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 .
Claims Status
Claim 1 is amended.
Claims 2-4 are cancelled.
Claims 1,5-15 are under examination.
Withdrawn Rejections
The double patent rejections over the claims of copending Application Nos. 18/658,741, 18/551,110, and 17/911,367 is withdrawn in light of Applicants amendment.
Edited Rejections Necessitated by Claims Amendments
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 1,9, and 12-15 are rejected under 35 U.S.C. 103 as being unpatentable over High et al ( WO 2015006743 A1), in view of Sadelain et al (EP 3620521 A1), Schaack et al ( Virology, 2011), and Wit et al ( Molecular Cell, 2015) .
Regarding claims 1 and 9, High et al disclose, “In more particular embodiments of the invention, a vector or vector sequence includes a first inverted terminal repeat (ITR) of an AAV; a promoter operable in mammalian cells; the reporter transgene; a polyadenylation signal; and optionally a second ITR of an AAV.” (paragraph 0020). Additionally, they disclose, “As used herein, a "vector" can refer to a viral particle, such as a parvovirus (e.g., AAV) that can be used to deliver nucleic acid (e.g., reporter transgene) into cells, and which vector includes nucleic acid (e.g., reporter transgene) packaged into virions or encapsidated by viral proteins (envelope proteins or capsid proteins, such as AAV capsid). (paragraph 0047). Accordingly, High et al teach the claimed basic rAAV architecture, including from the 5’ to the 3’: a 5’ AAV ITR; an expression promoter ; a transgene; a 3’ AAV ITR; and expression of the transgene from the recombinant AAV vector. In other words, High et al provide the claimed basic architecture of rAAV expression vector upon which the claimed modification could be made. However, High et al does not expressly teach the CTCF elements required by amended claim 1.
Sadelain et al disclose, “In certain embodiments, a presently disclosed expression cassette comprises at least one insulator comprising the CTCF binding site sequence.” (paragraph 0017) “In one embodiment, the expression cassette comprises two of the insulator…where one insulator is positioned at the 3' end and the other insulator is positioned at the 5' end of the expression cassette.” (paragraph 0017). Additionally, “Also provided are vectors comprising such expression cassettes, cells transduced with such expression cassettes or such vectors…” (paragraph 0016). Furthermore, “Other viral vectors that can be used include, for example, adenoviral, lentiviral, and adeno-associated viral vectors…” (paragraph 0149). Additionally, Sadelain et al disclose, “ the presently disclosed subject matter provides cells transduced with the above-described expression cassettes, cells transduced with the above-described recombinant vectors…” (paragraph 0025). Furthermore, “The vector itself, which encodes the therapeutic transgene or cDNA, retains the minimal viral sequences needed to enable packaging in viral particles in a packaging cell line, reverse transcription, and integration. The packaging cell expresses the necessary structural proteins and enzymes that are required to assemble an infectious recombinant particle that contains the vector sequence and the machinery needed for its reverse transcription and integration in the transduced cell.” (paragraph 0143). Sadelain et al further disclose “ when a presently disclosed insulator is incorporated into a vector, the insulator does not adversely affect vector titers of the vector. In certain embodiments, the insulators (e.g., insulator A 1) increase the in vivo expression of the globin gene or functional portion thereof”. ( See [0131]). Finally, “The presently disclosed subject matter contemplates that the vectors and other delivery systems (eg, nucleases or CRISPR-Cas systems), viral particles…”(paragraph 087). Accordingly. Sadelain et al supplement Hight et al by teaching an expression cassettes for gene therapy comprising CTCF-containing insulators, and specifically teach the claimed arrangement of ( 5’ “CTCF-containing insulator”-expression cassette-3’ “CTCF-containing insulator”).
Wit et al 2015 disclose, “As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR/Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal, convergent CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher-order chromatin structure.” (summary paragraph). Accordingly, Wit et al supplement High and Sadelain et al by providing the specific teaching supporting the selection of convergent orientation of two CTCF sites when the objective is to obtain CTCF-mediated chromatin looping effects.
