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 .
Application Status
The action is written in response to the applicant’s correspondence received on 7/21/2026. Claims 1-6, 9-10, 14, 17-18, 22, 26-27, 29-32, 40-43, 45-48, and 50-51 are currently pending in the instant application.
Priority
The instant application claims foreign priority to GB2103256.0, filed on 3/9/2021. The Certified Copy of Foreign Priority, filed on 9/8/2023, has been acknowledged.
Election/Restriction
Applicant’s election without traverse of the inventions of Group I (claims 1-4, 6, 9-10, 14, 17-18, 22, 26-27, 30-32, 40-43, and 45-46), drawn to a method of reducing the expression of a first target gene comprising of inserting a silencing insertion into the genome of a eukaryote cell, wherein the method produces a plant or plant seed comprising the eukaryotic cell, in the reply filed on 7/21/2026 is acknowledged.
Applicant elects the following species:
A plant cell, regarding claim 6;
Option (d), as recited in claim 18, wherein the selectable marker is a mutated version of an ALS gene that confers herbicide resistance;
Option (a), as recited in claim 22, wherein the silencing insertion is inserted into the genome of the eukaryotic cell in a construct that additionally comprises sequence encoding an RNA-guided DNA endonuclease and sequence encoding a guide RNA targeted to the endogenous silencing sequence;
Option (e), as recited in claim 32, wherein the target gene is exogenous to the eukaryotic cell.
Claims 5, 29, 47-48, and 50-51 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 7/21/2026.
Claims 1-4, 6, 9-10, 14, 17-18, 22, 26-27, 30-32, 40-43, and 45-46 are currently under examination on the merits.
Drawings
The drawings are objected to because the figures presented are labeled as “Figure”. Under MPEP and 37 CFR § 1.84(u), individual drawing views must be labeled with the abbreviation “FIG.” followed by a consecutive Arabic numeral (e.g. FIG. 1, FIG. 2).
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. 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.
Hyperlinks can be found throughout the specification but are not limited to (page 56, line 30), (page 57, lines 2 and 9), (page 59, lines 19, 24, 27-28, and 31), (page 60, lines 2, 4-5, 16, and 18), (page 61, line 4), (page 64, lines 12, 15, 18, and 20-21), (page 69, line 4), (page 72, line 24), (page 74, lines 5 and 9), (page 75, lines 12-13), (page 77, line 30), (page 78, lines 10 and 14), (page 79, line 16), and (page 82, line 21).
The use of the term GEiGS™, which is a trade name or a mark used in commerce, has been noted in this application. The term 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.
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. Figs. 3A-C, and 4A-B contain sequences without associated SEQ ID NOs present in the drawings or the brief description of the figures.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
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 6 and 10 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.
Regarding claim 6 and 10, the phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Improper Markush Groups
Claims 6 and 9 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of claim 6 and 9 are improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons:
Regarding claim 6, the method of claim 1 is drawn to a eukaryotic cell that is a plant cell or a human or animal cell. Here, the use of a silencing insertion to target a gene present in a plant cell would be structurally different from that used to target a human or animal cell, as different sequence of genes, promoters, and terminators would have to be incorporated.
Regarding claim 9, claim recites where the silencing RNA of the insertion is encoded by siRNA, miRNA, piRNA, phasiRNA, tasiRNA, shRNA, an inverted repeat RNA forming double stranded RNA, snRNA or U-RNA, snoRNA, scaRNA, tRNA, rRNA, a repeat-derived RNA, an autonomous or non-autonomous transposable or retro-transposable element-derived RNA, tRF, or a lncRNA.
Here, the alternatives do not share a common structure as microRNAs are naturally occurring endogenous sequences to the organism, while siRNAs, or other types of RNAs listed, are modified or artificial sequences, inserted into the organism. Furthermore, claim 9 recites transfer RNA and ribosomal RNA. Absent evidence to the contrary, one skilled in the art would recognize ribosomal RNAs function as the core structural and catalytic components of ribosomes utilized in protein synthesis and would not be used in a silencing insertion for targeting a gene.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim Interpretation
Regarding claim 1, examiner will interpret “wherein the silencing RNA encoded by the endogenous silencing sequence is not active or silences the expression of a second target gene that is different from the first target gene” as the original sequence, prior to modification of the silencing insertion, is no longer active or where the new endogenous sequence, created by the silencing insertion, targets a second gene that is different from the first, but not the first.
