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
Election/Restriction
1. Applicant’s election without traverse of Group I (claims 1-14) in the reply filed on August 15, 2025 is acknowledged.
Claims 1-29 are pending. Claims 15-29 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions, there being no allowable generic or linking claim.
Accordingly, Claims 1-14 are examined on merits in this Office action. This restriction is made FINAL.
Applicant is reminded that upon the cancellation of claims to a non-elected invention, the inventorship must be amended in compliance with 37 CFR 1.48(b) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. Any amendment of inventorship must be accompanied by a request under 37 CFR 1.48(b) and by the fee required under 37 CFR 1.17(i).
Information Disclosure Statement
2. Initialed and dated copy of Applicant’s IDS form 1449 filed in the papers of 10/09/2024 is attached to the instant Office action. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
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.
3. Claims 1-14 are rejected under 35 U.S.C. 112, first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor(s), at the time the application was filed, had possession of the claimed invention.
The Federal Circuit has recently clarified the application of the written description requirement. The court stated that a written description of an invention "requires a precise definition, such as by structure, formula, [or] chemical name, of the claimed subject matter sufficient to distinguish it from other materials." University of California v. Eli Lilly and Co., 119 F.3d 1559, 1568; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997). The court also concluded that "naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not a description of that material." Id. Further, the court held that to adequately describe a claimed genus, Patent Owner must describe a representative number of the species of the claimed genus, and that one of skill in the art should be able to "visualize or recognize the identity of the members of the genus." Id.
Finally, the court held:
A description of a genus of cDNAs may be achieved by means of a recitation of a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus. Id.
See also MPEP Section 2163, page 174 of Chapter 2100 of the August 2005 version, column 1, bottom paragraph, where it is taught that
[T]he claimed invention as a whole may not be adequately described where an invention is described solely in terms of a method of its making coupled with its function and there is no described or art-recognized correlation or relationship between the structure of the invention and its function. A biomolecule sequence described only by a functional characteristic, without any known or disclosed correlation between that function and the structure of the sequence, normally is not a sufficient identifying characteristic for written description purposes, even when accompanied by a method of obtaining the claimed sequence.
See also Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ 2d 1016 at 1021, (Fed. Cir. 1991) where it is taught that a gene is not reduced to practice until the inventor can define it by "its physical or chemical properties" (e.g. a DNA sequence).
Claims are broadly drawn to a method of genome editing in an explant, comprising: obtaining a seed of a bridge transgenic plant having a stably integrated Cas expression cassette containing a nucleic acid encoding a Cas protein or a bridge intermediate plant; treating the seed to obtain a germinated seed, wherein the germinated seed contains a viable epicotyl and the Cas protein is expressed in the epicotyl; and carrying out genome editing in the germinated seed, or the method further comprising:
prior to the genome editing step, cutting the germinated seed to produce a seed section in which a portion of shoot apical meristem is exposed or proximate to an exposed surface of the seed section; and
applying a genome editing reagent directly in vivo to the portion of shoot apical meristem or the exposed surface of the seed section under conditions allowing delivery of the genome editing reagent into a cell of the shoot apical meristem, wherein the cell expresses the Cas protein, whereby genome editing occurs in the cell to produce at least one genomic edit, or wherein the bridge transgenic plant or the bridge intermediate plant is a monocotyledonous, dicotyledonous, monoploid, diploid, triploid, or polyploid plant, or wherein the seed section is produced by cutting the germinated seed longitudinally, or wherein the seed section is produced by isolating a section of the germinated seed containing the shoot apical meristem, or wherein the genome editing reagent includes a guide RNA (gRNA), or wherein the genome editing reagent contains two or more gRNAs for making at least two different genome edits, whereby genome editing of at least two loci occurs in the cell of the shoot apical meristem, and wherein at least one of the genome edits confers a selective advantage under a selective agent or condition, or wherein the selective advantage is resistance or tolerance to a condition or toxic agent, or wherein the method, further comprising applying the selective agent or condition to the seed section before, after or at the same time that the genome editing reagent is applied, whereby conferring the selective advantage to the cell containing the at least two genome edits, or wherein the applying step includes substantially covering the portion of shoot apical meristem or the exposed surface with a composition containing the genome editing reagent, or wherein the method further comprising subjecting the seed section to (i) vacuum filtration or (ii) microprojectile bombardment, or wherein the method further comprising subjecting the seed section to one or both of a cold pretreatment and osmotic pretreatment prior to or at the same time with the applying step, or wherein the genome editing reagent includes a vector or delivery vehicle carrying a nucleic acid, or wherein the vector is a viral vector or the delivery vehicle is a carbon nanotube.
