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 .
Status of the Claims
Amended claims, 1-23, were filed on 3/6/2023 and are under examination in this Office action.
Information Disclosure Statement
The information disclosure statements (IDS’s) submitted on 4/3/2023 and 6/2/2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Drawings
The drawings, filed 12/13/2022, are accepted.
Specification
The disclosure is objected to because of the following informalities:
The use of the term Flp-in™, and Lipofectamine™ which are trade names or marks used in commerce, have been noted in this application, at least on Pg 60 and 61. The terms should be accompanied by the generic terminology; furthermore the term 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.
Appropriate correction is required.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim interpretation
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art.
Regarding “stable” transformation, the term ‘stable’ is found in the specification (on Pg 44, line 11) to reference transformation or transfection that is not transient but is nucleic acid sequence introduced into a host cell of interest and subsequently integrated into the host’s genome by means of stable transformation/transfection (not transient transformation, lacking stable integration/inheritance of introduction).
“Substantially the same” is referenced on Pg 47 (line 29+) in regard to efficiency and/or activity of an editing system, referring to a quantitative measure of activity (e.g. a number of indels (e.g. an indel percentage) and/or a number of base edits) in one cell (e.g. a mammalian cell) that is within about ±10% of the amount of the same editing activity in a different cell (e.g. a plant cell). Pg. 55 recited, in some embodiments, the modification in the plant cell is the same as the modification in the transgenic cell and/or the editing efficiency for the editing system in the plant cell is substantially the same as (e.g. within about ±10%) of the editing efficiency of the same editing system in the transgenic cell.
Thus, here “substantially the same” will be considered to reference the value of interest plus or minus 10% as well as a few additional percentage points (e.g. 1-3%).
The term use, in reference to ranking editing systems, this refers to a difference in order or rank for 20% or less of the editing systems (Pg 48, line 28+).
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 8 and 16 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 8 is indefinite in the recitation of ”a desired modification. “Desired” is a relative term. As used in this claim, two individuals of ordinary skill may have different opinions on what “a desired modification” is, to which the modification in the plant is compared.
The specification provides no explicit definitions section, or definition that clarifies, with the closest statement addressing “a modification in a plant polynucleotide in a transgenic cell that is compared to a desired modification (e.g. a modification the editing system is configured to make optionally given the plant polynucleotide sequence).” There is also reference to the subjective “desired edited alleles” and “desired edit” and “desired editing outcome” (Pg 60).
Claim 16 is indefinite over the recitation of “The method of claim 15, further comprising comparing the first sequence to the sequence of the plant polynucleotide prior to contacting the plant polynucleotide in the transgenic cell with the editing system.
Claim 15 states, The method of claim 1 further comprising, after contacting the plant polynucleotide in the transgenic cell with the editing system, sequencing the plant polynucleotide to obtain a first sequence.
The chronology of events in claim 16, can be confusing, in-part because claim 16 depends from claim 15, which is: The method of claim 1, further comprising “after contacting the plant polynucleotide in the transgenic cell with the editing system…” but claim 16 says prior to contacting the plant polynucleotide…
The phraseology of claim 16 can be interpreted as saying that sequences will be compared before taking the action of contacting the plant polynucleotide with the editing system. However, the true meaning may differ from this.
The intent may be to state that the first sequence and the plant polynucleotide sequence will be compared, and this comparison will involve “the first sequence” which is the plant polynucleotide after contact with the editing system, with the plant polynucleotide (of claim 1 that was introduced into a mammalian cell, so perhaps this is sequenced prior to being part of a transgenic cell), and this “latter” sequence not has not been edited because this sequence is the original plant polynucleotide.
Or, the meaning may be something different entirely, so further clarification is warranted.
Claim 16 recites the limitation "the sequence” (of the plant polynucleotide) in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 112(a)
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 1-23 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the method of transfecting a plant polynucleotide comprising a portion of the corn gene Glossy2, or the corn gene CenH3, or the blackberry SEEDSTICK gene, into a mammalian cell line (HEK293 cells) to provide transgenic cells using “a CRISPR-Cas system” or CRISPR-Cas12a, does not reasonably provide enablement for using any means of introduction or by transfecting any plant polynucleotide into a mammalian cell line. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims. Notably, this is a scope of enablement rejection.
To address whether sufficient evidence supports the determination that the disclosure does not satisfy the enablement requirement and whether undue experimentation might be needed, the below factors are considered:
In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
Nature of the Invention:
The claims are directed to a method of evaluating an editing system. The claims require introducing a plant polynucleotide into a mammalian cells. Accordingly, enablement of the claims requires that one of ordinary skill in the art be able to introduce plant polynucleotides into mammalian cells to provide a transgenic cell commensurate with the full scope of the claims without undue experimentation.
