DETAILED ACTION
Applicant’s amendment and Arguments/Remarks received on 28 December 2025 have been entered. Claims 1-30, 32-38, and 40-41 were previously pending in the application. Claims 4, 19, and 20 have been cancelled, and new claims 93-94 have been added by Applicant. Claims 1-3, 5-18, 21-30, 32-38, 40-41, and 93-94 are currently pending in the application. Claims 1, 2, and 38 are independent claims.
The following election of species remains in effect in the instant application:
Kozak sequences: a. SEQ ID NO: 125 (RNNATG) or SEQ ID NO: 28 (RVVATG)
Overlapping Kozak sequence and/or start codon and TRAP binding site sequences: a. SEQ ID NO: 29;
Nucleic acid sequences according to claim 17-18: f. SEQ ID NO: 70;
Sequence elements proximal to the TRAP binding site: Promoter: i. Leader sequences: 2. SEQ ID NO: 26.
Claims 18 and 25-30 remain withdrawn from consideration as being directed to a nonelected species, there being no allowable generic or linking claim.
Claims 1-3, 5-17, 21-24, 32-38, 40-41, and 93-94 are currently pending and under examination in the instant application. An action on the merits follows.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Priority
The present application is a 35 U.S.C. 371 national stage filing of International Application No. PCT/GB2020/052873, filed 11 November 2020, which claims priority to United Kingdom 1916452.4, filed 12 November 2019, and United Kingdom 2001998.0, filed 13 February 2020. Filing of a certified copy of the United Kingdom 1916452.4, filed 12 November 2019, and the United Kingdom 2001998.0, filed 13 February 2020 is acknowledged.
Thus, the earliest possible priority for the instant application is 12 November 2019.
Information Disclosure Statement
The information disclosure statement filed 28 December 2025 has been considered by the Examiner. Examiner notes the filing of IDS Size Fee assertions for the IDS filed 28 December 2025, as required under 37 CFR 1.98, indicating that no IDS size fee is required under 37 CFR 1.17(v) at this time.
37 CFR 1.821-1.825
Applicant has provided a substitute sequence listing the sequences previously recited without an accompanying SEQ ID NO: and a substitute specification reciting the appropriate SEQ ID NOs, which are now in compliance with the requirements of 37 CFR 1.821 through 1.825.
Specification
The objection to the specification of the disclosure for reciting trade names and/or marks without the appropriate symbols and/or generic terminology is withdrawn in view of the amendment to the specification.
Claim Objections
The objection to amended claims 13 and 32 for an apparent typographical error (claim 13) and reciting an abbreviation without first writing out the term (claim 32) is withdrawn in view of the amendment to claims 13 and 32.
Claim Rejections - 35 USC § 112(b)
The rejection of amended and cancelled claims 16, 19, 21, and 36 under 35 U.S.C. 112(b) as failing to particularly point out and distinctly claim the subject matter which the inventor(s) regards as the invention for issues of indefiniteness is withdrawn in view of Applicant’s cancellation of claim 19 and amendments to claims 16, 21, and 36 resolving the issues of indefiniteness.
**The following new rejection is necessitated by amendments to the claims.**
Amended, previously presented, original, and new claims 1-3, 5-17, 21-24, 32-38, 40-41, and 93-94 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. Claims 2-3, 5-17, 21-24, 32-38, 40-41, and 93-94 are included in this rejection due to their dependence on and/or encompassing of independent claim 1.
Independent claim 1 has multiple issues of indefiniteness.
Claim 1 was amended to recite, “a nucleotide of interest comprising an ATG start codon, a Kozak sequence comprising the start codon, and a tryptophan RNA-binding attenuation protein (TRAP) binding site” in lines 1-3, which is indefinite because it is unclear whether the nucleotide of interest itself is meant to comprise the recited ATG start codon, Kozak sequences, and TRAP binding site, or whether the nucleic acid sequence is meant to comprise 1) a nucleotide of interest comprising an ATG start codon, 2) a Kozak sequence comprising the start codon, and 3) a TRAP binding site, such that the non-ATG nucleotides of the Kozak sequence and the TRAP binding site are comprised within the nucleic acid sequence by not (necessarily) comprised within the nucleotide of interest.
