DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Claims 59, and 61-76 are under exam. Claims 55-58 are withdrawn from examination. Claims 1-55 and 60 were cancelled.
WITHDRAWN REJECTION
Claim Rejections - 35 USC § 112
Claims 65, 67 and 74 were rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as failing to set forth 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.
Claims 65 and 67 required that the library of modulatory compounds comprise at least 3 molecules from Tables 2-3 or at least about 15 contiguous nucleotides of a gene encoding a protein of Tables 3-5D. The rejection is withdrawn following cancellation of references to Tables.
MAINTAINED REJECTION
Claim Rejections - 35 USC § 103
Claims 59, 61-63, 70-73 and 75 remain rejected under 35 U.S.C. 103 as being unpatentable over Martinez-Lage et al (Biomedicines. 2018 Nov 12; hereinafter "Martinez-Lage;" See PTO-892) in view of Sharma et al (Int J Mol Sci. 2018 Mar 21; hereinafter "Sharma;" See PTO-892).
Regarding claim 59 and 70-73: Martinez-Lage is directed to use of CRISPR/Cas9 in therapeutic settings such as cancer. (See Martinez-Lage Abstract). Martinez-Lage taught “High-throughput RNAi genomic library screens have provided important information on causal links between individual genes and loss-of-function phenotypes.” It is also noted that Martinez-Lage taught a CRISPR library and indicated that “CRISPR/Cas9 provides some advantages over RNAi including complete inactivation (total knockdown), high reproducibility, and the capability to target the whole genome, including enhancers, promoters, introns, and intergenic regions.” (See Martinez-Lage p. 4, para 4). Further Martinez-Lage taught that “cells can be treated with a CRISPR library and then exposed to an anti-cancer drug.” “Negative selection is used to detect dead or slow-growing cells efficiently under a specific condition.” Martinez-Lage taught that “[f]or example, if a pool of gRNAs is used to make a set of random mutants, those cells that carry gRNAs targeting a survival-essential gene will not survive, and after several passages only surviving cells with targeted non-essential genes will remain. Thus, by sequencing a pool of gRNAs from the initial status and survival status (using next-generation sequencing), it would be possible to identify those survival-essential candidate genes.”
Cells treated with a CRISPR library and then exposed to an anti-cancer drug as taught by Martinez-Lage reads on the claimed contacting a sample of cancer cells with a library of gene modulatory agents, where the gene modulatory agent knocks down function of a gene as recited in step (a). Culturing for several passages as taught by Martinez-Lage reads on step (b) of claimed method. Sequencing a pool of gRNAs from the initial status and survival status (using next-generation sequencing) to identify those survival-essential candidate genes reads on the claimed sequencing step (c). It is also indicated that Martinez taught that their method identifies “promising candidates for molecularly targeted drugs.” (See Martinez Lage p. 5, line 1). As such, Martinez taught using a therapeutic molecule to treat cancer, wherein the cancer is determined to be susceptible to the therapeutic molecule as required by claim 59.
Further, Martinez-Lage taught that high-throughput library screening using CRISPR-Cas9 in primary cells as the next step in their proposed method. Martinez-Lage indicated that CRISPR delivery to primary tumor cells is a "challenge for the future". It is also pointed out that Martinez-Lage taught viral delivery systems for delivery of CRISPR-Cas9 components. Martinez-Lage explicitly taught that “viruses are highly versatile particles because they can be applied in vitro, ex vivo or in vivo, which eases both efficacy and safety testing” (See Martinez-Lage pp. 8; 4th para). In addition, Martinez-Lage taught hat non-viral delivery of CRISPR-Cas9 particles is also feasible. For example, Martinez-Lage taught “non-viral delivery of vectors or short-lived and preassembled Cas9 RNP complexes may provide an alternative strategy to meet these challenges. Non-viral methods include lipid nanoparticles/liposomes, gold nanoparticles or inorganic nanoparticles, among many others” (See Martinez-Lage, p. 8, last para). It is clear that Martinez envisioned the use of primary cells as the natural next step in the claimed method. A reference may be relied upon for all it would have reasonably suggested to one having ordinary skill in the art, including non-preferred embodiments. Merck & Co. v Biocraft Laboratories, 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir.), cert. denied, 493 U.S. 975 (1989), See also > Upsher-Smith Labs v. Pamlab, LLC, 412 F.3d 1319, 1323, 75 USPQ2d 1213 (Fed. Cir. 2005). MPEP 2123.