Breadth of the claims:
The claims broadly recite "introducing", which is not limited to any particular method of introduction. This phrase broadly encompasses any and all possible means of introducing the plant polynucleotide into the mammalian cell. The claims further recite "plant polynucleotide", which broadly encompasses any plant polynucleotide, which is a massive genus of possible plant polynucleotides, including plants of all ploidy levels.
Teachings of the Specification:
The specification only teaches two methods of transfection for introduction of plant polynucleotides into mammalian cells and in the first example (Example 1), the CRISPR-Cas system used with it, is not identified (Example 1, by use of Flp recombinase, Flp-in293 cells with an FRT site, and using Lipofectamine to introduce a “CRISPR-Cas” (a generalized term) construct with varied spacers). The second teaching is found in Example 4, SEEDSTICK in model cell line with plasmids expressing Cas12a and a cRNA with spacer. The specification does not describe any other means for introducing plant polynucleotides into mammalian cells. The specification further only teaches introducing “a portion” of three plant genes, namely Glossy2, CenH3 and SEEDSTICK, into mammalian cells. There are no other working examples in which a plant gene was successfully introduced into a mammalian cell.
State of the Art:
The state of the art was such that introducing plant polynucleotides into mammalian cells was highly unpredictable. Wada (Wada et al. (2017) ACS Synthetic Biology, 6:301-310) teaches that interkingdom fusions between human cells and tobacco hybrid protoplasts were not viable beyond 6 days and that several more attempts to make fusion cells between human and plant cells have not been successful (see page 301, column 2). Similarly, Liu (Liu et al. (2021) Scientific Reports, 11:7160, pages 1-13) teaches attempting to study a fusion of plant genetic material in human cells and determined that "Most of the introgressed Arabidopsis DNA was eliminated during the culture" (abstract). Liu reiterates that cell fusion often induces chromosomal instability (page 1, paragraph 2). These teachings indicate that the breadth of the claims which broadly encompass introduction of the plant polynucleotide by cell fusion is not well understood and would have been highly unpredictable. These teachings further indicate that the breadth of the plant polynucleotide that would have been capable of being introduced into the mammalian cell is also highly unpredictable given the instability of the plant polynucleotides in mammalian cells as demonstrated by Wada and Liu.
The level of one of ordinary skill:
Artisans in biotechnology are generally considered highly-skilled and hold a relevant PhD, where the courts have considered this person at least a junior faculty member with one or two years of relevant experience or a postdoctoral student with several years of experience Enzo Biochem, Inc. v. Calgene, Inc., 188 F.3d 1362, 1373 (Fed. Cir. 1999) (citing Enzo Biochem, Inc. v. Calgene, Inc., 14 F. Supp. 2d 536, 567 (D. Del 1998)).
Amount of Experimentation:
Given the limited number of teachings provided by the specification and the unpredictability in the art, substantive experimentation would be necessary in order to practice the full scope of the claimed invention. It would have been necessary to test many different plant polynucleotides and to have attempted to introduce these plant polynucleotides into mammalian cells by numerous different means, including, for example, cell fusion. However, given the teachings of the art of Wada and Liu showing the difficulties associated with such introduction, such experimentation would have been highly unpredictable. Accordingly, this would have amounted to an extremely large amount of unpredictable experimentation.
In conclusion, the factors weigh strongly against patentability of the scope of claims, as presented.
Claims 22 and 23 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 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 or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
Nature of the Invention: Broad.
Claim 1 recites a method of evaluating an editing system, where a plant polynucleotide is introduced into a mammalian cell to provide a transgenic cell that is contacted with an editing system. This broad claim encompasses the Genus comprised of any/all editing systems, without limitation. Claims 22 and 23 ultimately depend from claim 1.
Claim 22, the method of claim 18, introduces the any editing system of claim 1 into a plant cell, wherein the modification in the plant cell is the same as the modification in the transgenic cell and/or wherein the editing efficiency for the editing system in the plant cell is substantially the same in the transgenic cell.
Claim 22 therefore requires possession of a specific editing system that meets the functional limitation of having substantially the same editing efficiency for mammalian cells and plant cells. It is therefore expected that the instant application will provide substantive disclosure of a method where any editing system can be used and demonstrates editing efficiency that is substantially the same when the editing system is used in mammalian or plant cells.
