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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 2/9/2026 has been entered.
Claims status
Claims 2, 4, 5, 24, 25, 27, 30 is/are cancelled. Claims 1, 3, 6, 7, 9, 10, 12, 13, 16, 20, 22, 23 is/are currently pending and is/are under examination.
Claim Rejections - 35 USC § 112(b)
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.
Rejection of Claims 1, 2-7, 9, 10, 12, 13, 16, 20, 22, 23 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention is withdrawn in light of claim amendment or cancellation.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Rejection of Claim(s) 1, 2, 3, 4-7, 9-10, 12, 13, 16, 20, 22, 23 under 35 U.S.C. 103 as being unpatentable over Wang et al (Science Advances, 4, February 2018; ref of record), Wertz (Neuron, 106, 2020, ref of record) and Carbonaro et al (MOLECULAR THERAPY Vol. 13, No. 6, June 2006; ref of record) as evidenced by Platt et al (Cell, 159, October 2014; ref of record), and Breschi et al (Comparative transcriptomics in human and mouse. Nat Rev Genet. 2017 July ; 18(7): 425–440) is withdrawn in light of claim amendment.
Claim(s) 1, 3, 6, 7, 9, 10, 12, 13, 16, 20, 22, 23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Doench et al (Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotech. Vol. 34, Feb 2016), Wertz et al (Neuron, 106, 2020, ref of record) and Carbonaro et al (MOLECULAR THERAPY Vol. 13, No. 6, June 2006; ref of record) as evidenced by Platt et al (Cell, 159, October 2014; ref of record).
Claims are directed to a method for generating a genome-scale in vivo library for genomic screening in mice comprising intravenous delivery of genomic sgRNA library (=plurality of sgRNAs that target at least 10,000 or more genes expressed in developing, quiescent or regenerating liver) comprised in a retroviral vector at the recited dose to a neonatal mouse, wherein the mouse expresses a Cas protein or its variants in its cells, including liver tissue, and the intravenous delivery of the genomic sgRNA library results in transduction of at least the liver cells with at least one sgRNA per transduced cell.
Taken together, the claimed method uses a mouse genomic sgRNA library in vivo by delivering the library to a mouse that expresses a Cas protein or its variants in its cells, including liver tissue. The means of delivery recited is intravenous that results in transduction of cells in the mouse, including liver cells.
Further, the claims require the neonatal mouse to have or have a predisposition for a non-proliferative, non-neurological inflammatory, cardiovascular or metabolic disease.
Regarding claims 1, 3, 12 and 16, Doench teaches a mouse genomic sgRNA library comprised in a retroviral vector, wherein the sgRNA library is genome-wide and targets about 20,077 genes in the entire mouse genome (Online Methods: Avana and Asiago libraries). Since the entire mouse genome encodes only about 22,000 protein-coding genes (as evidenced by Breschi, page 3, para 2), Doench’s library necessarily targets greater than 10,000 genes and/or greater than 13,190 genes and/or greater than 80% genes expressed in a mouse liver and/or at least one tumor suppressor gene (as required for claims 1, 3, 12 and 16). See also identification of tumor suppressor genes in the vemurafenib resistance screening, thus teaching that Doench’s library necessarily targets at least one tumor suppressor gene (Supplementary Table 6; pg. 185, col. 1, para 3).
Regarding claim 13, Doench teaches six sgRNAs per gene (Online Methods: Avana and Asiago libraries).
As noted by Doench, prior art taught mouse sgRNA libraries comprised in retroviral vectors (Figure 1). Such libraries, including Doench’s, were used by ordinary artisan to perform both in vitro and in vivo genomic screening. To this end, Doench exemplifies the use of their sgRNA library for in vitro genomic screening (Online Methods: Screening; Figures 2, 3; Table 1).
Wertz teaches the use of Doench’s sgRNA library for in vivo genomic screening in mice (In vivo Genetic Screening: Lentiviral library concentration). To use Doench’s sgRNA library for in vivo genomic screening in mice, Wertz delivers the library to Rosa26 Cas9 knockin mice (see Rosa26 Cas9 knockin mice in Experimental model and subject details: Animals). These mice express Cas9 protein in their cells, including liver cells, and Cas9 comprises a EGFP detectable label and is under the control of a Cre-inducible promoter (as required by claim 1a, 7, 9 and 10; as evidenced by Figure 1A and 1B in Platt).
