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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 7/2/26 has been entered.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Specific to SEQ ID NO: 42:
Claim(s) 1, 4-7, 12-16, 18, 20-22, 25, 27, 28, and 31 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chung (Identification and evaluation of guide RNA design determinants for anti-HIV-1 therapy using CRISPR/Cas9, Drexel University, 02/2020, 1-297).
Chung teaches a gRNA consisting of the sequence of instant SEQ ID NO: 43 (see pages 86 and 157) (instant claims 1 and 18).
Chung teaches that the guide RNA further comprises a PAM sequence and sequences distal to PAM wherein CRISPR/Cas9 binds (pages 87-88) (instant claim 4).
Chung teaches that a lentiviral vector can encode Cas9/gRNA/RFP (page 101) (instant claims 5-7 and 25) and contacting cells with the composition (page 101) and teaches in vivo and in vitro delivery (page 17) (instant claims 27 and 28).
Chung teaches a method for inhibiting HIV-1: HIV-1 inactivation using RNA-guided CRISPR/Cas9 system- CRISPR/Cas9 recognize target sequence (designated as protospacer) by RNA DNA sequence complementarity instead of protein-guided process. The targeted editing of the gRNA-bound SpCas9 has been first initiated by the recognition of the protospacer adjacent motif (PAM, 3-bp NGG for SpCas9) on the desired dsDNA via the PAM interacting domain in the Cas9 protein (43,44). The guide RNA (gRNA) on the gRNA/Cas9 ribonucleoprotein complex directs the complex to intended loci by matching the protospacer sequence adjacent to PAM, followed by the Cas9 endonuclease activity that induces the DSBs. The subsequent mechanism that induces sequence edits flanked by the DSBs remained the same as other genome editing system facilitated by NHEJ as mentioned above. Nevertheless, the molecular techniques required to design CRISPR/Cas9 that edits target of interest is much more versatile and scalable for experimental use than protein-guided systems such as ZFN and TALEN (page 8).
Chung teaches: Genome editing on HIV-1 latent provirus using CRISPR/Cas9 has shown promising therapeutic potential to cure HIV-1 infection (page 9) (instant claim 12).
Chung teaches that the method of delivering anti-human immunodeficiency virus type 1 (HIV-1) clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing strategies eliminate the residual latent HIV-1 reservoir during antiviral therapies (ART) treatment (page 16) (instant claim 13).
Chung teaches: CRISPR/Cas9-based gene editing is highly versatile as it can be targeted to any genomic locus by choice of a guide RNA (gRNA) complementary to the intended target. The 20-bp spacer sequence in the gRNAs determines the target DNA, also designated as the protospacer, through sequence complementarity. The Cas9 protein begins target determination through the recognition of a protospacer adjacent motif (PAM), a three to six nucleotide recognition sequence particular to each Cas9 protein. The PAM binding provides energy to unwind the DNA where base-pairing between the target and protospacer begins. If sufficient energy is produced through base-pairing, then Cas9 endonuclease activity generates a double-strand break (DSB) activating host DNA repair pathways. Due to the blunt-end nature of the DSBs, the non-homologous end joining 18 (NHEJ) process dominates inducing insertions and deletions (InDels). Recent research has shown that CRISPR-induced InDels exhibited deterministic patterns in eukaryotic cells (6-10) with the majority of the editing pattern being predictable, given the flanking sequence (pages 17 and 18).
It is noted that both claims 12 and 13 recite the same method step of delivery of the same gRNA sequence. Given that Chung teaches this method step, each of the methods are anticipated regardless of intended use language.
With regards to claims 14-16, the claims do not recite an additional method step but rather recite outcomes of delivery of the recited gRNA and would therefore necessarily occur from the recited method.
Chung teaches that the guide RNA and the cas protein form a complex. Chung teaches: The guide RNA (gRNA) on the gRNA/Cas9 ribonucleoprotein complex directs the complex to intended loci by matching the protospacer sequence adjacent to PAM, followed by the Cas9 endonuclease activity that induces the DSBs (page 8)(instant claims 20 and 22).
Instant claim 21 recites an outcome of the method of claim 20 and would therefore necessarily occur from the recited method. Additionally, Chung teaches that the LTR can be targeted (page 18)(instant claim 21). Chung teaches: The nomenclature system described above has captured 293 distinct spacer-PAM among 450 listed gRNAs (Table 1.1). The majority of them targeted the LTR due to its critical role on the regulation of HIV-1 transcription and potential for near full proviral genome excision (Figure 1.1A) (page 26).
Chung teaches: guide RNAs (gRNAs) targeting the 5’ LTR that also permanently inactivate transcription are an attractive strategy (page 59). Chung teaches: Another measurement required for determining the efficacy of designated gRNAs that target the LTR was excision rate, given their potential to cut at both the 5’ and 3’ LTR sites (page 106). Chung teaches 5’-LTR-3’-LTR excision (page 255).
Chung teaches that the components can be delivered via a Cas9 expression vector and a gRNA expression vector or via vectors for CAS9-gRNA (page 19)(instant claim 31).