Claim 23 introduces the any editing system of claim 1 into a plant cell, wherein the editing system has the functional limitation of an editing efficiency of 80% or more in plant cells.
It is therefore expected that a method employing an editing system, where the editing efficiency is ≥80% when editing plant cells, will be sufficiently described.
State of Art: Currently challenging with unpredictability in editing efficiency.
Zhang (Zhang Y et al, CRISPR ribonucleoprotein-mediated genetic engineering in plants, March 2021, Plant Comms 2, 1-13) disclosed that editing efficiency in plants highly dependent upon expression cassette design and its genomic insertion site (Abstract), and further while CRISPR ribonucleoprotein (RNP) mediated genetic engineering is attractive, even its editing efficiency is only modest, and its application in many plant species is limited by difficulties in plant regeneration and selection (Abstract). Plasmid-based CRISPR editing requires efficient species-specific editing systems with optimal promotors, terminators and codon optimization (Pg 1 left col, para 1). Particle bombardment (to deliver RNPs) into plants, without selection, typically has an editing efficiency of less than 10% (Pg. 4 left col, para 2). When this is improved using plasmids with selective markers co-transformed with RNPs into plants, then a higher frequency of random inserts may also occur (Pg. 4 left col, para 2). Editing efficiency of ~6% was obtained when RNPs were delivered into tobacco by lipofection, where notably, for plants, this also requires cell wall degradation (Pg 4, left col, para 3) but for LbCas12a editing efficiency was <1% (Pg. 4, right col, para 1). In soybeans editing efficiency was 1.6% max, using AsCas12a, but was 17.5% using LbCas12a. Recognition was made of problems: formation of secondary structures, low activity in some species, and temperature sensitivity impacting Cas12a, impacting results (Pg 4, right col para 1). Editing efficiencies for different plant species, using RNP delivered CRISPR reagents were presented in Table 1 and range widely (with most however, <10%), Zhang indicating “room for improvement to achieve much higher editing efficiencies” to make RNP based CRISPR genome editing more practical for plants (Pg 4 right col, para 1; Pg 8 Table 1). Variation occurred within species where editing systems varied, with editing efficiency of up to 3.4% with electrotransfection /Cas9 in cabbage ((Pg 4, left col, para 3) and up to 1.8-2% with other transformation methods/Cas9, though with one cabbage subspecies using PEG and Cas9, editing efficiency ranged from 3.7-24.5% for one gene, and 1.1-12.5% for another (Table 1). Soybean editing efficiency appeared as much as 10% higher with LbCas12a then with AsCas12a (Pg 6 Table 1).
Javaid (Javaid N and Choi S, CRISPR/Cas System and Factors Affecting Its Precision and Efficiency, Nov 2021, Front Cell & Dev Biol, 9 761709 ) generally addressed precision and efficiency issues using CRISPR-Cas system(s), reminding that challenges obtaining maximum genome editing efficiency with minimal off-targets remain (Abstract end), and that CRISPR is the most efficient of the classes of binding proteins available (Pg 1 end to Pg 2 left col first para). Javaid points out that spacers, in plants, with GC content 30-80% have been validated, but that editing efficiency decreases with 40% GC content relative to higher amounts (Pg 5 right col, first full para), while in mammalian cells, very low or very high GC content is less effective, with 40-60% GC content favorable for efficient editing (Pg 5, right col, first full para).
Malzahn (Malzahn A, et al., Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis, 2019, BMC Biol 17:9 1-14) commented that CRISPR-Cas12a provided new opportunity in genome editing but that only a few plant species had been edited, noting one study could not detect any activity in rice plants with AsCas12a, another barely found induced mutations in soybean protoplasts (Pg 2, left col, final sentence to right col first para). Editing efficiency in maize was up to 60% with LbCas12a (Pg 2, right col first para). Malzahn noted that the pace of adoption of Cas12a systems to a wide collection of plant species has been slow, suggesting barriers impact editing (Pg 2, right col, final para), and demonstrating Cas12a nucleases behave differently in different plant species (Pg 3, left col, first para), indicating experimental work would be necessary when moving from one plant system to another using Cas12a nucleases, with some nucleases (e.g. AsCas12a) not having been successfully applied for generating heritable mutations in plants (Pg 5 left col, para 1), prior to Malzahn’s first-time work garnering success (Pg 8, right col, final para). Even the Cas9 nuclease demonstrated optimal activity under different conditions for human cells relative to plants, which impacts editing (Pg 10, left col second para). Malzahn believed further exploration of different conditions would probably result in more robust genome editing in plants (Pg. 10, left col, final para).