Claims 1, 2 and claims dependent thereon are directed to any nucleic acid from any source encoding any Cas protein from any source whose expression in combination with any gRNA in any plant results in genome editing in said plant or seed thereof.
Claims 6, 7 and claims dependent thereon are directed to any gRNA from any source whose expression in combination with any Cas protein in any plant results in genome editing in said plant or seed thereof.
The breadth of the claims encompasses a very large genus comprising species with unknown and uncharacterized structures and having the function of altering expression of any gene product in a CRISPR-Cas system guide RNA as instantly claimed.
Thus breadth of the claims encompass a large genus comprising unspecified structures with undescribed, unpredictable and unknown function(s).
The instant specification however, only describes making independent transgenic lines of Sorghum bicolor expressing Cas9 nuclease protein and GFP marker protein. This transgenic plant was subsequently delivered with gRNA as set forth in SEQ ID NOs 1, 2 or 3 to target nucleic acid encoding GFP marker protein. The on-target score varied from 70 (SEQ ID NO: 1), 100 (SEQ ID NO: 2) and 85 (SEQ ID NO: 3. The single-walled carbon nanotubes were used for said delivery. GFP expression analysis by monitoring florescence levels indicated successful targeting of the desired nucleic acid sequence encoding GFP protein. See for example, Examples 1-4 at pages 16-27.
The specification does not describe the structure for representative members of Applicant’s broadly claimed genus comprising variants derived from diverse sources as encompassed by the breadth of claims and thus function of disrupting g (altering) expression of any gene product as encompassed by the breadth and scope of claims is either unknown or unpredictable.
The species (Cas 9, SEQ ID NOs: 1- (targeted to GFP) and SEQ ID NOs: 4-8 (targeted to bmr6 gene)) described in the specification are insufficient to describe the claimed genus as encompassed by the breadth and scope of claims.
There is no description of the structure required for the recited function, and no description of the necessary and sufficient elements of a of altering expression of any gene product in a CRISPR-Cas system guide RNA as instantly claimed. The only species described are Cas 9, SEQ ID NOs: 1- (targeted to GFP) and SEQ ID NOs: 4-8 (targeted to bmr6 gene).
One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the genus in view of the disclosed species. Since the disclosure fails to describe the common attributes that identify members of the genus, and because the genus is highly variant, instantly described species (e.g. Cas 9, SEQ ID NOs: 1- (targeted to GFP) and SEQ ID NOs: 4-8 (targeted to bmr6 gene)) are insufficient to describe the claimed genus.
Accordingly, there is lack of adequate description to inform a skilled artisan that applicant was in possession of the claimed invention at the time of filing. See Written Description guidelines published in Federal Register/Vol.66, No. 4/Friday, January 5, 2001/Notices; p. 1099-1111.
Given the claim breadth and lack of guidance as discussed above, the specification does not provide written description of the genus broadly claimed. Accordingly, one skilled in the art would not have recognized Applicants to have been in possession of the claimed invention at the time of filing.
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.
4. Claim(s) 1-6, 10 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Martin-Ortigosa et al. (WIPO, WO 2016/184989 A1, Published November 24, 2016, IDS).
Martin-Ortigosa et al. teach a method of genome editing in an plant explant and subsequently obtaining a transgenic plant, wherein the method comprises a plant transformation vector using CRISPR/Cas9 based system in targeting an endogenous plant gene to suppress or eliminate its expression in plant cells and transformed plants obtained thereof. The method comprised non-naturally occurring CRISPR/Cas9 based gene editing system incorporated into a plant transformation vector. The transformed plant cells present within transformed plant expressed a DNA molecule having a target sequence and encoding gene of interest. The reference further teach that Cas9 protein expresses in the transformed plant. The reference discloses targeting shoot meristems in plant explants. The reference teach that after approximately 4 days the apical shoot apices were excised from distal part of the first internode of the epicotyl and coleoptile was removed. The reference further discloses that once the meristem was exposed the in planta (in vivo) delivery methods like particle bombardment, microinjection were used deliver gRNA sequences within the cells of transformed plant expressing CRISPR/Cas9 protein. The reference further teaches that the transgenic plant is a monocotyledonous or dicotyledonous plant species.
