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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1/5/2026 has been entered.
Claims 1, 4, 98 and 110 have been amended.
In view of Applicants amendments to claim 1, the new matter rejection is withdrawn.
3. Claims 1-4, 7-11, 95, 97-101, 103, 104 and 106-110 are examined in the instant application.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1, 4, 7-11, 95, 98-101, 104 and 106-109 are rejected under 35 U.S.C. 103 as being unpatentable over Smidler et al. (WO 2015/105928 A1, published 7/16/2015) in view of Gantz et al. (4/2015, Science, Vol. 348(6233), pgs. 442-444), Esvelt K. (5/22/2015, addgene Blog, pages 1-6) and Esvelt et al. (2014, eLife, Vol. 3, pgs. 1-21).
Claim Interpretation:
The claimed method has been amended to recite “wherein the resulting organism is an engineered organism of the strain, and wherein…” the engineered organism is crossed with another organism of the same strain (step a) and then released into a wild population (step b). However, it is interpreted that the newly amended limitations of claims 1 and 98 are a preferred embodiment and not required steps of preparing an engineered organism. The claimed method only requires steps (i) and (ii), which is drawn to preparing an engineered organism. The newly amended wherein clause reciting (a) and (b) is an intended use of the engineered organism and are not required to prepare the engineered organism and it thus interpreted that they are not required by the claimed method.
Regarding claims 1, 98 and 104, Smidler et al. teach a method of preparing an engineered organism using a Cas9 gene drive system, the method comprising:
inserting one or more DNA cassettes each comprising an independently preselected DNA sequence into a plurality of repeated regions in the genome of an organism of a strain to prepare a first engineered organism, wherein:
(i) a first insertion DNA cassette comprises one or more CRISPR components and a plurality of the first insertion DNA cassettes is inserted into the plurality of repeated regions in the genome of the first organism;
and (ii) a second insertion DNA cassette is inserted into a single site in the genome of the organism, wherein the second insertion DNA cassette comprises DNA encoding: (a) one or more cargo genes, and optionally encoding (b) an independently selected CRISPR component that differs from that in the first insertion DNA cassette,
wherein a means of inserting the preselected DNA sequence comprises using a nuclease-class enzyme to cut one or more strands of a predetermined natural sequence repeat in the genome of the organism and inducing homologous recombination of the preselected DNA sequence with the predetermined natural sequence (Examples I-V on pgs. 21-23 and see Figs. 1-8).
Smidler teaches that “The foreign nucleic acid sequence may also include any other gene sequence or gene sequences desired to be expressed by the germline cell. Such a gene sequence or such gene sequences may be referred to as "cargo DNA." (pg. 3 lines 21-23).
Regarding claims 4 and 99, Smidler teaches that the DNA sequence encodes a desired organism trait, preparing a plurality of the engineered organisms and releasing the engineered organisms to introduce the desired trait into the local population of the organism (pg. 1 line 25 bridge pg. 2 lines 1-9).
Regarding claims 7-9, Smidler teaches that the second insertion cassette is copied in the presence of at least one guide RNA cassette, at least one copy of the nuclease gene or at least one copy of the first insertion cassette (pg. 24 lines 6-24 and particularly Examples II and IV).
Regarding claim 10, Smidler teaches that they can create a transgenic strain comprising the first and second cassettes (pg. 1 lines 25-31 and pg. 11 lines 24-32).
Regarding claims 11 and 100, Smidler teaches that the transgenic organisms will be released to introduce the copies of the insertion DNA cassette into a local population of organisms of the strain (pg. 6 line 34 bridge pg. 7 line 11 and pg. 75 claim 44).
Regarding claims 95 and 101, Smidler teaches that the organism can be a vertebrate or an invertebrate (pg. 1 lines 25-32, pgs. 41-43 and pg. 62 claim 8).
Smidler does not teach:
(i) the CRISPR components comprise a nuclease and the nuclease induces conversion of one or more of a germline cell of the organism that are heterozygous for the second insertion DNA cassette into homozygotes by nuclease mediated cutting and repair by homologous recombination, thereby copying the second insertion DNA cassette, and
(ii) unlinked gene loci.
(i) Regarding a nuclease inducing a conversion of a germline cell from a heterozygous to a homozygous regarding the inserted DNA cassette, Gantz et al. teach the development of a mutagenic chain reaction (MCR) which converts heterozygous mutations to homozygous mutations in germline cells (see Abstract).
Specifically, Gantz teaches that MCS comprises “a construct having three components: 1) a Cas9 gene (expressed in both somatic and germline cells), 2) a guide-RNA (gRNA) targeted to a genomic sequence of interest, and 3) homology arms flanking the Cas9/gRNA cassettes that match the two genomic sequences immediately adjacent to either side of the target cut site (Fig. 1A). In such a tripartite construct, Cas9 should cleave the genomic target at the site determined by the gRNA (Fig. 1A) and then insert the Cas9/gRNA cassette into that locus via homology-directed repair (HDR) (Fig. 1B,C). Cas9 and the gRNA produced from the insertion allele should then cleave the opposing allele (Fig. 1D), followed by HDR-driven propagation of the Cas9/gRNA cassette to the companion chromosome (Fig. 1E,F).” (pg. 1 parag. 1 lines 6-14).
