DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1, 6, 9, 11-12, 17, 21, 27, 32, 34-35, 247, 316-317, and 320 were previously pending.
Receipt is acknowledged of the Amendments to the claims filed on 31 July, 2026. Claims 1, 6, 9, 11-12, 17, 21, 27, 32, 247, 317, and 320 are amended. Claims 34-35, and 316 are canceled. Claims 321-324 are newly added.
Applicant’s election without traverse of the invention of group I drawn to a modified cell and a plurality of modified cells (Claims 1, 6, 9, 11-12, 17, 21, 27, 32, 247, and 320) in the reply filed on 05 January, 2026 was previously acknowledged.
Claim 317 remains withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Therefore, claims 1, 6, 9, 11-12, 17, 21, 27, 32, 247, and 320-324 are pending and under examination in the present Official Action.
Priority
The present application is a 35 U.S.C. 371 national stage filing of International Application No. PCT/US2021/037670, filed 16 June, 2021, which claims priority to United States Provisional Application Nos. 63/134,271, filed 06 January, 2021, 63/085,687, filed 30 September, 2020, 63/063,821, filed 10 August, 2020, and 63/039,933, filed 16 June, 2020. Acknowledgment is made of applicant’s claim for priority.
The earliest possible priority for the instant application is 16 June, 2020.
Drawings
The Drawings submitted on 15 December, 2022 were previously accepted by the Examiner.
Examiner’s Comment
Throughout the present Official Action, where reference is made to the instant specification, the Examiner will be referencing the publication of the instant Application (US2023/0235305).
Claim Objections
Claim 1 is objected to because of the following informalities: the claim uses the word “comprise” incorrectly. The claim should recite wherein the plurality of cells is not comprised within a human organism instead of its current wording. Appropriate correction is required. It is noted that this amendment appears to have been made to overcome a rejection under 35 U.S.C. 101 for reading on a human organism. The objection presented here is intended to correct the claim language to the proper usage of “comprise” while respecting the apparent goal of the amendment.
Claim 321 is objected to because of the following informalities: abbreviations/acronyms need to be spelled out upon their first encounter in the claims (for example: “CD3, B2M, TRAC, PDCD1, PDL1, CIITA, TTR, LDHA, and HAO1”). Appropriate correction is required.
Claim 322 is objected to because of the following informalities: the claim fails to recite either “and” or “or” in the fourth line of the claim to separate list items (i)-(iii). The claim also fails to recite either “and” or “or” in the fourth line of the claim to separate the listed cell types within list item (ii). Appropriate correction is required.
Claim 323 is objected to because of the following informalities: the claim recites a singular noun to refer to a plural noun. The claim should recite -----wherein the modified cells are T cells----- instead. Appropriate correction is required.
Withdrawn Objections/Rejections in view of Applicant’s Amendments to the Claims
Claim Objections
The objection to claim 21 is withdrawn in view of Applicant’s amendments to the claims. Applicant has added the required space and better separated the lists.
The objection to claim 320 is withdrawn in view of Applicant’s amendments to the claims. Applicant has amended claim 320 to recite a definite article before “silencer”.
Claim Rejections - 35 USC § 112
The rejection of claims 9, 35, and 316 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 s withdrawn in view of Applicant’s amendments to the claims. Applicant has amended the claims to correct all previously raised issues of indefiniteness or else to cancel previously rejected claims.
Claim Rejections - 35 USC § 101
The rejection of claims 1, 6, 9, 11, 12, 17, 21, 27, 32, 35, 247, 316, and 320 under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter is withdrawn in view of Applicant’s amendments to the claims. Applicant has amended claim 1 to expressly require the cells not to comprise a human organism. It is noted that this usage of the term “comprise” is incorrect (see Claim Objections above) yet the amendment appears sufficient to overcome this rejection.
Maintained Rejections in view of Applicant’s Amendments and Arguments
Claim Rejections - 35 USC § 112
Claims 1, 6, 9, 11-12, 17, 21, 27, 32, 247, and 320 remain rejected and claims 321-324 are newly 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 claims contain 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 rejection has been modified as necessitated by Applicant’s amendments to the claims.
