and in vitro culture and selection of transgenic plants (Rech, Page 410, Abstract).
At the time of filing it would have been obvious to combine the soybean codon optimized Cpf1 and guide RNA composition of Zetsche in view of Endo and Hudson with the biolistics delivery system of Rech in order to produce transgenic gene-edited soybean plants at high-frequency. This would have been obvious because the composition of Zetsche in view of Endo and Hudson is used by transformation into target soybean cells and Rech teaches an efficient and highly successful method for the transformation of soybean cells.
The ordinary artisan would have been motivated to combine these methods in order to use the efficient gene editing capability of the Cpf1 enzyme of Zetsche in view of Endo and Hudson by transforming this composition into soybean cells using the highly successful method of Rech.
As such claim 16 is rejected as obvious under Zetsche in view of Endo, Hudson and Rech.
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN JAMES SULLIVAN whose telephone number is (571)272-0561. The examiner can normally be reached on 7:30 to 5:00.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached on (571)270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see https://ppair-my.uspto.gov/pair/PrivatePair. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/BRIAN JAMES SULLIVAN/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
Prosecution Insights