Schaack et al further support the cited prior arts by teaching the incorporation of CTCF-binding sites into a viral transducing vector containing a CMV-GFP expression cassette. Specifically, Schaack et al teach a vector comprising a CTCF-binding sequences being introduced at the 5’ and 3’ of the CMV-GFP cassette. ( See Figure 1. E). Schaack et al also demonstrate that multiple CTCF-binding sites (i.e. four CTCF-binding sites) can be incorporated into a viral expression cassette on one or both sides of promoter/transgene to regulate transgene expression. ( See abstract). Thus, Schaak et al teach that a CTCF-containing region may comprise multiple sequences in a viral expression construct, this reads on claim 9. Most importantly, Schaack et al teach that the CTCF-containg vectors produced substantially prolonged GFP expression with the duration of GFP expression in liver more than doubling. ( See abstract and Fig.4). Schaack et al thus provide an express teaching that flanking an expression cassette with CTCF binding sequences improves/prolong transgene expression. Thus, providing an ordinary skill in the art with the motivation to consider incorporating CTCF-binding elements into a viral expression vector when seeking to improve transgene expression.
Taken together, it would have been prima facie obvious to one with ordinary skill in the art, before the effective filing date to include a CTCF site in an AAV vector, and in particular in an AAV vector with the format disclosed by High et al above (5’ITR, a promoter, a transgene, and a 3’ ITR) because it is well known in the art that these types of DNA sequences (i.e. CTCF binding sites) are used to control and regulate gene expression as taught by Wit el al and demonstrated by Schaack et al. Because High et al provide an established rAAV expression vector platform comprising 5’ITR, a promoter, a transgene, and 3’ ITR. Sadelain et al teach the use of CTCF-containing insulator elements at the boundaries of a viral expression cassette and further teach that such CTCF-containing elements can enhance expression of the encoded transgene. Schaack et al independently demonstrate that multiple CTCF-binding sites can be incorporated into a viral expression cassette on one or both sides of promoter/transgene to regulate transgene expression. Wit et al further teach that the orientation of CTCF binding sites is functionally significant for chromatin organization and that CTCF sites arranged in a convergent orientation promote chromatin-loop formation. Accordingly, one with ordinary skill in the art seeking to improve or regulate transgene expression from the known rAAV expression construct of High et al would have been motivated to incorporate the known CTCF-containing regulator elements taught by Sadelain and Schaak et al at the boundaries of the promoter/transgene and to arrange the CTCF sites in the convergent direction as taught by Wit et al. An ordinary skill in the art would have had a reasonable expectation of success in making the proposed modification because prior arts already had demonstrated before the filing date that CTCF-binding elements could be incorporated into viral expression constructs and used to influence transgene expression and that CTCF orientation could influence chromatin organization. In other words, instant claims are combining prior art elements according to known methods to yield predictable results. See MPEP 2143 (I)(A).
Regarding claim 5, following the discussion of claim 1 above, the combined teachings of the prior art applied above teach a construct for producing recombinant AAV vector comprising the claimed architecture, including the 5’ and 3’ ITRs, a promoter, a transgene, with CTCF binding sites positioned at the 5’ and 3’ of the expression cassette. Sadelain et al further teach CTCF-binding sites of human origin and teach incorporating the CTCF-containing insulator into an expression cassette. Sadelain et al also teach that when incorporated into a viral vectors the insulator can increase the expression of the encoded goblin gene.[0131]. Thus, Sadelain et al teach that the use of human CTCF-binding sequences as insulator elements in viral gene-expression cassettes, including positioning such elements at the 5’ and/or 3’ boundaries of an expression cassette.
Regarding claims 12-15, following the discussion of claims 1 and 9 above the cited prior art render obvious the modified rAAV vector of instant claims. Sadelain further provides explicit disclosure of an AAV particle containing the disclosed construct (claim 13), a cell line transduced with the AAV vector (claim 12), and a cell line designed specifically for progeny generation using trans complementation (claim 14-15). This renders claims 12-15 obvious.
Claims 7-8 are rejected under 35 U.S.C. 103 as being unpatentable over High et al in view of Sadelain et al ,Schaack et al , and Wit et al as applied to claims 1,5, 9 and 12-15 above, and further in view of Roa et al ( Cell, 2014) .