Claim 1 is broadly directed to any plurality of eukaryotic cells that has been modified by a Cas12i system to possess any genomic deletion in any gene wherein the deletion starts within about 5 to about 15 nucleotides of a 5’-NTTN-3’ sequence where N is any nucleotide, wherein the deletion is any size greater than 15 nucleotides, and wherein the cells “lack expression of the gene”. Encompassed by the vast genus of cells claimed is any eukaryotic cell (including any animal cell, any plant cell, any fungal cell with any size of deletion greater than 15 nucleotides in any gene (encompassing deletions of entire essential genes and partial deletions which would produce deleterious truncated protein species) wherein the cells “lack expression of the gene”. Dependent claims limit the size of the deletion the location within a gene, and limit the types of cell but these still read on deletions in any gene (including essential genes and deletions which would produce deleterious truncated proteins) and essentially any cell (because “a primary cell” and “terminally differentiated cell” does nothing to limit the type of cell, it only limits the source of a cell). In addition, where particular genes are specified (new claim 321) the claim continues to read on any size of deletion greater than about 15 nucleotides in length in any eukaryotic cell. Every dependent claim except for claim 11 depends directly from independent claim 1 and claim 11 only ups the deletion size to “greater than about 40 nucleotides”. Thus, every attempt to limit the scope of the genus of cells claimed occurs in a vacuum where the claims continue to read on vast genera independent of one another. This observation is noted for the purpose of compact prosecution.
The specification lists three genes (AAVS1, EMX1, and VEGF) which were targeted at several different loci (four loci for AAVS1, and three loci for EMX1 and VEGF) within each gene by Cas9 and a Cas12i2 (Specification TABLE 1). Working Example 1 describes the cloning of wild type Cas12i2 and two variants of Cas12i2 into a pET28 plasmid backbone, the expression of the Cas12i2 enzymes in E. coli BL21, the ordering of synthetic RNA oligos encoding RNA guides, the formation of ribonucleoprotein (RNP) complexes comprising Cas12i2 and guide RNA (Specification, [0519]-[0522]). Working Example 1 then describes the nucleofection of 293T cells (mammalian cells) with the RNPs followed by 72 hours of culture and extraction of genomic DNA from the 293T cells for analysis (Specification, [0522]). Working Example 2 merely analyses a separate result (insertions as opposed to indels more broadly) of the protocol of Working Example 1 (Specification [0534]). Working Examples 3-6 describe the generation of modified T cells by nucleofection of CD3+ T cells with Cas12i2 RNPs targeting four different loci within the B2M gene, four different loci within the TRAC gene, and four different loci within the PDCD1 gene (Specification, [0537]-[0539], TABLE 19, TABLE 20, TABLE 21). Working Example 7 describes the targeting of four different loci within the BCL11A enhancer in CD34+ HSPCs ([0569]-[0571], TABLE 22). With regard to deletion sizes, the specification describes deletions ranging from 0 to 50 nucleotides for AAVS1 (Figure 2A, 3A, 4A, and 5A), deletions ranging from 0 to around 50 nucleotides for EMX1 (Figure 6A, 7A, and 8A) deletions ranging from 0 to around 50 nucleotides for VEGF (Figure 9A, 10A, and 11A) in 293T cells. With regard to B2M, TRAC, and PDCD1 deletions, the specification describes only the percentage of indels occurring in a population of cells and does not describe the actual size of a given deletion achieved in these genes in either T cells or HSPCs (Figures 13-18). Thus, the specification describes only three different modified cells (293T cells, CD3+ T cells, and CD34+ HSPCs) only six different genes modified by Cas12i in these cells (AAVS1, EMX1, VEGF in 293T cells, B2M and TRAC in CD3+ T cells, and PDCD1 in CD34+ HSPCs), and only deletions as large as 50 nucleotides within AAVS1, EMX1, and VEGF in 293T cells. The specification does not describe any particular size of deletion within B2M or TRAC in CD3+ T cells or within PDCD1 in CD34+ HSPCs. The specification does not describe any cells other than 293T cells, CD3+ T cells, and CD34+ HSPCs. Thus, the specification describes only a few examples of modified cells comprising a Cas12i-induced genomic deletion in a gene wherein the deletion is greater than about 15 nucleotides in length (these examples are all within 293T cells only, they are all within only three genes (AAVS1, EMX1, and VEGF), and they are all only described up to deletions of about 50 nucleotides in length.