It is noted that Martinez-Lage did not explicitly teach that the gRNA that reduces the viability will have fewer reads than a gRNA that does not impair gene viability as required by claims 59 and 70. However, one of ordinary skill in the art would have expected that a gRNA having lower reads is essential. For example, Sharma taught “The purpose of a negative selection screen is to identify perturbations that affect the survival or proliferation of cells, which cause the perturbed cells to be depleted during selection. The approach here is to transduce two sets of cell populations and subject one set to the selection while the other serves as a non-selected control. The gRNA abundance in both populations is then analyzed in order to identify gRNAs that have been depleted because of the selection. One of the simplest forms of negative selection screen is the continued growth of cells for an extended amount of time to identify genes that are required for the proliferation of cells. Such screens have been used to identify both essential genes that are required for cell lines tested and a small set of genetic dependencies of specific cancer cell lines.” (See Sharma Sec. 2.1, first para).
As such it would have been obvious for a person of ordinary skill in the art to use the method taught by Martinez-Lage to arrive at a drug for treatment of cancer based on cancer cell screening using gRNAs by CRISPR library. The person would also have a reasonable expectation that gRNA having lower reads is essential for cell viability based on the explicit teachings of Sharma. As such one of ordinary skill would have a reasonable expectation of success in finding a therapeutic for cancer based on the teachings of Martinez-Lage that this method “promising candidates for molecularly targeted drugs.”
Regarding claims 61-63 and 75: Martinez-Lage taught that CRISPR/Cas systems can be delivered using viral delivery systems, such as AAV and lentiviral systems. (See Martinez-Lage p. 8, Section 7, 1st para). One of ordinary skill in the art would have found it obvious to deliver the gRNA library using viral delivery systems as required by claim 62.
Claims 64, 66-67, 69, 74, and 76 remain rejected under 35 U.S.C. 103 as being unpatentable over Martinez-Lage et al (Biomedicines. 2018 Nov 12; hereinafter "Martinez-Lage;" See PTO-892) in view of Sharma et al (Int J Mol Sci. 2018 Mar 21; hereinafter "Sharma;" See PTO-892), as applied to claims 59-63, 70-73 and 75 above, and further in view of Wong et al (Proc. Natl. Acad. Sci.; Published 2016; hereinafter "Wong;" See PTO-892).
Regarding claim 64: The teachings of Martinez-Lage and Sharma are set forth above. However, none of the cited references taught analyzing distribution of sequencing counts of barcoded gene modulatory agent. However, it is common to use barcoded gRNA while screening gRNA libraries for identifying drug targets/candidates and to analyze the distribution of sequencing counts. For example, Wong “created a platform for the massively parallel screening of barcoded combinatorial gene perturbations in human cells and translated these hits into effective drug combinations. This technology leverages the simplicity of the CRISPR-Cas9 system for multiplexed targeting of specific genomic loci and the versatility of combinatorial genetics en masse (CombiGEM) to rapidly assemble barcoded combinatorial genetic libraries that can be tracked with high-throughput sequencing. ” (See Wong Abstract). Wong taught to analyze the counts of barcoded gRNA in genetically modified cancer cells (See Wong FIG. 1A). One of ordinary skill in the art would have in view of the teachings of Martinez and Wong, and in view of Sharma easily envisioned analyzing counts of barcoded gRNAs.
Regarding claim 66: Wong used 153 barcoded gRNAs to screen epigenetic perturbations with anti-cancer phenotypes. (See Wong p. 2545, col. 2, 2nd para).
Regarding claim 67 and 74: Wong taught NF1, NF2, MED12, DNMT1, CREBBP, EP300, HDAC1, HDAC2, SIRT1, MLL, MLL2, NSD1, PRMT5, SETD2 and KDM1A among others as gRNA targets.
Regarding claim 69 and 76: Wong taught the use of instant SEQ ID NO: 1827 (HDAC2) gRNA for screening cancer.
Claims 65 and 68 remain rejected under 35 U.S.C. 103 as being unpatentable over Martinez-Lage et al (Biomedicines. 2018 Nov 12; hereinafter "Martinez-Lage;" See PTO-892) in view of Sharma et al (Int J Mol Sci. 2018 Mar 21; hereinafter "Sharma;" See PTO-892) as applied to claims 59-63, 70-73 and 75 above and further in view of Shepard et al (Clin Med (Lond). 2017 Jun; hereinafter "Shepard;" See PTO-892).