Gantz concludes by teaching:
“MCR technology should be applicable to different model systems and a broad array of situations including: enabling mutant F1-screens in pioneer organisms, accelerating genetic manipulations and genome engineering, providing a potent gene drive system for delivery of transgenes in disease vector or pest specie populations, and potentially serving as a disease-specific delivery system for gene therapy strategies. Although we provide an example in this study of an MCR element causing a viable insertional mutation within the coding region of a gene, by including two gRNAs in the MCR construct targeting separated sequences and appropriate flanking homology arms, one should also be able to efficiently generate viable deletions of coding or non-coding DNA. MCR using the simple core elements tested in this study is applicable to generating homozygous viable mutations, creating regulatory mutations of essential genes, or targeting other non-essential sequences. The method may also be adaptable to targeting essential genes if an in-frame recoded gRNA-resistant copy of the gene providing sufficient activity to support survival is included” (pg. 3 parag. 1 lines 1-13).
(ii) Regarding unlinked gene loci in claims 1 and 98 and claims 106-109, Esvelt K. teaches one of the ways to safeguard a gene drive system is via molecular confinement via unlinked gene loci. Specifically, Esvelt teaches:
“Molecular confinement involves building gene drives that can spread through populations of transgenic laboratory organisms but not wild organisms. For example, an sgRNA-only drive will spread exclusively through populations that already express Cas9 from an unlinked locus, while a Cas9+sgRNA drive targeting a synthetic sequence will only spread in transgenic laboratory populations with that sequence. Both methods are easy to implement and have been tested in yeast.” (pg. 3 parag. 2).
Further Smidler teaches placing the multiple guide RNAs across multiple target DNA sites (pg. 21 lines 24 bridge pg. 22 lines 1-8 and Example II).
Regarding claim 110, Esvelt 2014 teaches using independently preselected DNA sequences in a first insertion DNA cassette and a second insertion DNA cassette encoding one or more cargo genes (see Fig. 2 reproduced below and pg. 12 col. 1 parag. 2 bridge col. 2 parag. 2).
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Further, at the time of filing Esvelt 2014 teaches the detailed mechanism for assembling a gene drive system (Fig. 4) and its use (Fig. 5), both reproduced below.
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Thus at the time of filing the ordinary artisan would have found it prima facie obvious to combine the teachings of Smidler regarding a Cas9 gene drive system for the creation of transgenic organism such as an insect with the teachings of Gantz regarding the advantages of converting of one or more germline cells that are heterozygous for an insertion cassette to a homozygous insertion cassette and with the teachings of Esvelt regarding molecular confinement of gene drive systems to arrive at the claimed invention.
One of ordinary skill in the art would have been motivated to make such a combination since Gantz teaches that using MCR accelerates genetic manipulations and genome engineering by converting heterozygous mutations into homozygous mutations which copies the expression cassette to a second insertion site. While the claim is drawn to copying the second insertion DNA cassette this would have been obvious since Smidler and Esvelt 2014 teach that the second insertion cassette comprises cargo genes, which can then be expressed in the germline cell using the MCR of Gantz.
Further motivation is provided by Esvelt that guide RNAs should be placed on unlinked gene loci since this provides a means of confining the gene drive so that it cannot escape to wild-type populations.
There would have been a reasonable expectation of success that the second insertion cassette of Smidler could be converted from heterozygous expression to homozygous expression since Gantz teaches a method of converting and inducing heterozygous to homozygous mutations in an insect using a CRISPR components.
Thus the cited art provides the requisite teachings and motivations to make and use the invention as claimed.
Claim(s) 2, 3, 97 and 103 are rejected under 35 U.S.C. 103 as being unpatentable over Smidler et al. (WO 2015/105928 A1, published 7/16/2015), Gantz et al. (4/2015, Science, Vol. 348(6233), pgs. 442-444) and Esvelt K. (5/22/2015, addgene Blog, pages 1-6) and Esvelt et al. (2014, eLife, Vol. 3, pgs. 1-21) as applied to claims 1, 4, 7-11, 95, 98-101, 104 and 106-110 above, and further in view of Hammond et al. (1/2016, Nat. Biotechnol., Vol. 34(1), pgs. 78-83).
Smidler, Gantz and Esvelt are relied upon above in teaching a method of preparing an engineered organism using a Cas9 gene drive system.
Smidler, Gantz and Esvelt do not teach:
(i) using a recombinase enzyme (claims 2 and 3), and
(ii) Anopholes gambiae (claims 97 and 103).
Regarding a recombinase enzyme and Anopholes gambiae, Hammond teaches a Cas9 gene drive system targeting female reproduction in Anopholes gambiae (see Abstract).
Specifically, Hammond teaches using recombinase mediated cassette exchange (RMCE) to insert CRISPR alleles at a target locus in female Anopholes gambiae (pg. 4 parag. 1, pg. 7 parag. 4 and Table 1).
Hammond continues to teach that Anopholes gambiae is the main vector for malaria and a major insect pet (see Abstract and pg. 6 parag. 2).
Hammond continues to teach in Table 1 that RCME had a transmission rate of 94.4 to 100% into female Anopholes gambiae.
Thus at the time of filing the ordinary artisan would have found it prima facie obvious to combine the teachings of Smidler, Gantz and Esvelt regarding a Cas9 gene drive system for the creation of transgenic organism such as an insect with the teachings Hammond regarding a Cas9 gene drive system to modify Anopholes gambiae to arrive at the claimed invention.
One of ordinary skill in the art would have been motivated to make such a combination since Hammond teaches that their RMCE can achieve 100% transmission of their Cas9 gene drive system into female Anopholes gambiae and further motivates to select Anopholes gambiae since it is a major insect pest and is the main vector for malaria.
There would have been a reasonable expectation of success that the recombinase used by Hammond would work in the method of Smidler since Hammond also uses a Cas9 gene drive system for the creation of a transgenic insect.
Thus the cited art provides the requisite teachings and motivations to make and use the invention as claimed.
Conclusion
No claims are allowed.
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/DAVID A MONTANARI/Examiner, Art Unit 1632