The art at the time of filing teaches that Cas12i systems have only been known to skilled artisans in the field of CRISPR-Cas enzymes since December, 2018 (Yan, et al., Science 363.6422 (2019): 88-91, Published online: December, 2018, hereinafter “Yan”). Yan and colleagues appear to be the first to identify and characterize Cas12i enzymes (Yan, Abstract). Therefore, the depth of knowledge concerning Cas12i functionality was established only a year and a half prior to the earliest possible priority date of the instant Application. In other words, the use of Cas12i to modify cells was in a nascent state at the time of filing. Yan identified the 5’-TTN-3’ PAM that both Cas12i1 and Cas12i2 systems recognize (Yan, Figure 3). It is noted that a 5’-TTN-3’ PAM is functionally equivalent to a 5’-NTTN-3’ PAM since Yan also teaches that Cas12i enzymes cut downstream of the PAM (Yan, Figure 3). At the time of filing, the extent to which Cas12i was used to modify cells was far from vast. WO 2019201331 (published: 24, October, 2019) (English Machine Translation) (hereinafter “Lai”) teaches the modification of a “cell” with a Cas12i1 or a Cas12i2 system (Lai, pages 13, and 21) but only exemplifies in vitro cleavage of Cas12i (Lai, page 27) and merely suggests to modify eukaryotic cells, prokaryotic cells, mammalian cells, or plant cells (Lai, page 37). US 10,808,245 (published: 27 February, 2020) (hereinafter “Arbor”) teaches Cas12i proteins (Arbor, FIG 2A, col. 3, lines 8-10) and teaches the codon optimization of a Cas12i and transfection of HEK 293T cells with a dCas12i to effectuate genome editing of mammalian cells (Arbor, col. 83, col. 85, lines 44-46, col. 89, lines 39-45). Thus, the extent to which Cas12i systems were used to modify cells was limited to mammalian cells and more specifically to HEK293T cells at the time of filing. At the time of filing it was also known that some deletions can cause the formation of truncated proteins that can kill the cells being modified (Yoshizawa et al., Human Molecular Genetics, Volume 9, Issue 1, 1 January 2000, Pages 69–78, hereinafter “Yoshizawa). Yoshizawa teaches that some deletions within the ataxin-3 gene cause aggregates to form which kill BHK-21 cells in culture (Yoshizawa, Abstract). Thus, a skilled artisan would have understood that one cannot delete any portion of any gene and still wind up with a cell possessing said deletion because some of such deletions kill the cell being modified.
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 inventor was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021). Further, A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that "only describe[d] one type of structurally similar antibodies" that "are not representative of the full variety or scope of the genus."). The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure "indicates that the patentee has invented species sufficient to constitute the gen[us]." See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) ("[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated."). See MPEP 2163(II)(A)(3)(a)(ii).
In this case, there is unpredictability in the deletion of any amount of any gene within any eukaryotic cell using a Cas12i system in the same way there is unpredictability doing so with any other gene editing technology. One cannot have a cell which was modified in such a way so as to kill the cell. In such a case, the genetic modification and the cell itself are mutually exclusive (See Yoshizawa above). Further, there is substantial variation in the genus of cells claimed because the genus encompasses every possible eukaryotic cell known and yet to be discovered. The instant specification describes only a few examples of modified cells comprising a Cas12i-induced genomic deletion in a gene wherein the deletion is greater than about 15 nucleotides in length (these examples are all within 293T cells only, they are all within only three genes (AAVS1, EMX1, and VEGF), and they are all only described up to deletions of about 50 nucleotides in length. In addition, the only examples Applicant has provided are in vitro, whereas the claims read on a cell in vivo. Applicant has not described a sufficient variety of species to reflect variation within the genus. Therefore, the instant application lacks written description for the entire genus of eukaryotic cells claimed.
Response to Arguments
Applicant argues against the above rejection under 35 U.S.C. 112(a) for lack of written description by arguing that the “specification provides extensive description of eukaryotic cells comprising a Cas12i induced genomic deletion in a gene” (Remarks, page 9), that “the working examples of the instant specification describe editing with Cas12iin several different eukaryotic cells” (Remarks, page 9), and that “Applicant disagrees with the Office’s assertion that ‘there is unpredictability in the deletion of any amount of any gene within any cell using a Cas12i system’” (Remarks, page 9). These arguments have been fully considered but have not been found persuasive for the following reasons.