Regarding claim 40, the term “homeolog” provides no structural or functional limitation as defined by the specification. Applying broadest reasonable interpretation, a second gene being a homeolog of the first still reads as the first gene and second gene being two distinct target genes.
Claim Objections
Claim 18 is objected to because of the following informalities: Claim 18 recites “an ALS gene”. When claims are directed to a gene that is not well known, or could be mistaken for another gene (such as acetolactate synthase or a gene associated with the disease amyotrophic lateral sclerosis), the first time “ALS” is mentioned in the claims, the full name of the gene should be used to avoid confusion.
Appropriate correction is required.
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.
Claims 1-3, 6, 9-10, 14, 17-18, 22, 26-27, 30-32, 40-43, and 45-46 are rejected under 35 U.S.C. 103 as being unpatentable over Maori et al. (WO 2019058255 A1, published 3/28/2019) in view of Song et al. (Optimizing the DNA Donor Template for Homology-Direct Repair of Double-Stranded Breaks, Molecular Therapy Nucleic Acids, Volume 7, pgs. 53-60, published June 16, 2017).
Regarding claim 1, Maori teaches a method of reducing expression of a first target gene in a plant cell, which is a eukaryotic cell (see claim 1), where Maori presents both a method of modifying a gene encoding or processed into a non-coding RNA molecule that has no RNA silencing activity in a plant cell to confer silencing specificity towards a target RNA of interest and a method of modifying a gene encoding or processed into a RNA silencing molecule to (such modified to target a second target gene) (see abstract). For the first method, modifying a non-coding RNA molecule with no silencing activity reads on the endogenous silencing sequence as being “not active”. For the second method, where a gene encoding an RNA silencing molecule is modified, Maori teaches where “the method comprising introducing into the plant cell a DNA editing agent which redirects a silencing specificity of the RNA silencing molecule towards a second target RNA, the target RNA and the second target RNA being distinct, thereby modifying the gene encoding the RNA silencing molecule” (see page 4, line 13). For working examples, Fig. 18 of Maori teaches where modified silencing molecules reduce the target expression of AtPDS3 transcripts by 82% when miR-173 was redirected to the target gene (see page 12, line 4).
In the descriptive drawings, Maori teaches Fig. 1 which is a flow chart of Genome Editing Induced Gene Silencing (GEiGS) for the replacement of an endogenous miRNA with siRNA targeting the PDS gene, hence inducing gene silencing of the endogenous PDS gene (see page 9, line 8). The modification is a 2-component system involving a CRISPR/Cas9 system to promote homologous DNA repair at a specific site and a donor sequence with the desired modification of the miRNA sequence, to target the newly assigned genes (see page 9, line 8).
Maori teaches, in some embodiments, a non-coding RNA molecule has 100% sequence identity or at least about…95% sequence identity when compared to a sequence of 10-500 or more contiguous nucleotides in the target RNA (or family members of a given target gene) (see page 24, line 12). This is also supported further where Maori teaches the donor sequences different minimally from the endogenous sequence where “according to a specific embodiment, the modification comprises a modification of at most 5 nucleotides” (see page 38, line 1) and Fig. 11 which depicts the main stages required to design RNA silencing molecule with minimally edited miRNA gene bases (see page 10, line 21). Also Maori teaches the “Hit and run” method where an insertion type-vector containing a dual positive/negative selectable marker cassette is used to introduced the desired sequence alteration. The insertion vector contains a single continuous region of homology to the target locus and is modified to carry the mutation of interest (see page 34, line 29). Regarding claim 3, Maori teaches methods of modifying a gene encoding a non-coding RNA molecule with and without silencing activity to target RNA of interest, described above. Maori further teaches plant cells, plant seeds, plants, and methods of generating plants are also disclosed (see abstract).
Maori further teaches where in the “Hit and Run” method, the homologous recombinants contain a local duplication that is separated by intervening vector sequence, including the selection cassette (see page 35, line 2), therefore, eukaryotic cells with the insertion vector would have an endogenous sequence separated by the insertion vector.