Regarding claim 7-8, following the discussion of claim 1 above, the combined teachings of the cited prior art render obvious the modified rAAV vector of claim 1. Rao et al supplement the cited prior arts by describing CTCF binding motifs and their orientation in human chromatin. Rao et al further disclose CTCF-binding consequences corresponding to the recited sequences of instant claims. Specifically, Rao et al disclose the CTCF motif CCACAAGGTGGCGC, which corresponds to SEQ ID NO.1 and CCGCCCCCTGGTGG corresponding to SEQ ID NO.42 of instant claims 7 and 8. Rao et al further describe CTCF motifs in forward and revers orientations and their association with chromatin loop formation. Roa et al further teach that CTCF binding motif pairs possess orientation and that CTCF motif pairs associated with chromatin loops are predominantly arranged in convergent orientation. Accordingly, Rao et al provide the specific CTCF sequences recited by instant claims, as well as the teaching concerning their orientation in CTCF-mediated chromatin looping. ( See Fig.6 and section “ The Vast Majority of Loops Are Associated with Pairs of CTCF Motifs in a Convergent Orientation”. Thus, an ordinary skill in the art would be motivated to employ the known CTCF sequences of Rao et al in the rAAV expression construct of claim 1 because the combined teachings of the cited prior arts demonstrate the use of CTCF binding sites in viral expression constructs, while Rao et al teach that CTCF binding and the orientation of CTCF motifs are involved in higher order chromatin organization. Thus, an ordinary skill in the art would have had a reason to select known human CTCF motifs, including the sequences taught by Rao et al and arrange the motifs in the known convergent orientation. In other words, instant claims merely amounts to combining prior art elements according to known methods to yield predictable results. See MPEP 2143 (I)(A).
Claims 6, and 10 are rejected under 35 U.S.C. 103 as being unpatentable over High et al in view of Sadelain et al ,Schaack et al , and Wit et al as applied to claims 1,5, 9 and 12-15 above, and further in view of Chen et al Journal of Virology, 2007).
Regarding claims 6 and 10, following the discussion of claim 1 above, the combined teachings of the cited prior arts render obvious the modified rAAV vector of claim 1. Chen et al supplement the cited prior arts by describing CTCF binding insulator derived from HSV-1 genome, this reads on claim 6. Specifically, Chen et al identifies an approximately 800-bp region within the HSV-1 LAT intron that functions as a chromatin insulator. The 800-bp region includes an approximately 200-bp region containing nine copies of a 16-bp repeat, each repeat containing the CTCF-interacting sequence CTCCC. Chen demonstrates that CTCF specifically binds the repeated sequences by EMSA and demonstrate that the nine repeated CTCF-binding sequences are functionally associated with enhancer-blocking activity. Deletion of the repeated region, impaired insulator activity, and knockdown of CTCF disrupted the enhance blocking activity of LAT insulator. ( See abstract). Thus, Chen et al teach a CTCF-binding sites derived from HSV-1, a viral construct containing more than 5 CTCF-binding sequences. Thus, it would have been prima facie obvious to one with ordinary skill in the art at the time the invention was filed to employ the HSV-1 derived, multiple copy of CTCF-binding sites taught by Chen et al in a viral construct of claim 1. Because Chen et al expressly state that repeated CTCF-binding sequences derived from a virus can function collectively as a chromatin boundary/insulator. The selection of known viral CTCF-binding sites, including an element containing at least five binding sites, represent the use of known regulatory elements for its known function. In other words, instant claims are combining prior art elements according to known methods to yield predictable results. See MPEP 2143 (I)(A).
Claims 11 is rejected under 35 U.S.C. 103 as being unpatentable over High et al in view of Sadelain et al ,Schaack et al , and Wit et al as applied to claims 1,5, 9 and 12-15 above, and further in view of Clark et al ( WO 2021/138559 A1).
