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 .
Election/Restrictions
Applicant’s election without traverse of Genus A (Borrelia burgdorferi), Genus B (wild-type Cas9), Genus C (lp25 or lp28-1), and Genus D (shuttle vectors) in the reply filed on 12/24/2025 is acknowledged.
Claims 13-14 and 17-18 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/24/2025.
Status of Claims
Claims 1-21 are currently pending.
Claims 1-12, 15-16, and 19-21 are under consideration, as claims 13-14 and 17-18 are withdrawn.
Priority
Acknowledgment is made of applicant’s claim for benefit under 35 U.S.C. 119(e) of Provisional application No. 63/407,955, filed on 09/19/2022. The present application and all claims are being examined with an effective filing date of 09/19/2022. In future actions, the effective filing date may change due to amendments or further review of priority documents.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 01/02/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claim Objections
Claim 16, 20 and 21 are objected to because of the following informalities:
Lines 4-5 of claim 16 currently recite “whereby the efficacy of Cas9-targeting can be tested in mammalian subject”. The claim should be amended to recite “whereby the efficacy of Cas9-targeting can be tested in a mammalian subject”
Claim 20 (claim 21 dependent on) is objected to as being improperly dependent.
The preamble of claim 20 recites “the method of claim 20”, which is a self-referential dependency and therefore improper. It appears that the reference to claim 20 is a typographical error and may have been intended to depend from claim 19, which recites “the mammalian subject”, or from claim 1, which recites “a mammalian host or mammalian host cell”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 11-12 and 16 are rejected 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.
Claim 11 (Claim 12 dependent there from), which directly or indirectly depends on claims 10 and 11, recites the limitation "sgRNA" in line 2. There is insufficient antecedent basis for this limitation in the claim. Claim 10 does not recite “sgRNA”, whereas claim 1 recites “a guide RNA (gRNA)”. Therefore, it is unclear whether the “sgRNA” is referring to the gRNA in claim 1 or to a separate and distinct sgRNA that differs from the gRNA recited in claim 1. For examination purposes, the examiner is interpreting sgRNA and referring back to the gRNA in claim 1.
Claim 16, which depends on claim 1, recites the limitation “the inducible expression cassette” in line 3. There is insufficient antecedent basis for this limitation in the claim. In line 2 of claim 16, there is reference to “an expression cassette” for the gRNA, but not an inducible expression cassette for expressing both the gRNA and the RNA-guided nuclease. Claim 1 does not recite any expression cassettes. Accordingly, in addition to the lack of antecedent basis for “the inducible expression cassette”, it is unclear as to how many expression cassettes are required in claim 16. For example, in one interpretation only one expression cassette is required: an expression cassette for the gRNA. In another interpretation, two expression cassettes are required: an expression cassette for the gRNA and an inducible expression cassette expressing both the gRNA and the RNA guided nuclease. In yet another interpretation, one inducible expression cassette for expressing both the gRNA and the RNA guided nuclease is required.
Appropriate response and clarification for all of the above is requested.
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.
Claims 1-10, and 19-21 are rejected under 35 U.S.C. 103 as being unpatentable over Citorik et al. (Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases, Nat Biotechnol. 2014 November ; 32(11): 1141–1145, cited in PTO-892), Purser and Norris (Correlation between plasmid content and infectivity in Borrelia burgdorferi, PNAS, 2000, Vol 97, no. 25, pg. 13865-13870, herein “Purser”, cited in the IDS) and Takacs et al. (A CRISPR Interference Platform for Selective Downregulation of Gene Expression in Borrelia burgdorferi. Appl Environ Microbiol 87:e02519-20, cited in the IDS).
Pursuant to MPEP 2111.02 II: The claim preamble must be read in the context of the entire claim. The determination of whether preamble recitations are structural limitations or mere statements of purpose or use "can be resolved only on review of the entirety of the [record] to gain an understanding of what the inventors actually invented and intended to encompass by the claim" as drafted without importing "'extraneous' limitations from the specification." Corning Glass Works, 868 F.2d at 1257, 9 USPQ2d at 1966. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Therefore, “reducing virulence of a bacterial species…which has infected a mammalian host or mammalian host cell” recited in claim 1 will be interpreted as an intended use, and as such, thus not given patentable weight. Claim 1 is directed to exposing a (segmented) bacterial genome to an RNA-guided nuclease and a guide RNA and generating a double-stranded or single-stranded break in the bacterial genome, wherein the gRNA base pairs with a target sequence in the bacterial genome.