Regarding claims 1 and 3, Maori does not explicitly state the length of “the single continuous region of homology to the targeted locus” of the insertion to encompass regulatory elements present in the genome of the eukaryotic cell such as promoters and terminators, or parts thereof. Maori states where the DNA agent and gRNA are linked to a plant promoter (see page 44, line 27), however, these regulatory elements are directed to the vector encoding the DNA agent and gRNA, not the donor sequence which embodies the silencing insertion of claim 3.
However, it would have been obvious to one with ordinary skill in the art before the effective filing date to configure the insertion vector of Maori with a “continuous region of homology” to encompass at least a part of the promoter and a part of the terminator in the donor sequence for modifying the endogenous RNA sequence.
Regarding the “Hit and Run” method, Maori discloses the targeting construct is linearized with a restriction enzyme at one site within the region of homology (see page 34, line 32). One skilled in the art would recognize that linearization at a site within the homology region requires homology on both ends of the cut site, where the mutation of interest is inserted. This is exemplified in Maori where “homologous recombinants contain a local duplication that is separated by an intervening vector sequence” (see page 35, line 2), supporting that the region of homology extends in both directions of the flanking sequences of the target locus or gene. Furthermore, Fig. 10 of Maori depicts a donor cassette with 110 bp upstream and downstream of the siRNA sequence inserted, indicating the region of homology extends beyond the target RNA sequence.
Regarding claims 1 and 3, Song teaches the length of the homology arm also plays an important role increasing HDR rate because the efficiency of recombination increases as the length of homology arm increases (see Discussion).
It would have been obvious to one with ordinary skill in the art, before the effective filing date of the claimed invention, to combine the teachings of Maori and Song to arrive at a silencing insertion comprising a promoter and terminator, or a part thereof, for the function of silencing a target gene in the genome of a eukaryotic cell.
A skilled artisan would have been motivated to employ an extended region of homology for homologous DNA repair beyond merely the modified sequence, which is the mechanism of introducing a donor sequence via particle bombardment to endogenous miRNA (see page 103, line 29) in Maori, as homology region length is an art recognized result-effective variable in HDR and routine optimization of the length of the homologous sequence would include at least a part of a promoter and a terminator. This is supported further as Song teaches the length of the homology arm plays an important role increasing HDR rate because the efficiency of recombination increases as the length of homology arm increases (see Discussion).
One would expect a reasonable chance of success as Song teaches different lengths of homologous regions, from 300-700 bp, were used to test the effects of homology length on HDR frequency (see HDR Frequency Depends on the Characteristics of the DNA Template).
Absent evidence to the contrary, one skilled in the art would modify and extend the “Hit and Run” method’s single region of homology, wherein a donor sequence is inserted into the genome of a cell, to include at least a part thereof of a promoter and a terminator, as it order to improve the frequency and efficiency of HDR.
In view of the foregoing, claims 1 and 3 are rejected under 35 U.S.C. 103 as being prima facie obvious, before the effective filing date.
Claims 2, 4, 6, 9-10, 14, 17-18, 22, 26-27, 30-32, 40-43, and 45-46 are rejected under 35 U.S.C. 103 as being unpatentable over being unpatentable over Maori et al. (WO 2019058255 A1, published 3/28/2019) in view of Song et al. (Optimizing the DNA Donor Template for Homology-Direct Repair of Double-Stranded Breaks, Molecular Therapy Nucleic Acids, Volume 7, pgs. 53-60, published June 16, 2017).
Regarding claims 2, 4, 6, 9-10, 14, 17-18, 22, 26-27, 30-32, 40-43, and 45-46 , the methods of claim 1 (a method of reducing the expression of a first target gene comprising inserting a silencing insertion into the genome of a eukaryotic cell), and the eukaryotic cell of claim 3 are taught by the combined teachings of Maori and Song, as described above.
Regarding claim 2, Maori teaches where exogenous nucleic acid (e.g. a silencing insertion) can be introduced via particle bombardment, into the cells (see pg. 57, line 19).
