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 .
Application Status
This action is written in response to applicant’s correspondence received 09/19/2025. Claims 1-2, 8-10, 12, and 14-25 are currently pending. Claims 3-5 were canceled by the applicant in the amendments filed 09/19/2025. Claim 25 was added. No claims are withdrawn from prosecution as being drawn to non-elected subject matter. Accordingly, claims 1-2, 8-10, 12, and 14-25 are examined herein.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
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:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
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.
Claims 1-2, 9-10, 12, 14, 16-20 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Feng et al. (Lytic Induction Therapy for Epstein-Barr Virus-Positive B-Cell Lymphomas. J Virol. 2004 Feb;78(4):1893–1902.) in view of WIPO Publication 2017/058795 to Quake (applicant’s submission, hereinafter ‘Quake’).
Regarding claims 1-2, 9 and 14:
Feng et al. teach a method for treating EBV-positive tumors which comprises activating lytic EBV by introducing into the cell a transcriptional activator (i.e., gemcitabine and doxorubicin) that is capable of activating transcription of lytic EBV genes (the two viral immediate-early transactivator genes, BZLF1 and/or BRLF1)(§Abstract).
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Please note that Feng et al.’s method comprised activating transcription from the promoters, i.e., transcriptional regulatory sequences (see above).
Feng et al. further note that the ability of various chemotherapy drugs to induce lytic EBV induction is cell type dependent:
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Feng et al. further provide a teaching, suggestion or motivation to use gene therapy/delivery methods to induce lytic EBV infection by expressing the BZLF1 or BRLF1 genes (p. 1901):
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Feng et al. do not teach that the method of activating EBV uses a programmable DNA binding protein system (dCas9) that is linked to a transcriptional activator.
Quake teaches methods of upregulating viral transcription using a Cas9 system targeting a viral promoter:
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Quake further teaches that EBV promoters may be targeted with said method:
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Quake further teaches activation of viral transcription by fusing a transcriptional activator to dCas9 (p. 10/30) (relevant to claims 1 and 9-10):
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Quake further teaches that the system may be delivered via AAVs, which allow for preferential infection of certain tissues and would have addressed the issue of cell type dependence noted by Feng et al. (p. 15/30):
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It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of activating lytic EBV in tumor cells to treat EBV-driven lymphoproliferative disease via administration of gemcitabine and GCV , as taught by Feng et al., to induce the lytic form of EBV via introduction of dCas9 fused to a transcriptional activator, as taught by Quake. The skilled artisan would have been motivated by Feng et al. to induce lytic EBV, via transcriptional activation of viral lytic genes, as a way to treat EBV-associated tumors, but to do so via gene therapy rather than administration of chemotherapeutic drugs. As Feng et al. note, the chemotherapy-based method has the limitation that it is cell type dependent. Quake, instead, provides an alternative method for activating lytic EBV by using a dCas9/transcriptional activator system which may be delivered via AAV, which would have permitted preferential infection of target tissues. One having ordinary skill would have recognized that Quake’s method followed Feng et al.’s suggestion of a gene therapy approach while overcoming the limitations of Feng et al.’s chemotherapy-based approach.
Regarding claim 12, Quake teaches wherein the programmable DNA binding protein system comprises a transcription activator-like effector (TALE) or zinc finger nuclease (ZFN) (p 9/30):
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Regarding claim 14, Quake and Feng et al. both teach wherein the transcriptional activator binds to the transcriptional regulatory sequence (promoter) (see above).
Regarding claims 16-18, Feng et al. teaches that the cell is a mammalian and/or cancer cell (Abstract; lymphoblastoid cells), and teaches the introduction of an antiviral prodrug, ganciclovir (GCV) into the cell (Abstract and p. 1893):
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Regarding claim 19, it is noted that the claim recites the same limitations present in claims 1-4 and 14 with regard to the method steps, genes targeted, and gene regions targeted. Claim 19 differs from the previous claims in that it further recites intended outcomes of the same method steps, i.e., at least 2-fold higher expression of BZLF1 and BRLF1 when both genes are targeted simultaneously compared to a method in which either gene is targeted alone. However, the limitation is not considered to have patentable weight over the prior art method which renders the method steps obvious, because specification does not appear to show at least a 2-fold increase in expression of BZLF1 and BRLF1 when transcription of both genes is activated.