Despite Applicant’s usage of the terms “describe” and “description” in the first two arguments, no attempt was made to engage with the breadth of the genus as set forth in the amended claims to argue for the position that the skilled artisan in the field of CRISPR gene editing would understand Applicant to have possession of the entire genus of cells claimed. Thus, these first two arguments appear to be more of a conclusory statement that the claims are described rather than an argument for the disclosure to have met the standard for written description under 35 U.S.C. 112(a). Indeed, the Examiner has discussed the specification and the working examples at length in the above rejection and provided art as well as legal support for drawing the conclusion that the skilled artisan would not understand Applicants to have possession of the entire genus of cells claimed. Of particular note is the fact that the claims still encompass any eukaryotic cell, any sized deletion (greater than about 15 nucleotides in length) which results in the cell lacking expression of the gene and which still allows for one to have the cell itself. The claims encompass a significant number of inoperative embodiments insofar as there are many cases in which the skilled artisan would understand a deletion of a particular size in a particular gene to be a characteristic which is mutually exclusive with the continued existence of that cell (i.e. one cannot possess what cannot exist in the first place). There is substantial variation in the genus of cells claimed because the genus encompasses every possible eukaryotic cell known and yet to be discovered. The instant specification describes only a few examples of modified cells comprising a Cas12i-induced genomic deletion in a gene wherein the deletion is greater than about 15 nucleotides in length (these examples are all within 293T cells only, they are all within only three genes (AAVS1, EMX1, and VEGF), and they are all only described up to deletions of about 50 nucleotides in length. In addition, the only examples Applicant has provided are in vitro, whereas the claims read on a cell in vivo. Accordingly, the first to arguments have been fully considered but have not been found to be persuasive.
Applicant also argues that one of skill in the art would be able to make RNA guides directed to their gene of choice and make precise edits in said gene citing the Examiner’s words that “precisely deleting various lengths of genomic DNA using CRISPR systems is well within the level of ordinary skill in the art” (Remarks, page 9). This argument misses the point of the instant rejection. The claims are not directed to the CRISPR system itself or even to a method of using a CRISPR system but rather cells having a genomic deletion. It is true that the skilled artisan knows how to design RNA guides to target specific genes and that doing so to induce deletions is well within the level of ordinary skill in the art. However, it is not true that this knowledge gives the skilled artisan the ability to predictably generate any eukaryotic cell having any sized deletion in any gene using any CRISPR system. This is exactly the position that the Examiner is arguing with the rejection set forth above and it is this position that Applicant has missed with their arguments. The Examiner agrees that the skilled artisan “would understand that a Cas12i system could be utilized to make deletions of greater than 15 nucleotides in a gene of choice in a eukaryotic cell” (Remarks, page 10, emphasis added). However, this possibility does not in itself represent to all other skilled artisans that the former has possession of every possible eukaryotic cell possessing any sized deletion greater than 15 nucleotides in any gene. Especially when considering the limited working examples provided in the instant Application coupled with the art at the time of filing. Accordingly, this argument has been fully considered but has not been found to be persuasive.
Claim Rejections - 35 USC § 103
Claims 1, 6, 9, 11-12, 17, 21, 27, 32, 247, and 320 remain rejected and claims 321-324 are newly rejected under 35 U.S.C. 103 as being unpatentable over WO 2019201331 (published: 24, October, 2019) (English Machine Translation) (hereinafter “Lai”) in view of Yan, et al., Science 363.6422 (2019): 88-91, Published online: December, 2018, hereinafter “Yan”, Zheng, et al., Biotechniques 57.3 (2014): 115-124, hereinafter “Zheng”, König, et al. Bio-protocol 8.2 (2018): e2688-e2688, hereinafter “Konig”, Zheng, et al., Supplementary Materials, Biotechniques 57.3 (2014): 115-124, hereinafter “Zheng Supplement”, and Stadtmauer, et al. Science 367.6481 (2020): eaba7365, hereinafter “Stadtmauer”, published 06 February 2020. This rejection has been modified as necessitated by Applicant’s amendments to the claims.
Lai teaches the modification of a “cell” with a Cas12i1 or a Cas12i2 system (Lai, pages 13, and 21) and suggests to modify eukaryotic cells, prokaryotic cells, mammalian cells, or plant cells (Lai, page 37). Lai teaches that the modification can be a deletion or a cleavage that results in a decrease in transcription of the target gene (Lai, page 12, fourth and fifth paragraphs). Lai teaches that the PAM associated with the Cas12i is a 5’-TTN where N is any nucleotide (Lai, page 36, second paragraph).
Lai does not explicitly teach at least 1000 modified cells comprising a Cas12i-induced genomic deletion in a gene wherein the deletion starts within about 5 nucleotides downstream of a 5’-NTTN-3’ sequence, wherein the deletion is greater than 15 nucleotides, wherein the cells lack expression of the gene.
Yan teaches that Cas12i cleaves immediately downstream of the 5’-TTN PAM (Yan, Fig. 3). Therefore, a person having ordinary skill in the art would have understood from the combined teachings of Lai and Yan that the Cas12i PAM identified as 5’-TTN is functionally equivalent to a 5’-NTTN-3’ sequence claimed because the Cas12i necessarily cleaves downstream of the 5’-TTN sequence. Further, a person having ordinary skill in the art would have known from Yan that Cas12i cleaves within about 5 nucleotides of the PAM because Yan teaches cleavage immediately following the PAM.