Regarding claim 4, Maori teaches in one embodiment, a plant viral nucleic acid is provided in which the native coat protein coding sequence has been deleted from a viral nucleic acid, a non-native viral coat protein coding sequence and a non-native promoter, preferably the sub genomic promoter of the non-native coat protein coding sequence, capable of expression in the plant host, has been inserted (see page 56, line 16). Furthermore, Maori teaches Fig. 1 which discloses the mechanism of swapping siRNA targeting PDS with miRNA through 2-component GEiGS. Fig. 1 further discloses a CRISPR/Cas9 system generates a cleavage in the chosen loci to promote HDR. Under the broadest interpretation of the word deleted, one skilled in the art would recognize that swapping the siRNA with the endogenous miRNA sequence in HDR would result in a deletion of the endogenous miRNA as the siRNA of PDS takes its place within the plant genome.
Regarding claim 6, Maori teaches a method of modifying a gene encoding or processed into a RNA silencing molecule in a plant cell (see abstract), therefore said eukaryotic cell is a plant cell.
Regarding claim 9, Maori teaches where according to some embodiments of the invention, the RNAi molecule is selected from the group consisting of a small interfering RNA (siRNA) (see page 7, line 2 and claim 10 of Maori).
Regarding claim 10, Maori teaches where in some embodiments of the invention, modifying the gene is effected by a modification selected from the group consisting of a deletion, an insertion, a point mutation, and a combination thereof (see page 7, line 12). Furthermore, Maori teaches where the modification comprises about 10-250 nucleotides, where the modification comprises a modification that is in a consecutive nucleic acid sequence (see page 37, line 25) or non-consecutive (see page 37, line 27).
Regarding claim 14, Maori teaches where in one embodiment, the non-coding RNA (e.g. RNA silencing molecule) is modified in the guide strand (silencing strand) as to comprise about 50-100% complementarity to the target RNA, while the passenger strand is modified to preserve the original (unmodified) non-coding RNA structure (see page 42, line 29). Maori further discloses the guide strand of the non-coding RNA molecule (e.g. RNA silencing molecule such as miRNA precursors or siRNA precursors is modified to preserve originality of structure and keep the same base pairing profile. The term “originality of structure” refers to the secondary RNA structure (i.e. base pairing profile). Keeping the originality of structure is important for correct and efficient biogenesis/processing of the non-coding RNA (see page 42, line 22).
Regarding claim 17, Maori teaches where exogenous nucleic acid includes a selectable marker, which serves by sequential selection procedures to ascertain that all or substantially all of the copies of the chloroplast genomes following such selection will include the exogenous nucleic acid (see page 57, line 27).
Regarding claim 18, Maori teaches the “hit and run” procedure, which comprises an insertion-type vector containing a dual positive/negative selectable marker cassette (see page 34, line 29) or where the exogenous nucleic acid includes a selectable marker, which serves by sequential selection procedures to ascertain that all or substantially all of the copies of the chloroplast genomes following such selection will include the exogenous nucleic acid (see page 57, line 28). Furthermore, Maori teaches an embodiment where the reporter is a toxic selection marker. An exemplary toxic selection marker that can be used is allyl alcohol selection using the Alcohol dehydrogenase (ADH1) gene, present in plants (see page 36, line 27).
Regarding claim 22, Maori teaches where the DNA editing agent comprises a nuclease (e.g. an endonuclease) and a DNA targeting module (e.g., gRNA) (see page 35, line 22). Maori further teaches where the DNA carrying the homologous sequence can be provided as a plasmid, single or double stranded oligo (see pg. 35 line 1) and the DNA is used to introduce the desired sequence alteration, which can comprise of changes to endogenous genes of the genome.
Regarding claim 26, Maori teaches a working example where guide RNAs targeting miR-173 and miR-390 were introduced into CRISPR/Cas9 vector system in order to generate a DNA cleavage in the desired miRNA loci. These were co-introduced to the plants with the DONOR vectors via gene bombardment protocol, to introduced desired modifications through HDR. The donor vector comprised of SWAPs to target GFP, AtPDS3, and AtADH1, all which are genes present in Arabidopsis thalia (see page 103, line 16). Maori teaches the “Hit and run” or “in-out” method as described in the working examples (with CRISPR/Cas9 and a donor sequence in a vector) and further teaches where the local recombination event removes the duplication and, depending on the site of recombination, the allele either retains the introduced mutation or reverts to wild type. The end result is the introduction of the desired modification without retention of any exogenous sequences (see page 35, line 1).