Figure 11 (depicting the results discussed in Example 6 on p. 36) shows a gel comparing relative protein expression after administration of either sgRNA (BZLF1 or BRLF1) alone to both at once. However, the amounts are not quantified, and the strength of the bands does not clearly show a 2-fold increase. For example, the band intensity for BZLF1 is stronger in the BZLF1 sgRNA (A5) only lane (lanes 2 and 6) than in the BZLF1 + BRLF1 lanes (4 and 8), which would indicate that protein expression was higher for the single BZLF1 sgRNA than it was for the BZLF1 and BRLF1 sgRNAs combined. Example 13 on p. 41 discusses the synergistic activation of both genes. Applicant defines “synergistic EBV lytic activation” as, “activation of multiple EBV lytic genes.” (p. 15 ln 5). This is interpreted to encompass any non-zero amount of activation. The specification states that synergistic activation “may” be 2-fold to 100-fold relative to non-synergistic activation, but the use of the term “may” is exemplary, open-ended, and does not disavow the full scope of the term (MPEP 2111.01(IV). Example 13 does not describe the level of activation, stating only that the proteins “were detectable” (p. 41 ln 12), that synergistic protein production occurred, and that the co-expression of BZLF1sgRNA3 and BRLF1 sgRNA3 increased the number of cells expressing caspase-3, more cells were accumulated in sub G1 phase, and the cell viability was decreased compared with DOX treated dCas9-Tet on - p65HSF1-BZLF1 sgRNA3 SNU-719, C666-1, and C17 cells (p. 41 ln 14-17). Absent support in the specification which shows, “wherein expression of genes regulated by EBV BZLF1 and EBV BRLF1 is at least 2-fold higher than expression of the same genes resulting from introduction of a programmable DNA binding protein system that targets only EBV BZLF1 or only EBV BRLF1”, the limitation is not given patentable weight for the purposes of comparison to the prior art.
Regarding claims 20 and 22, Feng et al. teaches administering the system for inducing lytic EBV to the subject (and thus also teaches cells comprising the system), wherein the subject has cancer associated with EBV infection (§GCV enhances the therapeutic effect of gemcitabine and doxorubicin in EBV-positive lymphoproliferative disease in SCID mice).
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Feng et al. and Quake as applied to claims 1-2, 9-10, 12, 14, 16-20 and 22, further in view of Konermann.(Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature volume 517, pages583–588 (2015).; of record, applicant’s submission).
Feng et al. and Quake render obvious the method of claim 1, from which instantly rejected claim 8 depends, as described above
Feng et al. and Quake do not teach wherein the transcriptional activator comprises a heat shock factor transactivation domain.
Konerman teaches a transcriptional activation system comprising dCas9 and a transcriptional activator which comprises HSF1 and is linked to a component of the complex. Please see Figure 1b, which shows a dCas9-VP64 fusion protein complexed with sgRNA, which is linked to a MS2-p65-HSF1 fusion protein. In the figure caption, Konerman notes, “Addition of the HSF1 transactivation domain to MS2-p65 further increases the efficiency of the transcription activation”.
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 modified the method of claim 1 by substituting the generic transcriptional activator with a transcriptional activator comprising HSF1. The skilled artisan would have been motivated to do so, and would have had a reasonable expectation of success, based on Konerman’s teachings that addition of the HSF1 transactivation domain enhanced the efficiency of the transcription activation.
Claims 23-25 are rejected under 35 U.S.C. 103 as being unpatentable over Feng et al. and Quake as applied to claims 1-2, 9-10, 12, 14, 16-20 and 22, further in view of Cheng et al. (Casilio: a versatile CRISPR-Cas9-Pumilio hybrid for gene regulation and genomic labeling. Cell Res. 2016 Feb;26(2):254-7.; applicant’s submission).
Feng et al. and Quake render obvious the method of claim 1, from which instantly rejected claims 23-25 depend, as described above.
Feng et al. and Quake do not teach wherein the transcriptional activator comprises P65HSF1 (relevant to claim 25), or wherein the Cas9 system further comprises a PUF domain binding sequence (PBS) linked to the guide RNA and a PUF domain that binds to the PBS of the gRNA, and the PUF domain is linked to the transcriptional activator (claims 23-24).
Cheng et al. teach the Casilio system, a CRISPR-Cas9-Pumilio hybrid having the recited components:
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Cheng et al. further teach that they were able to achieve “robust activation…in the corresponding Casilio experiments” (p. 256 first ¶; Figure 1C).
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 modified the method for activating a lytic Epstein-Barr virus gene comprising introducing into the cell a programmable DNA binding system linked to a transcriptional activator, as taught by Feng et al. and Quake, by using the transcriptional activator comprising P65HSF1/a PUF domain binding sequence (PBS) linked to the guide RNA and a PUF domain that binds to the PBS of the gRNA, and the PUF domain is linked to the transcriptional activator, as taught by Cheng et al., in place of the generic transcriptional activator taught by Feng et al./Quake. The skilled artisan would have had a reasonable expectation of success based on Cheng et al.’s successful application of the Casilio system to achieve transcriptional activation of target genes.