Citorik et al. teaches the use of CRISPR-Cas technology to “create antimicrobials whose spectrum of activity is chosen by design”, wherein RNA-guided nucleases (RGNs) “targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation”. Citorik et al. expressly teaches that Type II CRISPR-Cas system of Streptococcus pyogenes is an effective and programmable tool for genome editing and that “with the aid of a transactivating small RNA (tracrRNA), crRNAs enable the Cas9 endonuclease to introduce double-stranded breaks in target DNA sequences (Abstract and pg. 1141, right column). Citorik et al. teaches preparing such RGN systems by constructing plasmid (phagemid) vectors encoding Cas9 and crRNA spacer sequences and packaging those constructs into bacteriophage particles for delivery (Online Methods, “Plasmid Construction). Citorik et al. further teaches that the DNA targets of RGNs can be undesirable genes or polymorphisms, including “antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli” (Abstract) and discloses administering prepared RGNs to bacterial cells by delivering phage packaged ΦRGNs to E. coli, resulting in sequence specific DNA cleavage and loss of viability. More specifically, Citorik et al. discloses ΦRGNgyrAD87G targeting the chromosomal gyrAD87G gene in quinolone-resistant E. coli, wherein treatment resulted in cytotoxicity only in cells harboring the gyrAD87G mutation (pg. 1143 and Fig. 1). Therefore, Citorik et al. teaches exposing bacterial genomes to the RNA guided nuclease and guide RNA in a treatment context, and is directed to therapeutic antimicrobial methods. However, Citorik et al. does not expressly disclose applying the disclosed RNA-guided nuclease system to a bacterial species having a segmented genome.
Purser teaches that Borrelia burgdorferi, which causes Lyme disease, possesses a segmented genome comprising a linear chromosome and multiple linear circular plasmids, including endogenous infectivity associated plasmids such as lp25 and lp28-1 and discloses that lp25 and lp28-1 “encode virulence factors important in the pathogenesis of B. burgdorferi” (Abstract and pg. 13865, right column). Therefore, Purser teaches that Borrelia burgdorferi comprises the endogenous virulence plasmids lp25 and lp28-1.
Takacs et al. teaches the functional implementation of a CRISPR interference (CRISPRi) system employing dCas9 in Borrelia burgdorferi, teaching the assembly and expression of sgRNA and dCas9 expression cassettes that target endogenous B. burgdorferi genes (Abstract, and Results pg. 3). Therefore, Takacs et al. demonstrates the feasibility of RNA-guided CRISPR systems in B. burgdorferi.
An invention would have been obvious to a person of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the claimed invention, the teachings of Citorik et al., which discloses RGN systems comprising Cas9 and gRNAs that direct sequence-specific cleavage of bacterial DNA, the teachings of Purser, that B. burgdorferi is a pathogenic bacterium possessing a segmented genome and identifies lp25 and lp28-1 as endogenous virulence plasmids, and the teachings of Takacs et al. which demonstrate the functional implementation of RNA guided CRISPR systems in B. burgdorferi, would have motivated said practitioner to apply the RGN systems taught by Citorik et al. to target lp25/lp28-1 in Borrelia burgdorferi (claims 1-10) in order to reduce the virulence of the infecting bacteria. Given that the method taught by Citorik et al. is not dependent on genome architecture, but rather on sequence-specific guide RNA base pairing and nuclease mediated cleavage of DNA, and given that Takacs et al. demonstrate the feasibility of implementing such systems in B. burgdorferi, a person of ordinary skill in the art would have readily predicted that the combination of teachings would result in a method of reducing virulence of B. burgdorferi, comprising exposing the segmented genome of B. burgdorferi to an RNA-guided nuclease and guide RNA, with a reasonable expectation of success. A person or ordinary skill in the art would be further motivated to apply the disclosed RGN systems to mammalian subjects harboring the targeting bacteria, including rodents routinely used as experimental models and humans as intended recipients of antimicrobial treatment, with a reasonable expectation of success (claims 19-20) and to further administer an antibiotic to the subject, as combination antimicrobial therapies were well known and routinely employed to enhance bacterial killing or exploit restored antibiotic susceptibility (claim 21). Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Citorik et al., Purser, and Takacs et al., as applied to claims 1 and 10 above, and further in view of Revel et al. (DNA microarray analysis of differential gene expression in Borrelia burgdorferi, the Lyme disease spirochete, PNAS, 2002, vol. 99, no. 3, pg. 1562-1567, cited in PTO-892).
The teaching of Citorik et al., Purser, and Takacs et al., as they apply to claims 1 and 10 have already been discussed above. Briefly, Citorik et al. discloses RNA guided nuclease systems comprising Cas9 and guide RNAs that direct sequence-specific cleavage of bacterial DNA to reduce bacterial viability and virulence. Purser teaches that Borrelia burgdorferi is a bacterium with a segmented genome comprising endogenous virulence plasmids lp25 and lp-281, while Takacs et al. teaches the functional implementation of CRISPR-Cas systems in B. burgdorferi. However, neither Citorik et al., Purser, nor Takacs et al. teach wherein the sgRNA base pairs with a bbe10 or bbe17 gene.
Revel et al. discloses that lp25 has been closely associated with Borrelia burgdorferi infectivity and further identify bbe16 and bbe17 as lp25 encoded genes, with bbe17 being upregulated during mammalian host adaptation, suggesting a role in virulence expression (pg. 1565, left column).