Wertz notes the advantage of genomic screens wherein large number of genes are targeted by stating that “Unbiased in vivo genome-wide genetic screening is a powerful approach to elucidate new molecular mechanisms” (Summary). Wertz shows the utility of such an unbiased genomic screen in identifying disease-related genetic factors by applying the genomic screen to an Huntington disease model (Figure 4).
Since Wertz applies genomic screen to study Huntington disease, Wertz delivers Doench’s sgRNA library to the Cas9-expressing mice via intracranial injection (Figure 1).
Although Wertz exemplifies the in vivo use of Doench’s sgRNA library in screening disease-related genetic factors by applying the genomic screen to an Huntington disease model, neither Wertz nor Doench deliver the sgRNA library comprised in a retroviral vector intravenously to a neonatal mouse that has or is predisposed to a non-proliferative, non-neurological inflammatory, cardiovascular or metabolic disease.
However, intravenous delivery of retroviral vectors to transduce liver cells in neonatal mice was known.
Carbonaro teaches a method for delivering transgenes to neonatal mice that are wild type and also to neonatal mice that have or are predisposed to SCID, a non-proliferative, non-neurological inflammatory disease (as required by claim 1; Abstract; Methods: Mice). Carbonaro delivers lentiviral injection to neonatal mice intravenously at a dose of 107-108 TU which results in long-term transduction of liver cells into adulthood (Abstract, Figure 4, 5, Methods: Injection of lentivirus; as required by claim 1). The range taught by Carbonaro overlaps with the range recited in claim 20. According to MPEP 2144.05(I), “In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists”. Furthermore, as noted above, an ordinary artisan would use routine optimization to inject the amount of viral vector that results in desired percent of liver cells to be transduced. According to MPEP 2144.05 (II), “It is a settled principle of law that a mere carrying forward of an original patented conception involving only change of form, proportions, or degree, or the substitution of equivalents doing the same thing as the original invention, by substantially the same means, is not such an invention as will sustain a patent, even though the changes of the kind may produce better results than prior inventions."). See also KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416, 82 USPQ2d 1385, 1395 (2007) (identifying "the need for caution in granting a patent based on the combination of elements found in the prior art."). Therefore, in teaching lentiviral injection at a dose of 107-108 TU, Carbonaro also renders the dose of 4x107-6x107 TU/ml (as required by claim 20) prima facie obvious. Furthermore, since Carbonaro delivers the lentiviral vector to neonatal mice, some of the transduced cells, including transduced liver cells, in these developing mice would be in a state of proliferation (as required by claim 6).
Although Carbonaro does not quantify the %cells in the liver that were transduced by their dose of lentiviral vector, Carbonaro shows that increasing dose resulted in increasing copy number/cell and increased number of cells transduced and in the data shown, at least 25% of liver cells appear to be transduced (Figure 6). Furthermore, based on Carbonaro’s teachings, an ordinary artisan could transduce desired % of liver cells by optimizing lentiviral dose (See MPEP 2144.05(II) regarding routine optimization above).
The combination of prior art cited above under 35 U.S.C. 103 satisfies the factual inquiries as set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966). Once this has been accomplished the holdings in KSR can be applied (KSR International Co. v. Teleflex Inc. (KSR), 550 U.S., 82 USPQ2d 1385 (2007): Exemplary rationales that may support a conclusion of obviousness are from MPEP 2143.
In the present situation, rationale (A) Combining prior art elements according to known methods to yield predictable results is applicable. MPEP 2143 guides that for rationale A “Office personnel must articulate the following: (1) a finding that the prior art included each element claimed, although not necessarily in a single prior art reference, with the only difference between the claimed invention and the prior art being the lack of actual combination of the elements in a single prior art reference; (2) a finding that one of ordinary skill in the art could have combined the elements as claimed by known methods, and that in combination, each element merely performs the same function as it does separately; (3) a finding that one of ordinary skill in the art would have recognized that the results of the combination were predictable; and (4) whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness”.
(1) The prior art of Doench, Wertz and Carbonaro included each element claimed.
Doench taught a mouse genome-wide sgRNA library (Asiago library). Doench also taught methods to optimize sgRNAs included in the library and methods to generate the library (see Criterion A-C in Online Methods: Avana and Asiago libraries, Library Creation).
Wertz taught methods to use genome-wide sgRNA library, such as that of Doench, to perform in vivo genomic screening in mouse disease models by delivering the sgRNA library to a Cas9-expressing mouse (Abstract, Figure 1, Methods: In vivo Genetic Screening). Wertz also provides guidance regarding how to optimize the dose of lentiviral vector comprising the sgRNA library to achieve desired spread in a tissue with desired multiplicity of infection (i.e. ratio between number of viral particles/cells transduced) (Methods: In vivo lentiviral injection parameters, Multiplicity of infection (MOI), Lentiviral spread).