Regarding claim 27, Maori teaches the limitations of claim 3, as described above. Maori further teaches a construct comprising a DNA editing agent comprises a nuclease (e.g. an endonuclease) and a DNA targeting module (e.g., gRNA) (see page 35, line 22). Maori further teaches where the vectors comprising the DNA agent and gRNA are co-introduced to the plants with the DONOR vectors via gene bombardment protocol, to introduced desired modifications through HDR (see page 103, line 16).
Regarding claim 30, Maori teaches where tobacco mosaic virus (TMV), is a single-stranded RNA virus that commonly infects solanaceous plants and TMV-based vectors have led to recombinant protein yield as high as 80% of total soluble protein. Agroinfection is inexpensive and reproducible, making it a preferred method of delivering viral expression vectors into plant tissues as part of the T-DNA of a binary vector carried by Agrobacterium tumefaciens (see page 118, line 3).
Regarding claim 31, Maori teaches where the present inventors use TuMV-GFP for infection of Arabidopsis or tobacco plants. The present inventors are using an engineered virus that expresses GFP upon plant infection (a selectable marker). Maori further teaches where using a virus will enable to use the same constructs as described in example 3, above (see page 118, line 19). Maori teaches the construct above as a GEiGS construct which comprises CRISPR/Cas9 to express small siRNA molecules (see page. 116-117, line 30).
Regarding claim 32, Maori teaches example 1B where endogenous plant gene PDS was targeted in Arabidopsis or Nicatiana benthamiana (see page 114, line 10).
Regarding claim 40, Maori teaches example 1B, which discloses the use of GEiGS to target PDS in Arabidopsis plants and N. benthamiana. Under the broadest reasonable interpretation of homeolog, an undefined “homeolog” limitation reads on any duplicated/paralogous gene pair as no definition in the specification ties homeolog to a specific allopolyploid subgenome origin. In this case, two orthologs, such as a PDS gene in two separate plants, would read on a homeolog as the limitation does not provide any structural or functional distinction. Furthermore, as homeolog does not provide any structural or functional limitation, the two genes would be distinct targets of the silencing insertion. It would be obvious to one skilled in the art that the methods of targeting a gene, as presented by Maori, could easily be modified to implemented to target a second distinct gene that is a homeolog of the first.
Regarding claim 41, Maori teaches where “plant-expressible” or “active in plant cells” refers to a promoter sequence, including any additional regulatory elements added thereto or contained therein, that is at least capable of inducing, conferring, activating, or enhancing expression in a plant cell, tissue, or organ. The plant promoter employed can be a constitutive promoter, a tissue specific promoter, an inducible promoter, or a developmentally regulated promoter (see page 45, line 4).
Regarding claim 42, the composition (a eukaryotic cell comprising in its genome) of claim 3 is taught above. Maori further teaches where according to some aspects of the present invention, there is a method of generating a plant with increased stress tolerance, increase yield, increased growth rate, or increased yield quality, the method comprising modifying a gene encoding or processed into a non-coding RNA molecule or into a RNA silencing molecule in a plant cell according o some embodiments of the invention (see page 5, line 1).
Regarding claim 43 and 45, Maori teaches a method of generating a plant (see page 5, line 1), which one skilled in the art would recognize as growing a plant from a cell. Maori further specifies that following stable transformation, plant propagation is exercised, where the most common method of plant propagation is by seed (see page 54, line 29).
Regarding claim 46, Maori teaches the method of claim 3, as described above. Maori further teaches where according to one embodiment, there is provided a seed of the plant generated according to the method of some embodiments of the invention (see page 92, line 31).
Regarding the teachings of Maori and Song, the rationale to combine these arts to arrive at the method of claim 1 and the cell of claim 3 are described above. However, to restate:
It would have been obvious to one with ordinary skill in the art before the effective filing date to configure the insertion vector of Maori with a “continuous region of homology” to encompass at least a part of the promoter and a part of the terminator in the donor sequence for modifying the endogenous RNA sequence.