It may be noted that the reference teaches through several examples in many economically important plant crop species, methods of genome editing which also includes altering expression of at least one gene product comprising transforming plant with a plant transformation vector using CRISPR/Cas9 based system in targeting an endogenous plant gene to suppress or eliminate its expression in plant cells and transformed plants obtained thereof. The method comprised non-naturally occurring CRISPR/Cas9 based gene editing system incorporated into a plant transformation vector. The transformed plant cells present within transformed plant expressed a DNA molecule having a target sequence and encoding gene of interest. The reference further discloses that said method comprising: (a) a first regulatory element (promoter) operable in a plant cell and operably linked to at least one nucleotide sequence encoding a CRISPR-Cas system guide RNA (gRNA) that hybridizes with the target sequence, and (b) a second regulatory element operable in a plant cell and operably linked to a nucleotide sequence encoding a Type-ll CRISPR- associated nuclease (Cas9), wherein components (a) and (b) were located on same plant transformation vector of the system or on different plant transformation vector delivery system. For example, a transgenic plant expressing Cas9 protein is further transformed in vivo (in planta) with genome editing agent gRNA that was previously designed to specifically target endogenous plant gene of interest. The reference further teaches that the guide RNA targeted the target sequence and the CRISPR-associated nuclease (Cas9) cleaved the DNA molecule, and whereby expression of the gene product is altered, resulting to expected phenotype to the transformed plant. The reference further teaches that the CRISPR- associated nuclease and the guide RNA do not naturally occur together. The reference further disclose that nucleotide encoding said guide RNA and nucleotide sequence encoding said CRISPR-associated nuclease are also operably linked to a terminator at 3’ end to terminate transcription. The reference also teaches using cold pretreatment to meristem tissues prior to treating with said editing solution using said particle bombardment or other in vivo or in planta delivery systems. See in particular, examples 1-13 at pages 45-75, including plant transformation and in vivo/planta delivery methods of editing agent gRNAs, Figures 1-7.
Martin-Ortigosa et al. do not specifically teach bridge transgenic plant/bridge intermediate transgenic, or germinating seeds expressing Cas protein and using explants derived from said germinated seed to do genome editing using gRNA.
Martin-Ortigosa et al. teaches (i) in planta application of editing reagents comprising gRNAs targeting endogenous plant genes, (ii) delivery into the shoot apical meristem, and (iii) either transformation with a construct expressing Cas9 or co-application of Cas9 and gRNAs. Accordingly, it would have been obvious to one of ordinary skill in the art, prior to the earliest filing date, to first generate a stable transgenic plant expressing Cas9 and then apply gRNAs in planta to achieve desired genome editing. A skilled artisan would have been motivated to adopt this “bridge” Cas9 transgenic plant approach because it enables efficient editing of multiple endogenous genes with different gRNAs, thereby conserving time and resources, with a reasonable expectation of success. Further, use of any plant tissue, including seeds germinated into Cas9-expressing seedlings, would have been a matter of routine design choice. Routine assays of seed viability and Cas9 expression, such as dissecting germinated seeds while preserving the apical meristem, would also have been standard practice.
Thus, the claimed invention as a whole is prima facie obvious teachings of the prior art.
5. Claim(s) 1-13 are rejected under 35 U.S.C. 103 as being unpatentable over Martin-Ortigosa et al. (WIPO, WO 2016/184989 A1, Published November 24, 2016), and further in view of Zhu et al. (Molecular Cell Biology, 21:661-677, Published 2020).
Martin-Ortigosa et al. teachings are discussed as supra.
Martin-Ortigosa et al. do not teach one of genome edits confers a selective advantage under a selective agent or condition.
Zhu et al. teach using CRISP-Cas/gRNA based approach in editing herbicide-targeted genes to confer endogenous resistance to a plant. The reference further teaches that introduction of a particular base mutation into endogenous plant ALS (Acetolactate synthase) gene with the use of CBEs (cytosine based editing) conferred herbicide (selective agent) resistance to plants while retaining ALS activity. Zhou et al. cites several examples (e.g. Huang et al. (Mol. Plant 13,565-572, 2020); Sun et al. (Mol. Plant 9, 628-631, 2016)) were herbicide resistance was achieved using similar approach. See in particular, 2nd paragraph at page 666, abstract at page 661; Figures 1-5; Table 1).
Given Zhu et al., teach using gene editing approach to produce herbicide-resistant (a selective agent) by targeting plant’s endogenous gene (ALS), it would have been obvious and within the scope of an ordinary skill in the art prior to earliest filing date of the claimed invention to have edited any endogenous plant gene to confer resistance to any selective agent, including herbicide resistance to the plant. It would have been obvious to modify Martin-Ortigosa et al. method of genome editing as discussed above to incorporate multiple gRNAs in editing solution, including the one that can target endogenous plant gene to confer resistance to a selective agent, such as herbicide resistance and thus arrive at the Applicant’s claimed invention with a reasonable expectation of success and without any surprising results. Obviously, one of skilled in the art would have been motivated to do so by incorporating multiple useful traits to a plant genetically engineered using a precise CRISPR/cas9 gRNA based approach as discussed above.
Thus, the claimed invention as a whole is prima facie obvious teachings of the prior art.