Carbonaro taught intravenous injection of lentiviral vector in neonatal mice such that liver cells are transduced.
(2) An ordinary artisan could combine the elements taught by Doench, Wertz and Carbonaro with each element performing the same function as it does separately. As noted by Doench and Wertz, using genome-wide sgRNA libraries in vitro and in vivo for genomic screening of genetic factors related to diseases was known. Thus, an ordinary artisan recognizes that genomic screening of genetic factors related to a disease, such as the claimed non-proliferative, non-neurological inflammatory, metabolic or infectious diseases associated with the liver could be performed by delivering Doench sgRNA library to Wertz’s Cas9 mouse using intravenous delivery of Carbonaro when the mouse is a neonate and is a model for a non-proliferative, non-neurological inflammatory, metabolic or infectious disease. An ordinary artisan recognizes that in such a combination, the sgRNA library will perform its function of identifying target genes along with Cas9 while intravenous delivery would result in sgRNA expression in the liver cells of the neonate.
(3) An ordinary artisan would recognize that the combination of these elements would result in a predictable result of a mouse comprising the genome scale sgRNA library, at least in the liver of the mouse (as required by claim 23).
Therefore, the teachings of the cited prior art in the obviousness rejection above provide the requisite teachings with a clear, reasonable expectation. The cited prior art meets the criteria set forth in both Graham and KSR. Therefore, it would be obvious to a person of ordinary skill in the art to combine the teachings of Doench, Wertz and Carbonaro to arrive at a method that generates a genome-scale in vivo library for genomic screening. Furthermore, an ordinary artisan would be motivated to by deliver Doench sgRNA library to Wertz’s Cas9 mouse using intravenous delivery of Carbonaro when the mouse is a neonate and is a model for a non-proliferative, non-neurological inflammatory, metabolic or infectious disease to identify genetic factors related to such a disease.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in
the art at the effective time of filing of the invention, especially in the absence of evidence to the
contrary.
Response to Arguments
Applicant’s arguments with respect to the U.S.C. 103 rejection of claim(s) 1, 3, 6-7, 9-10, 12-13, 16, 20, and 22-23 have been considered but are moot because the new ground of rejection necessitated by claim amendments.
Arguments pertinent to instant U.S.C. 103 rejection are addressed below.
Applicant argue that “Wertz is directed to an in vivo Huntington's disease screen in mouse brain requiring VSV-G coated lentivirus that have high neuronal tropism in the striatum, and thus is directed to the use of a mouse having a neurological disease excluded from the claims” and “Carbonaro provides a study investigating adenosine deaminase replacement therapy, and was cited primarily for disclosure of viral vector dose. None of these references teach or suggest the invention as presently claimed. Moreover, modification of any of these references to arrive at the claimed methods would render them unsuitable for their primary purposes (i.e. proliferative disease screen, Huntington's disease screen, ADA replacement therapy).” (page 6, para 1)
In response, Wertz indeed develops a genome-wide genetic screen targeting the brain but teachings from Wertz’s are applicable to developing genome-wide genetic screen targeting other organs. Specifically, Wertz teachings about the advantages of using the unbiased mouse genome-wide sgRNA library (Summary) and use of Cas9 mouse for in vivo CRISPR-based screening (Figure 1). Thus, Wertz’s teachings remain pertinent to the U.S.C. 103 rejection of the claims.
Carbonaro provides teachings pertinent to delivery of lentiviral vectors, such as used by Wertz to deliver the sgRNA library, to the liver of a neonatal mouse using intravenous route. Thus, Carbonaro’s teachings remain pertinent to the U.S.C. 103 rejection of the claims.
None of the references are modifies, instead key teachings are combined to arrive at the claimed invention. Critically, application of genome-wide sgRNA library for genomic screening of various genetic factors, including genetic factors related to diseases, was known. Even the instant application does not apply the method to a non-proliferative, non-neurological inflammatory, metabolic or infectious disease. However, an ordinary artisan interested in genetic factors related to a non-proliferative, non-neurological inflammatory, metabolic or infectious disease could deliver a sgRNA library to a Cas9 mouse with the disease of interest without requiring inventive ingenuity.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MATASHA DHAR whose telephone number is (571)272-1680. The examiner can normally be reached M-F 8am-4pm (EST).
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/MATASHA DHAR/Examiner, Art Unit 1632
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