Neither Lai nor Yan teaches a deletion greater than about 15 nucleotides in length or at least 1000 cells or the cells lacking expression of the gene.
However, precisely deleting various lengths of genomic DNA using CRISPR systems (including the deletion of entire genes) is well within the level of ordinary skill in the art. A person having ordinary skill in the art knows that all that is needed is to design gRNA molecules flanking the area desired to be deleted to effectuate a precise deletion. Zheng describes such a system of using two gRNAs to precisely delete genomic DNA in human cells (Zheng, Abstract). Zheng teaches that using two gRNAs with a CRISPR-Cas system enabled the deletion of 10,000 bases encompassing the entire CDC42 gene (Zheng, page 116, first full paragraph, Figure 2). Further, a person having ordinary skill in the art knows that any number of cells can be modified to produce a plurality of any number of modified cells (simultaneously or at different times) by simply increasing the amount of reaction components and cells. In fact, Zheng teaches to modify 100,000 HEK293T cells (Zheng, page 116, “Targeted DNA deletion”).
Therefore, it would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have used the Cas12i system to have induced a deletion of more than 15 nucleotides in length and to have arrived at the invention claimed with a reasonable expectation of success because Lai suggests to use the Cas12i system in mammalian cells, Yan teaches the immediate cleavage of the Cas12i enzyme following the PAM sequence, and Zheng evidences the level of ordinary skill in the art of CRISPR-Cas genetic modifications in mammalian cells to encompass the use of two gRNAs to delete precise regions of genomic DNA well over 15 nucleotides in length. There would have been a reasonable expectation of success insofar as Lai suggested to use the Cas12i system in mammalian cells and Yan and Zheng teach that Cas12i cleaves efficiently immediately following 5’-TTN PAMs and that two gRNA systems can be used to delete large portions of genomic DNA from mammalian cells respectively.
Regarding claim 6, Lai, Yan, and Zheng do not teach a deletion within about 30 nucleotides specifically.
However, Konig teaches a method for the stepwise knockout of genes from E. coli using CRISPR and recommends to delete 30 nucleotides at a time within the target gene to avoid post-mutation cleavage (Konig, Abstract, page 9, last partial paragraph).
Therefore, it would have been prima facie obvious to a person having ordinary skill in the art to have deleted around 30 nucleotides at a time in the case of a stepwise knockout of a gene to avoid post-mutation cleavage as taught by Konig.
Regarding claim 9, were a person having ordinary skill in the art to have used two gRNAs as taught by Zheng to delete a portion of genomic DNA using the Cas12i system of Lai and Yan, the second guide RNA (the downstream gRNA) would necessarily facilitate cleavage within about 5 nucleotides of a 5’-NAAN-3’ sequence on the sense strand because said second guide RNA would be designed complementary to the antisense strand (which would mean there would be a 5’-NAAN-3’ on the sense strand at the second cleavage site) according to Zheng (Zheng Supplement, Fig. S3).
Regarding claim 11, Zheng teaches a deletion of 10,000 nucleotides.
Regarding claim 12, the deletion in Zheng encompassed exons within the CCL2 locus (Zheng, Figure 3).
Regarding claim 17, Konig recommends the stepwise deletion of 30 nucleotides at a time in E. coli to knock out a gene with multiple 30 nucleotide deletions.
Regarding claim 21, Lai and Yan teach a 5’-TTN-3’ PAM sequence. The listed possible 5’-NTTN-3’ sequences in claim 21 are encompassed by the teachings of Lai and Yan.
Regarding claim 27, Zheng teaches the modification of HEK293T cells which are cells from a cell line (Zheng, page 116, “Cell Culture”).
Regarding claim 32, Lai claims progeny of the modified cells (Lai, page 38).
Regarding claim 247, the culture of modified HEK293T cells of Zheng is interpreted as meeting the “composition” comprising the modified cells limitation.
Regarding claim 320, Lai teaches to induce a cleavage that results in a decrease in transcription of the target gene (Lai, page 12, fourth paragraph). Thus, Lai suggests deleting a region that regulates transcription of the gene.
Regarding claim 322, Lai teaches that the cell can be a stem cell (Lai, page 15, second paragraph).
Regarding claims 321 and 323, neither Lai, Yan, Konig, nor Zheng teach to delete the TRAC gene or to modify a T cell specifically.