Claim 1 was amended to recite, “a nucleotide of interest comprising an ATG start codon, a Kozak sequence comprising the start codon, and a tryptophan RNA-binding attenuation protein (TRAP) binding site” in lines 1-3 and “wherein the TRAP binding site is capable of interacting with tryptophan RNA-binding attenuation protein, such that translation of the nucleotide of interest is repressed in a viral vector production cell” in lines 8-10, which is indefinite because Applicant has claimed a DNA start codon, but has also indicated that the TRAP binding site (tbs) comprised within the same molecule is interacting with an RNA binding protein (TRAP) to modify translation. As such, it is unclear how the TRAP is interacting with a nucleic acid sequence comprising a DNA start codon. Additionally, dependent claims 15-17, 24, and 36-37 recite DNA sequences comprised within the claimed nucleic acid sequence.
As such, the metes and bounds of the claims cannot be determined.
Claim Interpretation
Amended independent claim 1 now recites, “wherein the TRAP binding site is capable of interacting with tryptophan RNA-binding attenuation protein, such that translation of the nucleotide of interest is repressed in a viral vector production cell”, has been interpreted to encompass an inherent functional attribute of the claimed nucleic acid sequence without requiring that the claimed nucleic acid be present in a viral vector production cell. Further, “wherein the TRAP binding site is capable of interacting with tryptophan RNA-binding attenuation protein” has been interpreted to encompass wherein the corresponding TRAP binding site present in an mRNA transcribed from the nucleotide of interest is capable of interacting with TRAP. Additionally, “such that translation of the nucleotide of interest is repressed in a viral vector production cell” has been interpreted such that the interaction of the RNA tbs with TRAP in a viral vector production cell results in the translational repression.
Claim 21 has been amended to recite, “wherein the TRAP binding site does not comprise a type II restriction enzyme site”, which has been afforded its broadest reasonable interpretation to encompass wherein the TRAP binding site does not comprise any single individual type II restriction enzyme, such that at least one type II restriction enzyme site is not found within the sequence. Specifically, the TRAP binding site may comprise any number of type II restriction enzyme recognition sites as long as at least one type II restriction site is not present in the sequence.
Claims 16, 17, and 37 recite, “a nucleotide sequence set forth in any one of SEQ ID NOs:” (claims 16 and 17) or “a sequence as defined in SEQ ID NO: 114 or SEQ ID NO: 116” (claim 37) [emphasis added], which has been afforded its broadest reasonable interpretation to encompass comprising any fragment having 2 or more consecutive nucleotides of the sequence according to any one of the recited SEQ ID NOs, such that the claims do not require the full length sequences according to the recited SEQ ID NOs.
Claim 24 recites, “wherein said leader sequence comprises a sequence as defined in SEQ ID NO: 25 or SEQ ID NO: 26”. Note that Applicant elected a leader sequences: of SEQ ID NO: 26. Therefore, the elected leader sequence has been interpreted such that the leader sequence comprises a sequence derived from the non-coding EF1α exon 1 region (as recited in claim 23 upon which claim 24 depends) and comprises a sequence as defined in SEQ ID NO: 26, which requires inclusion of any fragment having 2 or more consecutive nucleotides of the sequence according to SEQ ID NO: 26 and does not require the full length sequence of SEQ ID NO: 26.
Claim Rejections - 35 USC § 101
The rejection of amended, previously presented, and original claims 1-3, 6-7, 15-16, and 22-24 under 35 U.S.C. 101 as being directed to a product of nature without significantly more is withdrawn in view of Applicant’s amendments to independent claim 1 and Applicant’s declaration filed under 37 CFR 1.132 attesting that the Kozak sequence as recited in the claims is defined specifically to be “a consensus sequence in a eukaryotic mRNA which is recognized by the ribosome as the translational start site” [Declaration point 9 and instant specification page 33, lines 9-11], and therefore excludes a bacterial nucleic acid sequence even when the elected core Kozak sequence is present within the bacterial sequence.
Claim Rejections - 35 USC § 102
The rejection of amended, previously presented, and original claims 1-3, 6-7, 15-16, and 22-24 under 35 U.S.C. 102(a)(1) as being anticipated by Babitzke [2004, Current Opinion in Microbiology, 7, 132-139], as evidenced by NCBI GenBank [CP120587.2 Bacillus subtilis strain PRO121 chromosome, complete genome, retrieved on 8 August 2025 from the Internet: <https://www.ncbi.nlm.nih.gov/nuccore/CP120587.2?report=fasta>], is withdrawn in view of Applicant’s amendments to independent claim 1 and Applicant’s declaration filed under 37 CFR 1.31 asserting that the Kozak sequence as recited in the claims is defined specifically to be “a consensus sequence in a eukaryotic mRNA which is recognized by the ribosome as the translational start site” [Declaration point 9 and instant specification page 33, lines 9-11], and therefore excludes a bacterial nucleic acid sequence even when the elected core Kozak sequence is present within the bacterial sequence. Babitzke does not teach wherein the ycbK gene sequence is present within a eukaryotic cell, and as such, does not teach wherein the sequence is a eukaryotic DNA or mRNA sequence.