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Feng et al. and Quake as applied to claims 1-2, 9-10, 12, 14, 16-20 and 22, further in view of Guo et al. (An inducible CRISPR-ON system for controllable gene activation in human pluripotent stem cells. Protein Cell 2017, 8(5):379–393.).
Feng et al. and Quake render obvious the method of claim 1, from which instantly rejected claim 15 depends, as described above. Specifically, Feng et al. in view of Quake teach a system with a dCas9 protein fused to a transcriptional activator (see above).
Feng et al. and Quake do not teach wherein expression of the DNA binding protein and/or transcriptional activator is inducible.
Guo et al. teach an inducible CRISPR-ON system for controllable gene activation (Title), in which a dCas9 protein is fused to a transcriptional activator and placed under the control of an inducible promoter. The system comprises a doxycycline inducible dCas9-VP64-p65-Rta transcription activator (§Abstract). The DCas9-VPR was constructed by fusing the nuclease deficient Cas9 (dCas9) with transcription activator VP64, p65 and Rta in tandem (p. 390 §Plasmid construction). For inducible expression, dCas9-VPR was placed behind a TRE promoter (p. 391 §Plasmid construction first ¶). Guo et al. note that the system can be a valuable system to control gene expression from endogenous loci (p. 380 second ¶).
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 modified the method as taught by Feng et al. and Quake by making the expression of the DNA binding protein and/or transcriptional activator inducible. The skilled artisan would have been motivated to do so by Guo et al.’s teachings, which demonstrated that a system placing the dCas9/transcription activator fusion protein under the control of an inducible promoter was effective and could be a valuable system to control gene expression from endogenous loci, such as latent viral genomes in EBV-infected cells.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Feng et al. and Quake as applied to claims 1-2, 9-10, 12, 14, 16-20 and 22, further in view of Ahern (Biochemical, Reagents Kits Offer Scientists Good Return On Investment. The Scientist, Vol:9, #15, pg 20, July 24, 1995).
Feng et al. and Quake render obvious the method of claim 1, from which instantly rejected claim 21 depends, as described above.
Feng et al. and Quake do not teach a kit comprising the system of the method of claim 1.
Ahern teaches that premade reagents and kits are convenient and save time for researchers. Rather than browsing through catalogs and buying individual chemicals from one or several suppliers, investigators can instead purchase a kit that supplies all of the necessary reagents for a particular research application and even provides them with detailed instructions (p. 5/10 last ¶).
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 modified the method of claim 1, as taught by Feng et al. and Quake, by including the necessary components in a kit so that the method could be carried out with greater ease and in less time, as taught by Ahern.
Response to Arguments
Applicant's arguments filed 09/19/2025 have been fully considered but they are not persuasive for the reasons that follow.
On page 7 of the remarks, Applicant argues that, “…nowhere in Quake is there any teaching or suggestion for one to activate viral gene expression for the purpose of causing the lysis of host cells”. Respectfully, this is not persuasive because it argues against Quake individually when the rejection is based on the combination of Feng (providing a motivation to activate viral expression for the purpose of causing the lysis of host cells, as described above) and Quake (providing a gene therapy method of activating expression of the viral lytic genes, as suggested by Feng). 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). The same logic applies to Applicant’s argument that, “Quake states that a transcription factor fused with dCas9 may be used for activating viral gene transcription, this is a generic and vacuous statement without naming any benefits for activating viral gene expression”, (Id.) because these benefits are taught by Feng.
Applicant further argues that, “Multiple paragraphs in Quake describe the benefits of inhibiting, not activating, viral gene expression…These passages effectively teach away from the claimed invention…” (Id.). Respectfully, this argument is not persuasive for the reasons already discussed and because it does not criticize, discredit or otherwise discourage the solution claimed (MPEP 2143.01(I)).
Applicant further argues that, “Example 7 shows that targeting EBV lytic gene BGLF4 did not achieve the same level of success. These results indicate that, regardless of whatever relevant teaching one might derive from Feng and Quake, not all EBV lytic genes can be targeted for successfully inducing lysis of the host cells.” Respectfully, this argument is not persuasive because the amended claims merely recite targeting BZLF1 or BRLF1, not BGLF4. As discussed in the above rejection, Feng clearly teaches that activation of transcription of BZLF1 or BRLF1 induced the lytic state of EBV.
Conclusion
No claim is allowed at this time.
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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/A.M.Z./ Examiner, Art Unit 1636
/BRIAN WHITEMAN/Primary Examiner, Art Unit 1636