Stadtmauer teaches that T cell therapy can increase the natural antitumor response of a cancer patient and that combining the redirection of immune specificity with genome editing using CRISPR has the potential to improve the efficacy and increase the safety of T cell therapies (Stadtmauer, Introduction). Thus, a person having ordinary skill in the art would have been motivated to use CRISPR techniques to modify T cells to improve the efficacy and increase the safety of T cell therapies. Stadtmauer specifically teaches the deletion of the TRAC gene from T cells to reduce TCR mispairing and to enhance expression of a synthetic cancer-specific TCR transgene (Stadtmauer, Abstract). Thus, a person having ordinary skill in the art would have been motivated to delete the TRAC gene specifically from T cells to reduce TCR mispairing and to enhance expression of a synthetic cancer-specific TCR transgene in T cell therapies.
Regarding claim 324, Konig recommends to delete 30 nucleotides at a time within the target gene to avoid post-mutation cleavage (Konig, Abstract, page 9, last partial paragraph) and Zheng teaches a deletion of 10,000 nucleotides. 100% of the cells possessing the deletions of Konig and Zheng possess the deletions of Konig and Zheng.
Response to Arguments
Applicant argues that there would have been no reasonable expectation of success in combining Lai, Yan, and Zheng because Lai does not provide working examples, Yan does not teach deletion, and Zheng and Konig do not relate to Cas12i at all (Remarks, page 12). Applicant additionally argues that Cas9 and Cas12i yield a different pattern of deletions and that the Cas12i induced indels represent a distinct pattern (Remarks, pages 12-13). These arguments have been fully considered but have not been found persuasive for the following reasons.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). In addition, the fact that Lai does not provide any working examples does not preclude a prima facie finding of obviousness. The specification need not contain an example if the invention is otherwise disclosed in such manner that one skilled in the art will be able to practice it without an undue amount of experimentation. In re Borkowski, 422 F.2d 904, 908, 164 USPQ 642, 645 (CCPA 1970). Thus, the fact that Lai does not have a working example in itself does not lead to the conclusion that Lai is not an enabling disclosure. Lai teaches Cas12i systems and suggests using those systems to delete DNA in a eukaryotic cell. Yan operationalizes the suggestion of Lai by teaching the precise sites where Cas12i systems cleave and Zheng teaches the level of ordinary skill in the art with regard to the use of multiple gRNAs to delete large portions of genomic DNA using CRISPR systems. Applicant has not argued nor required the claims to preclude the use of multiple gRNAs to delete entire genes. In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., “a different pattern of deletions”) are not recited in the rejected claims. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Accordingly, these arguments have been fully considered but have not been found to be persuasive.
Double Patenting
Claims 1, 6, 9, 11-12, 17, 21, 27, 32, 247, and 320 remain rejected and claims 321-324 are newly rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of U.S. Patent No. 11,912,992, claims 1-55 of U.S. Patent No. 11,168,324, claims 1-20 of U.S. Patent No. 10,808,245, and claims 1-10, 12-15, 17-18, 20-22, and 24-33 of U.S. Patent Application No. 17,020,414 (allowed but yet to be issued). Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are directed to an obvious variant of the inventions claimed in each of the reference patents.
Claim 1 of the ‘992 patent recites: An engineered, non-naturally occurring Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)—associated (Cas) system comprising: (a) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence; and (b) a CRISPR-Cas effector protein or a nucleic acid encoding the CRISPR-Cas effector protein, wherein the CRISPR-Cas effector protein comprises an amino acid sequence with at least 95% identity to SEQ ID NO: 5, and a nuclear localization sequence (NLS) having an amino acid sequence having at least 90% identical to KRPAATKKAGQAKKKK (SEQ ID NO: 301); wherein the CRISPR-Cas effector protein binds to the RNA guide, and wherein the spacer sequence is complementary to at least 15 nucleotides of a target nucleic acid.
Claim 1 of the ‘324 patent recites: An engineered, non-naturally occurring Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated (Cas) system comprising: (a) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence; and (b) a CRISPR-Cas effector protein or a nucleic acid encoding the CRISPR-Cas effector protein, wherein the CRISPR-Cas effector protein comprises an amino acid sequence with at least 95% identity to SEQ ID NO: 5, wherein the CRISPR-Cas effector protein binds to the RNA guide, and wherein the spacer sequence is complementary to at least 15 nucleotides of a target nucleic acid.