Regarding the “Hit and Run” method, Maori discloses the targeting construct is linearized with a restriction enzyme at one site within the region of homology (see page 34, line 32). One skilled in the art would recognize that linearization at a site within the homology region requires homology on both ends of the cut site, where the mutation of interest is inserted. This is exemplified in Maori where “homologous recombinants contain a local duplication that is separated by an intervening vector sequence” (see page 35, line 2), supporting that the region of homology extends in both directions of the flanking sequences of the target locus or gene. Furthermore, Fig. 10 of Maori depicts a donor cassette with 110 bp upstream and downstream of the siRNA sequence inserted, indicating the region of homology extends beyond the target RNA sequence.
A skilled artisan would have been motivated to employ an extended region of homology for homologous DNA repair beyond merely the modified sequence, which is the mechanism of introducing a donor sequence via particle bombardment to endogenous miRNA (see page 103, line 29) in Maori, as homology region length is an art recognized result-effective variable in HDR and routine optimization of the length of the homologous sequence would likely include at least a part of a promoter and a terminator. This is supported further as Song teaches the length of the homology arm also plays an important role increasing HDR rate because the efficiency of recombination increases as the length of homology arm increases (see Discussion).
Absent evidence to the contrary, one skilled in the art would modify and extend the “Hit and Run” method’s single region of homology, wherein a donor sequence is inserted into the genome of a cell, to include at least a part thereof of a promoter and a terminator, as extending the region of homology is known in the art to increase HDR efficiency.
In view of the foregoing, claims 2, 4, 6, 9-10, 14, 17-18, 22, 26-27, 30-32, 40-43, and 45-46 are rejected under 35 U.S.C. 103 as being prima facie obvious, before the effective filing date.
Claim 18 is rejected under 35 U.S.C. 103 as being unpatentable over being Maori et al. (WO 2019058255 A1, published 3/28/2019) in view of Song et al. (Optimizing the DNA Donor Template for Homology-Direct Repair of Double-Stranded Breaks, Molecular Therapy Nucleic Acids, Volume 7, pgs. 53-60, published June 16, 2017), in further view of Carbonell et al. (US 2017/0159064 A1, published 6/8/2017).
Regarding claim 18, the teachings of the method of claim 1, directed towards a method of reducing the expression of a first target gene comprising inserting a silencing insertion into the genome of a eukaryotic cell, is taught by the combined teachings of Maori and Song, as described above.
Regarding claim 18, Maori teaches an embodiment where the reporter is a toxic selection marker. An exemplary toxic selection marker that can be used is allyl alcohol selection using the Alcohol dehydrogenase (ADH1) gene, present in plants (see page 36, line 27).
Per applicant’s election, Maori does not teach where the selectable marker is endogenous to the eukaryotic cell and is a mutated version of the ALS gene that confers herbicide resistance.
Regarding claim 18, Carbonell teaches a method to produce artificial miRNAs to target a gene in a plant cell (see abstract). Carbonell further teaches where, in one embodiment, the vector encoding an artificial or synthetic miRNA comprises a selectable marker or resistance genes, wherein one of the markers or resistance genes can be a gene coding for resistance to herbicides which act to inhibit the action of acetolactate synthase (ALS) (e.g. the ALS gene containing mutations leading to such resistance in the particular S4 and/or Hra mutations) (see paragraph 0130).
It would have been obvious to one with ordinary skill in the art, before the effective filing date, to combine the teachings of Maori and Carbonell to arrive at a method of reducing the expression of a target gene, wherein the selectable marker is a mutated version of the ALS gene.
One would expect a reasonable chance of success as Carbonell teaches a method of generating artificial or modified miRNAs to target genes of interest, wherein the vector carrying the miRNA sequence can comprise of selection markers or resistance genes, such as a mutated version of the ALS gene.
One would be motivated to do as mutated ALS genes are confer herbicide resistance to plants, as evidenced by Carbonell (see paragraph 0130). Therefore, by imparting this mutated gene as a selectable marker, one skilled in the art could use herbicides in order to select for plants that have successful integrated the silencing construct into its genome.
In view of the foregoing, claim 18 is rejected under 35 U.S.C. 103 as being prima facie obvious, before the effective filing date.
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 filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual 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/apply/applying-online/eterminal-disclaimer.