An invention would have been obvious to a person of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the claimed invention, given the combination of Citorik et al. and Purser which teaches RGN systems comprising Cas9 and gRNAs that direct sequence-specific cleavage of bacterial DNA, and that lp25 is an endogenous virulence plasmid in B. burgdorferi, the teachings of Revel et al. which identify bbe17 as an lp25 encoded gene associated with mammalian host adaptation and infectivity, would have motivated a person of ordinary skill in the art to apply the above RGN systems obvious by Citorik et al., Purser, and Takacs et al., to specifically target bbe17 in Borrelia burgdorferi. There is a reasonable expectation of success because Citorik et al. demonstrates a successful method of reducing virulence in bacteria using an RNA guided nuclease and gRNAs, and Takacs et al. demonstrates the successful implementation of CRISPRi in B. burdorferi using dCas9 and sgRNA. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Claims 15-16 are rejected under 35 U.S.C. 103 as being unpatentable over Citorik et al., Purser, and Takacs et al., as applied to claim 1 above, and further in view of additional teachings of Takacs et al. (A CRISPR Interference Platform for Selective Downregulation of Gene Expression in Borrelia burgdorferi. Appl Environ Microbiol 87:e02519-20, cited in the IDS).
The teaching of Citorik et al., Purser, and Takacs et al., as they apply to claim 1 have already been discussed above. Briefly, Citorik et al. discloses RNA guided nuclease systems comprising Cas9 and guide RNAs that direct sequence-specific cleavage of bacterial DNA to reduce bacterial viability and virulence. Purser teaches that Borrelia burgdorferi is a pathogenic bacterium with a segmented genome, while Takacs et al. teaches the functional implementation of CRISPR-Cas systems in B. burgdorferi. However, neither Citorik et al., Purser, nor Takacs et al. teach wherein the RGN and an expression cassette for the guide RNA are carried on a shuttle vector comprising an expression cassette for expressing the gRNA and an inducible expression cassette for expressing the RGN, wherein the shuttle vector can be replicated in E. coli and the bacteria with the segmented genome (as recited in claim 15), or a shuttle vector comprising an inducible expression cassette for expressing both the gRNA and the RGN.
With respect to the “whereby” clause in claim 16, reciting that “the efficacy of Cas9 targeting can be tested in a mammalian subject”, this language is understood as merely stating an intended result or inherency of the shuttle vector, and does not impart any additional structural or function limitation beyond those already recited in the claim. Accordingly, the whereby clause is not given patentable weight.
Takacs et al. in addition to the discussed above further teaches shuttle vectors comprising separate expression cassettes, including an inducible expression cassette for dCas9 and a separate cassette for sgRNA, generating “both the template and the mature sgRNA cassettes in B. burgdorferi/E. coli shuttle vectors. Takacs et al. further teaches “to express dcas9, we generated a dcas9-lacI cassette, which contains the dcas9 gene controlled by the isopropyl-b- D-thiogalactopyranoside (IPTG)-inducible PpQE30 promoter and a constitutively expressed lacI gene …expressed from a B. burgdorferi shuttle vector” (pg. 3, bottom). Additionally, Takacs et al. teaches all-in-one CRISPRi shuttle vectors in which both dCas9 and the sgRNA are expressed from a single inducible plasmid-based cassette. Specifically, “the others are all-in-one plasmid-based versions that express both dcas9 and the sgRNA from the same plasmid” (pg. 6, 3rd para) and “replacement of the rifampin cassette with sgRNA cassettes yielded all-in-one CRISPRi shuttle vectors” (pg. 3, bottom).
An invention would have been obvious to a person of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the claimed invention, it would have been obvious to a person of ordinary skill in the art to substitute the RNA-guided nuclease expression and delivery system as made obvious by Citorik et al., Purser, and Takacs et al., with the well-established shuttle vector-based expression systems further taught by Takacs et al., for use when targeting Borrelia burgdorferi, because Takacs et al. discloses B. burgdorferi/E. coli shuttle vectors containing origins of replication that function in both organisms, thereby permitting routine cloning and propagation of RGN constructs in E. coli while enabling functional expression of those constructs in bacterial species with segmented genomes, such as B. burgdorferi. There is a reasonable expectation of success, in view of Takacs et al.’s teachings, demonstrating the successful implementation of CRISPR-based systems, using shuttle vectors, in B. burgdorferi. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Conclusion
No claim is in condition for allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NAGHMEH NINA MOAZZAMI whose telephone number is (703)756-4770. The examiner can normally be reached Monday-Friday, 9:00-5:00.
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, Robert Mondesi can be reached at 408-918-7584. 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.
/NAGHMEH NINA MOAZZAMI/Examiner, Art Unit 1652
/RICHARD G HUTSON/Primary Examiner, Art Unit 1652