Therefore, the claims are anticipated by Chung.
Specific to SEQ ID NO: 43:
Claim(s) 1, 4-7, 12-16, 18, 20-22, 25, 27, 28, and 31 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Wigdahl et al. (US 2018/0334732 A1).
Wigdahl et al. teach a HIV-1 gRNA that is 100% identical to instant SEQ ID NO: 42 (see Figure 5, SEQ ID NO: 13, page 7) (instant claim 1 and 18).
Wigdahl et al. teach: [0041] FIG. 5 is a table showing the packages of gRNAs selected using three different methodologies (the gRNAs are represented by the DNA sequences that encode them). The Temple package was selected using previously described methods. The Top-10 gRNAs were selected as those with the highest average cleavage score across 100 patients in the training dataset. The SMRT-10 package was selected using numerical optimization from the same dataset. The values reported are the fraction of samples in each dataset that have a greater than 80% likelihood of being cleaved.
Wigdahl et al. teach: Cas9 recognizes a trinucleotide (NGG) protospacer adjacent motif (PAM) to specify the cut site (the 3rd nucleotide from the PAM) [0132] (instant claim 4).
Wigdahl et al. teach: [0130] In certain embodiments, a CRISPR enzyme in combination with (and optionally complexed with) a guide sequence is delivered to a cell. [0131] The enzyme is Cas9 (instant claim 20).
Wigdahl et al. teach: Such sgRNA can be synthesized or in vitro transcribed for direct RNA transfection, or expressed from a promoter-driven RNA expression vector [0132] (instant claims 5, 7, 25, and 31).
Wigdahl et al. teach: A humanized Cas9 nuclease sequence can be encoded by any of the expression vectors [0133] (instant claims 6, 22, 25, and 31).
Wigdahl et al. recite: A method of treating HIV-1 infection in an infected human, the method comprising the steps of: sequencing HIV-1 long terminal repeat (LTR) regions that are integrated in the human genomic DNA from a sample selected from the group consisting of a bodily sample from the HIV-1-infected human or bodily samples from a HIV-1-infected patient population; identifying a set of guide RNA sequences (gRNAs) that are at least partially identical to a fragment of the HIV-1 LTR regions; and, excising the HIV-1 chromosomally integrated genome from the human genomic DNA of the human using the set of gRNAs and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas)9 system (claim 15) (instant claims 12, 13, 20, 22, 27, and 28).
Wigdahl et al. recite: A method of treating HIV-1 infection in an infected human, the method comprising the steps of: obtaining a set of guide RNA sequences (gRNAs) that are at least partially identical to a fragment of the HIV-1 LTR regions; and, excising the HIV-1 genome from the genomic DNA of the human using the set of gRNAs targeted to the HIV-1 LTR or another region of the HIV-1 and the CRISPR-Cas9 system (claim 33).
Wigdahl et al. recite: The method of claim 15, wherein the excision step comprises administering to the human the set of gRNAs within at least one selected from the group consisting of a viral vector, microparticle, nanoparticle, liposome, hydrogel, and block copolymer micelle (claim 28) (instant claims 27 and 31).
With regards to claims 14-16, the claims do not recite an additional method step but rather recite outcomes of delivery of the recited gRNA and would therefore necessarily occur from the recited method.
Instant claim 21 recites an outcome of the method of claim 20 and would therefore necessarily occur from the recited method. Additionally, Khalili et al. teaches that the LTR can be targeted (claim 15).
Therefore, the claims are anticipated by Wigdahl et al.
Specific to SEQ ID NO: 44:
Claim(s) 1, 4-7, 12-16, 19-22, 25, 27, 28, and 31 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Khalili et al. (US 11,298,410 B2).
Khalili et al. teach a HIV-1 gRNA targeting the LTR that comprises instant SEQ ID NO: 44 (see Table 1, SEQ ID NO: 29, page 46, nucleotides 6-25) (instant claims 1 and 19).
Khalili et al. taches that the gRNA was identified as one of the best for targeting HIV-1 LTR and viral structural region and that it can efficiently eradicate the HIV-1 genome (page 46).
Khalili et al. teach: The present invention further provides a pharmaceutical composition for the inactivation of integrated retroviral proviral DNA in a mammalian subject. The composition includes an isolated nucleic acid sequence encoding a Cas endonuclease, and at least one isolated nucleic acid sequence encoding at least one gRNA complementary to a target sequence in a proviral retroviral DNA, such as HIV DNA (column 3) (instant claims 4-6).
Khalili et al. teach: FIG. 1A shows a diagram of Streptococcus pyogenes Cas9 (SpCas9), single guide RNA (sgRNA) and protospacer adjacent motif (PAM), showing the cutting site at the third nucleotide of both strand DNA from the PAM NGG or NAG and sequence of sgRNA. The sgRNA is composed of the CRISPR RNA (crRNA) containing 20 bp spacer (seed or target sequence) and 12 bp, the stem loop (GAAA) and the transactivation cRNA (tracRNA) (SEQ ID NO: 60) (column 3) (instant claims 4 and 22).