Claims 1, 6, 9, 10, 22, 26-27 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5, and 7-9 of U.S. Patent No. 11555199 B2 in view of over Maori et al. (WO 2019058255 A1, published 3/28/2019) in view of Song et al. (Optimizing the DNA Donor Template for Homology-Direct Repair of Double-Stranded Breaks, Molecular Therapy Nucleic Acids, Volume 7, pgs. 53-60, published June 16, 2017)
Although the claims at issue are not identical, they are not patentably distinct from each other because both patent and instant application are drawn to a method of reducing the expression of a target gene with a silencing insertion comprising of introducing to a cell, a DNA editing agent and donor oligonucleotide with a desired modification sequence which redirects the silencing specificity to a second target gene.
Regarding the claim 1 of the issued patent and the instant application, the issued patent is directed to a method of introducing a DNA editing agent and a donor oligonucleotide, which reads on a silencing insertion of the instant application (a sequence encoding a silencing RNA that silences the expression of the first target gene), and where the modification comprises nucleotide replacement and redirects the silencing specificity of said RNA molecule towards a distinct second target. Claim 1 of the issued patent explicitly discloses a plant cell which is disclosed in claim 6 of the instant application.
The limitations of claim 2 of the issued patent is also recited in claim 1 and 32 of instant application. The issued patent states where the DNA sequence encoding the RNA silencing molecule is endogenous to the plant cell while the instant application recites the silencing insertion targets an endogenous silencing sequence within a eukaryotic cell.
Furthermore, the limitations of claim 3, 5, and 7-9 of the issued patent are further recited in claims 6, 9, 10, 22, 26-27, and 32 of the instant application.
Regarding claim 3 of the issued patent, which recites wherein the RNA silencing molecule comprises at least 45% complementarity to the second target gene. Though the instant application does not recite percent complementarity, one skilled in the art would recognize that the second target gene recited in the instant application would require a silencing insertion with a high degree of complementarity in order to reduce gene expression. This is evidenced in Maori where it is disclosed “the present inventors are identifying well characterized short siRNA sequences in different plants that might be 100% match to the gene in Arabidopsis” (see example 1B). Therefore, a degree of complementarity to the second target gene, at least over 45%, would be required in order to reduce expression of said second target gene.
Regarding claim 5 of the issued patent, the RNA silencing molecule is recited as identical to the RNA molecules of claim 9 of the instant application.
Regarding claims 7-9 of the issued patent, claim 7 recites the same limitations of claim 10 of the instant application. Claim 8 and 9 of the issued patent recites the same limitations of claim 22, and 26-27 of the instant application.
Though the donor oligonucleotide is not recited to comprise a promoter and a terminator, or part thereof, as recited in the instant application, the issued patent recites a method of modifying a DNA sequence through homologous recombination. Integration of a construct through homologous recombination requires in fact regions of homology, which can be derived from terminal parts of the silencing elements, or from regions further upstream and downstream, including regulatory parts of the promoter and terminator, as evidenced by Song et al.
As described above in Maori in view of Song, it would have been obvious to modify the donor oligonucleotide of the issued patent to extend the region of homology to include regions (or at least a part thereof) of a promoter and a terminator of the donor sequence, as extended regions of homology leads to better efficiency of recombination (see discussion of Song).
Claims 1, 6, 9, 10, 22, 26-27 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5, 7-10, 13, and 16 of U.S. Patent No. US 12275939 B2 in view of over Maori et al. (WO 2019058255 A1, published 3/28/2019) in view of Song et al. (Optimizing the DNA Donor Template for Homology-Direct Repair of Double-Stranded Breaks, Molecular Therapy Nucleic Acids, Volume 7, pgs. 53-60, published June 16, 2017).
Although the claims at issue are not identical, they are not patentably distinct from each other because both patent and instant application are drawn to a method of reducing the expression of a target gene with a silencing insertion comprising of introducing to a cell, a DNA editing agent and donor oligonucleotide with a desired modification sequence which redirects the silencing specificity to a second target gene.
Regarding the claim 1 of the issued patent and the instant application, the issued patent is directed to a method of introducing a DNA editing agent and a donor oligonucleotide, which reads on a silencing insertion of the instant application (a sequence encoding a silencing RNA that silences the expression of the first target gene), and where the modification comprises nucleotide replacement and redirects the silencing specificity of said RNA molecule towards a distinct second target.