6. Claim(s) 1-14 are rejected under 35 U.S.C. 103 as being unpatentable over Martin-Ortigosa et al. (WIPO, WO 2016/184989 A1, Published November 24, 2016), in view of Zhu et al. (Molecular Cell Biology, 21:661-677, Published 2020) and further in view of Yin et al. (Sci Rep., 5:1038/srep14926, pp 1-10, 2015).
Martin-Ortigosa et al. teachings are discussed as supra.
Zhu et al. teachings are discussed as supra.
Neither Martin-Ortigosa et al. nor Zhu et al. teach using viral vector based method of delivering genome editing reagent comprising gRNA.
Yin et al. explicitly recognize the difficulty of transforming certain plant species and identify the desirability of improved transformation techniques. Specifically, Yin et al. (page 7, last five lines of the Discussion section) state:
“As we know, many non-model plants and some model crop plants (such as maize, cotton) are difficult to transform, which hinders their reverse genetic study. With the advancement of sequencing and reduction in cost, more and more genomes of non-model plants will be uncovered quickly. Together, VIGE approach is a promising method to enable efficient genome engineering for many plants.”
It would have been obvious to one of ordinary skill in the art, prior to the earliest effective filing date of the claimed invention, to employ any efficient nucleic acid delivery method into intact plant material, including the viral vector based method taught by Yin et al., as a matter of design choice. One of ordinary skill in the art would have had a reasonable expectation of success in doing so, and the record does not demonstrate that the claimed invention yields any unexpected or surprising results.
This disclosure would have motivated a person of ordinary skill in the art to utilize efficient nucleic acid delivery methods, such as those recited in the present claims, to enable genome engineering in a variety of plants. The combination of Yin et al. with routine skill in the art therefore renders the claimed subject matter obvious.
Furthermore, as explained in Ex parte Smith, slip op. at 20 (B.P.A.I. June 25, 2007), citing KSR Int’l Co. v. Teleflex Inc., 82 USPQ2d 1385, 1396 (2007), a finding of obviousness does not require an express teaching, suggestion, or motivation in the prior art. Rather, if a claimed invention represents no more than the predictable use of prior art elements according to their established functions, the invention is unpatentable as obvious. Here, the application of known nucleic acid delivery methods to intact plant materials represents such a predictable use.
Thus, the claimed invention as a whole is prima facie obvious teachings of the prior art.
7. Claim(s) 1-14 are rejected under 35 U.S.C. 103 as being unpatentable over Martin-Ortigosa et al. (WIPO, WO 2016/184989 A1, Published November 24, 2016), in view of Zhu et al. (Molecular Cell Biology, 21:661-677, Published 2020) and further in view of Alghuthaymi et al. (Int. J Mol Sci., 22(14),7456, pages 1-22, July 2021).
Martin-Ortigosa et al. teachings are discussed as supra.
Zhu et al. teachings are discussed as supra.
Neither Martin-Ortigosa et al. nor Zhu et al. teach using carbon nanotube based method of delivering genome editing reagent comprising gRNA.
Alghuthaymi et al. teach a carbon nanotube based delivery system for CRISPR/Cas9 mediated plant genome editing. The reference clearly demonstrates a carbon nanotube based guide RNA (gRNA) delivery system for CRISPR/Cas9 mediated plant genome editing that can be used to precisely target genome locations and cause mutations. See in particular, abstract, Figures 1-3; Tables 1-2, items 1-10 at pages 1-22.
It would have been obvious to a person of ordinary skill in the art, prior to the earliest effective filing date of the claimed invention, to employ any efficient nucleic acid delivery method into intact plant material, including that taught by Alghuthaymi et al., as a matter of routine design choice. Such a person would have had a reasonable expectation of success in doing so, without encountering any unexpected or surprising results. Moreover, one of ordinary skill in the art would have been motivated to adopt this approach because organic carbon nanotubes possess advantageous properties—including size, charge, stability, and low toxicity relative to other delivery systems—as disclosed by Alghuthaymi et al.
The Federal Circuit and the Board have clarified that a specific teaching, suggestion, or motivation is not required to establish obviousness. See Ex parte Smith, – USPQ2d –, slip op. at 20 (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR Int’l Co. v. Teleflex Inc., 82 USPQ2d 1385, 1396 (2007)). Consistent with KSR, the claimed invention would have been no more than the predictable use of prior art elements according to their established functions.
Thus, the claimed invention as a whole is prima facie obvious teachings of the prior art.
Conclusions
8. Claims 1-14 are rejected.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Vinod Kumar whose telephone number is (571) 272-4445. The examiner can normally be reached on 8.30 a.m. to 5.00 p.m.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad A. 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 http://pair-direct.uspto.gov. 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).
/VINOD KUMAR/Primary Examiner, Art Unit 1663