Claim 1 of the ‘245 patent recites: An engineered, non-naturally occurring Cluster Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated (Cas) system comprising: (a) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence; and (b) a CRISPR-Cas effector protein or a nucleic acid encoding the CRISPR-Cas effector protein, wherein the CRISPR-Cas effector protein comprises the amino acid sequence set forth in SEQ ID NO: 5, wherein the CRISPR-Cas effector protein binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid.
Claim 1 of the ‘414 application recites: An engineered, non-naturally occurring Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) - associated (Cas) system comprising:(a) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence; and(b) a CRISPR-Cas effector protein or a nucleic acid encoding the CRISPR-Cas effector protein, wherein the CRISPR-Cas effector protein comprises an amino acid sequence with at least 95% identity to SEQ ID NO: 14 or SEQ ID NO: 16, and the CRISPR- Cas effector protein further comprises at least one nuclear localization signal (NLS),at least one nuclear export signal (NES), or at least one NLS and at least one NES,wherein the CRISPR-Cas effector protein binds to the RNA guide, and wherein the spacer sequence is capable of hybridizing to a target nucleic acid in a eukaryotic cell.
Each of the reference patents and applications contain claims directed to a cell comprising “the system of claim 1” (‘992 claim 24, ‘324 claim 21, ‘245 claim 19, ‘414 claim 18). The reference patents share the same supporting disclosure, all of the reference patents and applications contain claims directed to a method of binding the system to DNA in a cell, and two of the reference patents and the reference application contain claims directed to that method wherein the binding results in “cleavage, or a formation of an insertion or a deletion” (‘245 claim 20, ‘992 claims 26-28, ‘324 claims 25-28, ‘414 claims 22, and 24-25).
Instant claim 1 recites: A modified cell comprising a Cas 12i-induced genomic deletion in a gene, wherein (a) the deletion starts within about 5 nucleotides to about 15 nucleotides downstream of a 5' - NTTN-3' sequence, wherein N is any nucleotide;(b) wherein the deletion is greater than about 15 nucleotides in length; and(c) wherein the modified cell substantially lacks expression of the gene.
The reference patents do not claim a Cas12i-induced deletion that starts within about 5 to about 15 nucleotides downstream of a 5’-NTTN-3’ sequence, wherein N is any nucleotide or wherein the deletion is greater than about 15 nucleotides in length, or wherein the cell substantially lacks expression of the gene.
Note that MPEP 804(II)(2)(a) sets forth instances where it is acceptable to utilize the disclosure of a U.S. patent document in conjunction with its claims for ODP rejections.
In particular, the MPEP notes that the portion of the specification that supports the patent claims may be considered. The court in AbbVie Inc. v. Kennedy Institute of Rheumatology Trust pointed out that “this use of the disclosure is not in contravention of the cases forbidding its use as prior art, nor is it applying the patent as a reference under 35 U.S.C. 103, since only the disclosure of the invention claimed in the patent may be examined.” In AbbVie Inc. v. Kennedy Institute of Rheumatology Trust, 764 F.3d 1366, 112 USPQ2d 1001 (Fed. Cir. 2014). The court explained that it is also proper to look at the disclosed utility in the reference disclosure to determine the overall question of obviousness in a nonstatutory double patenting context. See Pfizer, Inc. v. Teva Pharm. USA, Inc., 518 F.3d 1353, 86 USPQ2d 1001 (Fed. Cir. 2008); Geneva Pharmaceuticals Inc. v. GlaxoSmithKline PLC, 349 F3d 1373, 1385-86, 68 USPQ2d 1865, 1875 (Fed. Cir. 2003).
In this case, the shared disclosure teaches that the CRISPR-Cas enzyme in question is a Cas12i and that the PAM recognized by the Cas12i is a 5’-NTTN-3’ PAM (See FIG. 41B). In particular, the shared disclosure teaches that the enzyme encompassed by the SEQ ID NO: 5 claimed is a Cas12i2 enzyme (Col. 3, lines 46-49). The shared disclosure also teaches cleavage at two sites to result in a deletion (Col. 12, lines 10-12). The shared disclosure also teaches the production of deletions ranging from 50 to 2000 base pairs using the Cas12i system in a cell (Col. 39, lines 64-67, Col. 40, lines 1-3). Lastly, the shared disclosure teaches that the purpose of the systems is to control gene expression (Col. 1, lines 31-36).
Therefore, the instantly claimed invention would have been an obvious variant of the cells already claimed in each of the reference patents in view of the supporting disclosure which is shared between those reference patents.