Regarding claims 65, and 68: None of the cited references taught at least three drugs from the drugs listed in Tables 2-3. However, the listed drugs are known to be well known in the prior art for treatment of cancer or related conditions. For example, Shepard taught Tocilizumab, Nivolumab, Ipilimumab, Trastuzumab, Cetuximab, and Bevacizumab among many others. As such one of ordinary skill in the art would have expected to include the popular anti-cancer drugs in a drug library for treatment of cancer. The person would also be motivated to include these drugs, as they are known to treat cancer.
It would further have been obvious for a person of ordinary skill in the art to screen for gene knock outs of the claimed drug targets as required by claim 68 in order to use the drugs in treatment of cancer. It is further indicated that Martinez-Lage taught that “The sgRNA contains a unique 20 base-pair (bp) sequence that is designed to be complementary to the target DNA site.” It would have been obvious to a person of ordinary skill in the art to use gRNA comprising at least an 18 bp complementarity to a target gene for effective gene editing or knock down.
Response to Applicant Arguments and Amendments
Applicants amended the claims to indicate that the cancer cells are primary cancer cells. Applicants argued that there is no reasonable expectation of success because Martinez-Lage, explicitly acknowledged that CRISPR delivery to primary tumor cells is a "challenge for the future", and none of the other cited references provide any disclosure or examples that would provide a person of skill in the art any expectation that such editing in primary cancer cells could be achieved. Applicants indicated that primary tumor cells pose unique challenges because of their inherent difficulty in introducing gene editing reagents, limited proliferative ability, and sample scarcity. The Applicants also indicated unexpected results, because instant Example 3 showed demonstrated a clear loss of gRNAs corresponding to therapeutic vulnerabilities, which can be utilized to select a personalized therapeutic. Applicants indicated that the editing and profiling of primary cancer cells is unexpected in view of the cited references, further demonstrating unexpected results that support non-obviousness of the pending claims. Applicants’ arguments have been thoroughly considered but are not found persuasive.
A reference may be relied upon for all it would have reasonably suggested to one having ordinary skill in the art, including non-preferred embodiments. Merck & Co. v Biocraft Laboratories, 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir.), cert. denied, 493 U.S. 975 (1989), See also > Upsher-Smith Labs v. Pamlab, LLC, 412 F.3d 1319, 1323, 75 USPQ2d 1213 (Fed. Cir. 2005). MPEP 2123. As an initial matter, Martinez-Lage indicated that CRISPR delivery to primary tumor cells is a "challenge for the future". This phrase is reasonably interpreted as the next step or ongoing area of development in the field, rather than suggesting that the approach is unlikely to succeed or is technically infeasible. It is also pointed out that Martinez-Lage taught viral delivery systems for delivery of CRISPR-Cas9 components. Martinez-Lage explicitly taught that “viruses are highly versatile particles because they can be applied in vitro, ex vivo or in vivo, which eases both efficacy and safety testing” (See Martinez-Lage pp. 8; 4th para). In addition, Martinez-Lage taught that non-viral delivery of CRISPR-Cas9 particles is also feasible. For example, Martinez-Lage taught “non-viral delivery of vectors or short-lived and preassembled Cas9 RNP complexes may provide an alternative strategy to meet these challenges. Non-viral methods include lipid nanoparticles/liposomes, gold nanoparticles or inorganic nanoparticles, among many others” (See Martinez-Lage, p. 8, last para). As such Applicants statements about infeasibility of editing primary cancer cells is unconvincing given the teachings of Martinez-Lage.
Additionally, Applicants’ arguments about propagation of primary tumor being unexpected is also not persuasive. Mitra et al (Trends Biotechnol. 2013 Jun; hereinafter “Mitra;” See PTO-892), as an evidence, taught importance of short -term culture of primary cells from solid tumors in personalized medicine, and taught methods to propagate them. Mitra taught methods of dissociating cells from tumors, using enzymes, chemicals or mechanical force, as well as explants, 3D cultures, sandwich cultures among others to propagate primary cancer cells. Taken together, these teachings would have led a person of ordinary skill in the art to view CRISPR-delivery into primary cells and short-term culture of primary cells as a logical next step, albeit with routine optimizations, rather than unpredictable or unattainable objective.
Accordingly, Applicant’s interpretation improperly equates “challenge” with “impossibility,” whereas the more reasonable reading of the prior art is that it identifies primary tumor cells as an expected progression in the field.
Conclusion
No claim is free of art.
No claim is allowed.
THIS ACTION IS MADE FINAL. 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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/JAGAMYA NMN VIJAYARAGHAVAN/ Examiner, Art Unit 1633
/EVELYN Y PYLA/Primary Examiner, Art Unit 1633
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