Khalili et al. teach: FIG. 1B shows a map diagram for spCas9 expressing lentiviral vector (top) and sgRNA expressing lentiviral vector (bottom) (instant claims 7, 25, 27, 28, and 31).
Khalili et al. teach: The present invention also provides a method of inactivating a retrovirus in a mammalian cell by exposing the cell to a composition including one or more isolated nucleic acids encoding a gene editing complex. The gene editing complex includes a CRISPR-associated endonuclease and one or more gRNAs, wherein each gRNA is complementary to a target sequence in the retrovirus (columns 2- 3).
Khalili et al. teach: The present invention still further provides a method of treating a mammalian subject infected with a retrovirus, e.g. HIV. The method includes the steps of determining that a mammalian subject is infected with HIV, administering an effective amount of the previously stated pharmaceutical composition, and treating the mammalian subject for HIV infection (column 3) (instant claim 12).
Khalili et al. teach: Methods of the invention may be used to remove viral or other foreign genetic material from a host organism, without interfering with the integrity of the host's genetic material. A nuclease may be used to target viral nucleic acid, thereby interfering with viral replication or transcription or even excising the viral genetic material from the host genome. The nuclease may be specifically targeted to remove only the viral nucleic acid without acting on host material either when the viral nucleic acid exists as a particle within the cell or when it is integrated into the host genome (columns 12-13)(instant claim 13).
With regards to claims 14-16, the claims do not recite an additional method step but rather recite outcomes of delivery of the recited gRNA and would therefore necessarily occur from the recited method.
Khalili et al. teach: The guide RNA localizes the CRISPR/Cas complex to a viral target sequence. Binding of the complex localizes the Cas endonuclease to the viral genomic target sequence causing breaks in the viral genome (column 13)(instant claim 20).
Instant claim 21 recites an outcome of the method of claim 20 and would therefore necessarily occur from the recited method. Additionally, Khalili et al. teaches that the LTR can be targeted (HIV-1 gRNA targeting the LTR that comprises instant SEQ ID NO: 44 (see Table 1, SEQ ID NO: 29, page 46, nucleotides 6-25)).
Therefore, the claims are anticipated by Khalili et al.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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.
Claim(s) 1, 4-7, 12-16, 18, 20-22, 25, 27, 28, and 31 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chung (Identification and evaluation of guide RNA design determinants for anti-HIV-1 therapy using CRISPR/Cas9, Drexel University, 02/2020, 1-297) as applied to claims 1, 4-7, 12-16, 18, 20-22, 25, 27, 28, and 31 above, and further in view of Wigdahl et al. (US 2018/0334732 A1) and Khalili et al. (US 11,298,410 B2).
The claims are anticipated by Chung, as set forth above. The instant rejection is specific to SEQ ID NOs: 42 and 44, which are not taught by Chung.
However, it would have been obvious to utilize the gRNA of SEQ ID NO: 42 instead of the gRNA of SEQ ID NO: 43 that is taught by Chung because Wigdahl et al. teach a HIV-1 gRNA that is 100% identical to instant SEQ ID NO: 42 (see Figure 5, SEQ ID NO: 13, page 7).
One would have selected this specific gRNA because each are directed to HIV-1 and have the same intended use and Wigdahl et al. teaches that it was in the top 10 gRNAs that were selected as those with the highest average cleavage score across 100 patients in the training dataset. Wigdahl et al. teach: [0041] FIG. 5 is a table showing the packages of gRNAs selected using three different methodologies (the gRNAs are represented by the DNA sequences that encode them). The Temple package was selected using previously described methods. The Top-10 gRNAs were selected as those with the highest average cleavage score across 100 patients in the training dataset. The SMRT-10 package was selected using numerical optimization from the same dataset. The values reported are the fraction of samples in each dataset that have a greater than 80% likelihood of being cleaved.
Therefore, one would have reasonably expected successful activity of the complex of Chung with the gRNA of Wigdahl et al.
Additionally, it would have been obvious to utilize a gRNA comprising SEQ ID NO: 44 instead of the gRNA of SEQ ID NO: 43 that is taught by Chung because Khalili et al. teach a HIV-1 gRNA targeting the LTR that comprises instant SEQ ID NO: 44 (see Table 1, SEQ ID NO: 29, page 46, nucleotides 6-25).
One would have selected this specific gRNA because each are directed to HIV-1 and have the same intended use and Khalili et al. taches that the gRNA was identified as one of the best for targeting HIV-1 LTR and viral structural region and that it can efficiently eradicate the HIV-1 genome (page 46). Therefore, one would have reasonably expected successful activity of the complex of Chung with the gRNA of Khalili et al.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Amy R Hudson whose telephone number is (571)272-0755. The examiner can normally be reached M-F 8:00am-6:00pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached at 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/AMY ROSE HUDSON/Primary Examiner, Art Unit 1636
Prosecution Insights