Bernabe-Orts (Bernabe-Orts, JM et al, Assessment of Cas12a-mediated gene editing efficiency in plants, 2019, Plant Biotechnology Journal (2019) 17, pp. 1971–1984) compared efficiency of Acidaminoccoccus (As), Lachnospiraceae (Lb) Cas12 variants with S. pyogenes Cas9 in CRISPR/Cas12a as an editing system for plants, comparing editing efficiency of these two Cas12a variants with SpCas9 in benth (N. benthamiana) (Abstract). All three nucleases showed ‘drastic target-dependent differences in efficiency’ (Abstract). Genome editing was conducted in three plants tobacco, tomato and Arabidopsis thaliana and Bernabe-Orts concluded that while Cas12a may be used as a viable alternative to Cas9 for plant genome editing, more work is needed to make editing efficiency more predictable. (Pg. 1972, left col, first full para last line). Bernabe-Orts also did point out that Cas12a orthologs have been proven effective in mammalian cells (Pg. 1971, right col final para).
What the specification does and does not teach:
Foremost, the specification teaches the combination of Examples 1 and 2, which indicate that a construct was made in human cell line with an (undefined) “CRISPR-Cas” system, where one spacer, PWsp104, has an editing efficiency in the human cell line of ~37% for the corn gene Gl2, and at least 80%, in corn. Re: claim 22, this does not constitute an editing efficiency that is substantially the same in plant and mammal cells. Re: claim 23, a singular plant editing system has an efficiency of 80%, but the editing system is not disclosed beyond, “a CRISPR-Cas editing system”. Spacers for a second corn gene addressed were not tested in both mammalian and plant cells and does not meet claim 22 or 23. Editing systems and spacers vary structurally, meaning the Genus of all editing systems is not represented here.
Further, in Example 4, a blackberry gene in a human cell line, using C12a, was tested with six crRNAs, and resulted in two crRNAs that were ‘highly’ active, PWsp661 (%indels ≥82%) and PWSP662 (73%). The editing system is not introduced into a plant cell with the blackberry gene, so comparison cannot be made between plant and mammal cells for claims 22 or 23, though re: claim 23, editing efficiency for one spacer, PWsp661, in plant cells is over 80%. Here a different plant polynucleotide to Examples 1, 2 is used, and the editing system here is named, and a few different spacers are used compared to Example 1, 2, which is expected with a different plant polynucleotide, but this does not comprise the Genus of editing systems available. Very broad mention of different binding polypeptides, nucleases, editing systems is made in general (ZFN, TALEN, and even different CRISPR-Cas systems, and promotors) but nothing beyond recognition that these exist, despite each having different structural requirements and functioning differently (e.g. Pg 10, 16, 25).
The Specification points to the issue that plant genome editing is difficult for many specialty crops, making it challenging to identify promising genome editing strategies that produce a desired edit in the context of the plant genome (Pg 1). The Specification further states that identification of optimal gRNA, assessing editing outcomes and estimating editing efficiency at targets cannot be easily determined (Pg 1).
The specification does not teach the limitations in claims 22 and 23 in any working example that discloses a particular editing system and spacer and that introduces a plant polynucleotide into a plant and a mammal cell (line). The specification also broadly recognizes the limitations affecting testing, as explanation why varied systems are not tested. The Specification points to feasibility issues, where it indicates that many specific editing enzymes and gRNAs could be employed, but due to “laborious” (nature of the work) and expensive cost, extensive testing of reagents is not feasible (Example 1, Pg 60, lines 25-29).
Disclosure in the “Examples” Section of the Specification:
Example 1 addresses editing, where a portion of corn Glossy 2 (Gl2) gene or CenH3 gene, was integrated into a human cell line (HEK293T, specifically, Flp-in™ 293 cells) to test editing reagents in the newly generated 291Gl2 or 293CenH3 cell lines. CRISPR-Cas constructs were introduced using (individually) six Glossy2 spacers, four CenH3 spacer (Table 1) and tested for editing of the two genes. FIG. 1 depicts results: Indels (%) ranging from ~15% to 42% for Gl2, and ~20-79% for CenH3. Construing “indels %” directly as editing efficiency, the example fails to meet the limitations of claim 22 or 23 since there are no comparisons in plant/mammalian cell lines nor editing efficiency 80%+ in plant cell lines.