Regarding claim 11, Clark et al disclose an AAV2 p5 promoter as SEQ ID NO:720. In particular, Clark et al teach that an AAV2/9 Rep/Cap plasmid may comprise an AAV2 p5 promoter having the nucleic acid sequences of SEQ ID NO:710, and further identifies SEQ ID 710 as the AAV2 P5 promoter from which AAV2 Rep78 and Rep68 are transcribed. It should be noted that sequence search established that SEQ ID NO 3 is an exact 19-nucleotide match to nucleotides 42-60 of the AAV2 p5 sequence of SEQ ID NO:710. Thus, the specific nucleotide sequence relied upon in SEQ ID NO:3 was not newly created, but rather was part of a known AAV2 regulatory sequence that had been publicly disclosed before the effective filing date of instant application. Following the discussion of claim 1 above, prior arts have taught a modified rAAV comprising the construct of claim 1, and further identified that CTCF-binding elements were useful regulatory elements for viral expression constructs and that CTCF can be positioned at around the expression cassette to regulate chromatin organization and gene expression. Thus, an ordinary skill in the art would be motivated to identify and employ CTCF-binding motifs within a known AAV sequence rather than being required to generate unknown sequences. In other words, an ordinary skill in the art would have had a reason to examine known sequences for CTCF-binding sites and employ the identified motifs in an expression construct rather than being required to identify an entirely new sequences. Thus claim 11 is an example of combining prior art elements according to known methods to yield predictable results. See MPEP 2143 (I)(A).
Response to Arguments
Applicant's arguments filed 08/05/2026 have been fully considered but they are not persuasive.
Applicants argue that the present application demonstrates enhancement of gene
expression in multiple constructs containing convergent CTCF sites, and submits that one of skill in the art would have no motivation to use the convergent CTCF sites disclosed in Wit with the vector disclosed in High or the expression cassette disclosed in Sadelain.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully considered but are not found persuasive. It should be noted that Applicants have amended claim 1 to incorporate the limitations previously recited in claims 2-4. Applicants have further amended claim 1 to add the limitation“ a modified rAAV that expresses a transgene at a higher level than a wild type of the rAAV vector”, while High et al alone does not teach the recited limitations ; however, a new ground of rejection is made over High et al in view of Sadelain et al, Schaack et al , and Wit et al, that covers all of the added claim limitations ( as discussed above).
Applicant further argue that the cited prior arts disclose longer promoter or genomic sequences containing the claimed CTCF sequence and does not identify the particular nucleotides constituting a CTCF-binding site to provide a motivation to isolate the sequence for use in another construct.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully considered but are not found persuasive. This argument is addressed in part by amendment of the references relied upon for the sequences limitation. Specifically, Rao et al is now relied upon to disclose SEQ ID NO 1 and 42. This leaves Applicants remaining argument to be directed to Clark et al. To address this, first the rejection does not rely on Clark et al for the teaching that the sequence functions as a CTCF-binding site. Rather, Clark et al was relied upon to demonstrate that the particular nucleotide sequence (i.e. SEQ ID NO:3) was known in the art and publicly available as part of an AAV2 P5 promoter sequence, specifically SEQ ID NO:720. On the other hand, the cited prior arts applied toward claim 1 were relied upon to teach that CTCF-binding sites were useful regulatory elements that can be incorporated in viral expression vector and could be positioned at the boundaries of the expression cassette. Thus, the identification and use of a known nucleotide sequence would have been a sequence-selection exercise within the skill of the art where the prior art provided a reason to identify functional regulator motifs within the known viral sequences. The fact that SEQ ID NO 3 is disclosed with a longer promoter or genomic sequence does not by itself negate its availability to the skilled artisan because an ordinary skill in the art would have had a reason to examine known sequences for CTCF-binding sites and employ the identified motifs in an expression construct, rather than being required to identify an entirely new sequences.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FATIMAH KHALAF MATALKAH whose telephone number is (703)756-5652. The examiner can normally be reached Monday-Friday,7:30 am-4:30 pm EST.
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, Tracy Vivlemore can be reached at 571-272-2914. 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.
/FATIMAH KHALAF MATALKAH/Examiner, Art Unit 1638
/Tracy Vivlemore/Supervisory Primary Examiner, Art Unit 1638