Though the donor oligonucleotide is not recited to comprise a promoter and a terminator, or part thereof, as recited in the instant application, the issued patent recites a method of modifying a DNA sequence through homologous recombination. Integration of a construct through homologous recombination requires in fact regions of homology, which can be derived from terminal parts of the silencing elements, or from regions further upstream and downstream, including regulatory parts of the promoter and terminator.
As described above in Maori evidenced by Song, it would have been obvious to modify the donor oligonucleotide of the issued patent to extend the region of homology to include regions (or at least a part thereof) of a promoter and a terminator of the donor sequence, as extended regions of homology leads to better efficiency of recombination (see discussion of Song).
The limitations of claim 2 of the issued patent are also recited in claim 1 and 32 of the instant application. The issued patent states where the DNA sequence encoding the RNA silencing molecule is endogenous to the plant cell and the issued patent recites where the silencing insertion targets an endogenous silencing sequence. Claim 32 of the instant application specifically recites in (C) where the target gene is endogenous to the eukaryotic cell.
Regarding claim 3 of the issued patent, which recites wherein the RNA silencing molecule comprises at least 45% complementarity to the second target gene. Though the instant application does not recite percent complementarity, one skilled in the art would recognize that the second target gene recited in the instant application would require a silencing insertion with a high degree of complementarity in order to reduce gene expression, as disclosed in claim 1 of the instant application. This is evidenced in Maori where it is disclosed “the present inventors are identifying well characterized short siRNA sequences in different plants that might be 100% match to the gene in Arabidopsis” (see example 1B). Therefore, a degree of complementarity to the second target gene, at least over 45%, would be required in order to reduce expression of said second target gene.
Claim 5, 7-10, 13, and 16 of the issued patent read on claims 6, 9, 10, 22, 26-27 and 32 of the instant application.
Claims 1, 6, 9, 10, 22, 26-27 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-3, 6-8, 11, and 15 of U.S. Patent No. US 12331295 B2 in view of in view of over Maori et al. (WO 2019058255 A1, published 3/28/2019) in view of Song et al. (Optimizing the DNA Donor Template for Homology-Direct Repair of Double-Stranded Breaks, Molecular Therapy Nucleic Acids, Volume 7, pgs. 53-60, published June 16, 2017).
Although the claims at issue are not identical, they are not patentably distinct from each other because both patent and instant application are drawn to a method of reducing the expression of a target gene with a silencing insertion comprising of introducing to a cell.
Regarding the claims 1 and 2 of the issued patent and the instant application, the issued patent is directed to a method of introducing a DNA editing agent and a donor oligonucleotide, which reads on a silencing insertion of the instant application (a sequence encoding a silencing RNA that silences the expression of the first target gene), and where the modification comprises nucleotide replacement and redirects the silencing specificity of said RNA molecule towards a distinct second target. This matches with claim 1 and 32 of the instant application.
Though the method of modifying a gene encoding or processed into a non-coding RNA in the issued patent does comprise a promoter and a terminator, or part thereof, as recited in the instant application, the issued patent recites a method of modifying a DNA sequence through homologous recombination. Integration of a construct through homologous recombination requires in fact regions of homology, which can be derived from terminal parts of the silencing elements, or from regions further upstream and downstream, including regulatory parts of the promoter and terminator.
As described above in Maori evidenced by Song, it would have been obvious to modify the donor oligonucleotide of the issued patent to extend the region of homology to include regions (or at least a part thereof) of a promoter and a terminator of the donor sequence, as extended regions of homology leads to better efficiency of recombination (see discussion of Song).
Regarding claims 3, 6-8, 11, and 15 of the issued patent, claims 6, 9, 10, 22, 26-27 of the instant applications teaches these limitations such as the DNA editing agent comprising at least one operatively linked gRNA, wherein the target RNA of interest is exogenous to the plant and the structure of the RNAi molecule.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID YU whose telephone number is (571)272-1118. The examiner can normally be reached Monday-Friday 7:30 am -5 pm.
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, Ram Shukla can be reached at 571-272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/D.T.Y./Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
Prosecution Insights