Claims 1, 6, 9, 11-12, 17, 21, 27, 32, 247, and 320 remain provisionally rejected and claims 321-324 are newly provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-33 of copending Application No. 17,497,725 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are directed to an obvious variant of the inventions claimed in the reference application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 1 of the reference application recites: An engineered, non-naturally occurring Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) - associated (Cas) system comprising:(a) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence, wherein the direct repeat sequence comprises 5'-CCGUCNNNNNNUGACGG-3' (SEQ ID NO: 202), wherein N is any nucleobase; and (b) a CRISPR-Cas effector protein or a nucleic acid encoding the CRISPR-Cas effector protein, wherein the CRISPR-Cas effector protein comprises at lease one nuclear localization signal (NLS), at least one nuclear export signal (NES), or at least one NLS and at least one NES; and wherein the CRISPR-Cas effector protein binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid.
The reference application contains claims directed to a cell comprising “the system of claim 1” (claims 26-29). The reference application shares the same supporting disclosure as the reference patents referenced above, and the reference application contains claims directed to a method of binding the system to DNA in a cell wherein the binding results in cleavage, or a “formation of an insertion or a deletion” (claims 30-33).
Instant claim 1 recites: A modified cell comprising a Cas 12i-induced genomic deletion in a gene, wherein (a) the deletion starts within about 5 nucleotides to about 15 nucleotides downstream of a 5' - NTTN-3' sequence, wherein N is any nucleotide;(b) wherein the deletion is greater than about 15 nucleotides in length; and(c) wherein the modified cell substantially lacks expression of the gene.
The reference application does not claim a Cas12i-induced deletion that starts within about 5 to about 15 nucleotides downstream of a 5’-NTTN-3’ sequence, wherein N is any nucleotide or wherein the deletion is greater than about 15 nucleotides in length, or wherein the cell substantially lacks expression of the gene.
Note that MPEP 804(II)(2)(a) sets forth instances where it is acceptable to utilize the disclosure of a U.S. patent document in conjunction with its claims for ODP rejections.
In particular, the MPEP notes that the portion of the specification that supports the patent claims may be considered. The court in AbbVie Inc. v. Kennedy Institute of Rheumatology Trust pointed out that “this use of the disclosure is not in contravention of the cases forbidding its use as prior art, nor is it applying the patent as a reference under 35 U.S.C. 103, since only the disclosure of the invention claimed in the patent may be examined.” In AbbVie Inc. v. Kennedy Institute of Rheumatology Trust, 764 F.3d 1366, 112 USPQ2d 1001 (Fed. Cir. 2014). The court explained that it is also proper to look at the disclosed utility in the reference disclosure to determine the overall question of obviousness in a nonstatutory double patenting context. See Pfizer, Inc. v. Teva Pharm. USA, Inc., 518 F.3d 1353, 86 USPQ2d 1001 (Fed. Cir. 2008); Geneva Pharmaceuticals Inc. v. GlaxoSmithKline PLC, 349 F3d 1373, 1385-86, 68 USPQ2d 1865, 1875 (Fed. Cir. 2003).
In this case, the disclosure of the reference application (reference made to the shared disclosure of the reference patents above) teaches that the CRISPR-Cas enzyme in question is a Cas12i and that the PAM recognized by the Cas12i is a 5’-NTTN-3’ PAM (See FIG. 41B). In particular, the shared disclosure teaches that the enzyme encompassed by the SEQ ID NO: 5 claimed is a Cas12i2 enzyme (Col. 3, lines 46-49). The shared disclosure also teaches cleavage at two sites to result in a deletion (Col. 12, lines 10-12). The shared disclosure also teaches the production of deletions ranging from 50 to 2000 base pairs using the Cas12i system in a cell (Col. 39, lines 64-67, Col. 40, lines 1-3). Lastly, the shared disclosure teaches that the purpose of the systems is to control gene expression (Col. 1, lines 31-36).
Therefore, the instantly claimed invention would have been an obvious variant of the cells already claimed in each of the reference patents in view of the supporting disclosure which is shared between those reference patents.
Applicant requests that the double patenting rejections above be held in abeyance (Remarks p. 13-14). A request to hold a rejection in abeyance is not a proper response to a rejection. Rather, a request to hold a matter in abeyance may only be made in response to an OBJECTION or REQUIREMENTS AS TO FORM (see 37 CFR 1.111(b) and MPEP §714.02). Thus, the double patenting rejections of record have been maintained as no response to these rejections has been filled by applicant at this time.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/BRENDAN THOMAS TINSLEY/Examiner, Art Unit 1634
/MARIA G LEAVITT/Supervisory Patent Examiner, Art Unit 1634
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