Example 2 discloses edited Gl2 alleles, generated in corn, by plant transformation using CRISPR-Cas editing components of Example 1. Transformation constructs employed Gl2 spacers, were introduced into dried maize embryos via Agrobacterium, transformed tissue maintained with selection, and tissue from E0 plants was screened for Gl2 edits. Editing efficiency with one spacer (PWsp104) was calculated and reported as the percentage of plants with ≥10% of sequencing reads with an edit in Glossy2 (relative to total number plants screened). PWsp104 was evaluated twice and demonstrated editing efficiency of 93.8% and 80% in corn.
Prophetic Example 3: considers editing the CenH3 gene in corn with the same CRISPR-Cas components employed for Gl2. No results provided, since prophetic example.
Example 4: Blackberry SEEDSTICK gene in human cell line transfected with Cas12a and one crRNA including a spacer from Table 2. Six crRNAs were tested, two were ‘highly’ active, where data for PWsp661 is 82% for % indels, and PWSP662 is 73%. No work in plant cells is presented.
Prophetic Example 5: Edited SEEDSTICK allele constructs are proposed to be generated with same CRISPR-Cas components as in Ex 4. No results provided since prophetic example.
Example 6: Human cell line with corn fea2, using Cas12a, one crRNA with spacer from Table 3. Editing efficiency reported: all <50%.
Prophetic Example 6 (the second example 6): edited fea2 alleles in corn with spacers of Table 3 for fea2. No data presented.
Figures, and related text (Pg. 61) indicate “highly active spacers” (Pg 61, line 19, within Example 1) were identified. The figures depict indels (%) for the six spacers for Gl2, and four for CenH3 which show variability in editing efficiency in Ex 1, 2. One is used in one example of introduction of one plant gene into plant and mammalian cells.
Conclusion regarding possession:
Taking into consideration the factors outlined above, including the nature of the invention, the state of the art, the guidance provided by the applicant and the specific example, it is the conclusion that Applicant does not possess the invention as recited in the claims.
There is not sufficient specific written example in the Specification that would lead one with ordinary skill in the art to a different conclusion. Written description (possession) for claims 22 and 23 is not supported, given the narrow and fractional disclosures in the working examples of pieces of the Genus of editing systems, or spacers, or of editing efficiency in one but not both cell line types, and a lack of broad implementation.
Related art that is not relied upon:
Ghogare (Ghogare, R. et al., Genome editing reagent deliver in plants, Transgenic Res 2023 30:321-355, cited on IDS) references editing in plants, but does not use mammalian cell lines for insertion of plant material.
Bradley (US20150079680 A1, published 3/19/2015) disclosed (Bradley, claim 10, the method of claim 1), a method of recombination, with Cas mediated cuts, deletion of sequence that is followed by (Bradley, claim 6) inserting a sequence between cut ends, wherein claim 17, the method is carried out in a cell and claim 18, the cell is a rodent cell. Motivation to insert into mammal cells, from plant genome could come from [0024] addressing orthologous (here proteins) in general, but this application does not teach or suggest introduction of plant genes/material into mammalian cells, and thus does not measure said editing efficiency and has no motivation to do so. [0024] The pathway of NHEJ in S. cerevisiae and mammals has been extensively characterized. In mammals, conserved proteins that are involved in classic NHEJ include the following: DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the heterodimer Ku70/80, DNA ligase IV (Lig4), Xrcc4, Cernunnos/XLF and Artemis. See, e.g., Figure 1. Orthologs of these proteins have been identified also in yeast, fungi and plants with the exception of DNA-PKcs, which is not required for efficient NHEJ in these organisms.
Zhang (US 2021/0163944 A1, published June 3, 2021) disclosed systems, methods and compositions for targeting nucleic acids (Abstract) and addressed designing optimized CRISPR-Cas systems for mammals or plants and agricultural application of plants, and the improvement of specificity and efficacy and reduction of off target effects [0148] but does not incorporate plant genetic material into mammalian cell lines.
Additionally, it is noted for this application some dependent claim material was considered under 35 USC § 101, including the “comparing” performed in claim 8, the “determining the presence or absence of the modification” in claim 9, and the ”quantifying the amount of indels..and/or base edits” in claim 10.
Consideration was made that these may be judicial exceptions as mental processes not integrated into practical application under step 2A, however under step 2B, the claims would not be considered to contain subject matter that is well-understood, routine and conventional given the processes disclosed in claim 1 which they rely upon, and these claims therefore, do recite significantly more than the judicial exception.
Conclusion
Claims 1-23 are rejected. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Lisa Horth whose telephone number is (703)756-4557. The examiner can normally be reached Monday-Friday 8-4 EST.
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/LISA HORTH/Examiner, Art Unit 1681
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636