Claim Rejections - 35 USC § 103
The rejection of amended, previously presented, original, and cancelled claims 1-17, 19-24, 32-38, and 40-41 under 35 U.S.C. 103 as being unpatentable over Farley [US20160333373A1, published 17 November 2016]; in view of Babitzke [2004, Current Opinion in Microbiology, 7, 132-139]; REBASE [1999, BamHI, retrieved on 9 August 2025 from the Internet: <https://web.archive.org/web/19991111001358/http://rebase.neb.com/rebase/enz/BamHI.html>, archived on 11 November 1999]; Zhu et al. [2001, Biochimica & Biophysica Acta, 1521, 19-29]; and Schlatter et al. [2003, Biotechnology & Bioengineering, 81(1), 1-12]; is withdrawn over cancelled claims 4, and 19-20; maintained over amended, previously presented, and original claims 1-3, 5-17, 21-24, 32-38, and 40-41; and newly applied to new claims 93-94. Applicant's amendments to the claims and arguments have been fully considered but have not been found persuasive in overcoming the rejection for reasons of record as discussed in detail below.
The limitations newly introduced into independent claim 1 were previously rejected with respect to cancelled claims 4 and 19-20. Applicant has not introduced new limitations which would alter the scope of the claims to overcome the rejection of record.
Regarding new claim 93, Farley teaches a 5’UTR leader sequences upstream of the TRAP binding site which is 34 nt long [0123, 0602, Figure 24i-24ii]. Farley also teaches including a 5’ Stem-loop (SL) sequence upstream of the tbs sequence, wherein the 5’SL is taken from the Bacillus subtilis trpEDCFBA operon, which has been shown to be important for TRAB-tbs binding [0075, 0597, Figure 13]. Babitzke teaches that the 5’SL from the Bacillus subtilis trpEDCFBA operon comprises 31 nucleotides [Figure 3].
As discussed in the prior action, Zhu and Schlatter teach the motivation to include the EF1α TOP leader sequence within the 5’ UTR of an mRNA encoding a transgene to allow translational control of the transgene expression, including increasing the repression of the gene by blocking ribosomal binding to the transcript.
Additionally, Zhu teaches that the EF1A 5’UTR region is 33 nucleotides long [Figure 1]. Zhu also teaches inclusion of the EF1A 5’UTR in a nucleic acid construct encoding a transgene to assess the role of the 5’ TOP sequence in gene expression regulation, wherein the intact 5’ TOP element contributes to rapamycin-dependent repression of translation of the mRNA comprising the EF1A 5’ UTR [Figure 1]. Specifically, Zhu teaches that mutation of the +1 C to G and the +3 T to A is sufficient to eliminate the rapamycin-induced repression [column 3 ¶ 4- column 4 ¶ 1, Figure 1]. Further, Zhu teaches that the 5’ TOP element itself is 7 nucleotides long (CTTTTTC) [Figure 1]. Therefore, the ordinarily skilled artisan would be motivated to use either the full length EF1A 5’UTR of 33 nucleotides or to specifically use the EF1A 5’ TOP sequence of 7 nucleotides within the 5’ UTR of an mRNA encoding a transgene to allow translational control of the transgene expression.
As such, it would have been prima facie obvious to an ordinarily skilled artisan at the time of filing the instant application to modify the nucleic acid of Farley use the 33 nucleotide-long EF1α 5’ UTR sequence or the 7 nucleotide-long EF1α 5’ TOP sequence as the EF1α TOP leader sequence for translational control of a transgene with a reasonable expectation of success.
Therefore, Applicant’s amendments do not overcome a finding of obviousness over Farley, Babitzke, Zhu, and Schlatter under 35 USC 103.
Applicant argues that:
Farley does not disclose or suggest an overlapping TRAP binding site (tbs) and Kozak sequence, but instead discloses a tbs that is adjacent to a truncated Kozak sequence (i.e., the “+0 spacer” construct);
Farley provides no motivation to make a nucleic acid sequence wherein the tbs overlaps the Kozak sequence, in that the data presented by Farley shows that moving the tbs closer to the start codon did not achieve increased translation repression;
the disclosure of Babitzke is irrelevant to the present invention because the nucleic acid sequence discussed in Babitzke is a bacterial sequence and does not comprise a Kozak sequence; and
with respect to claim 24 in particular, the present inventors surprisingly found that the sequence encoding the terminal oligopyrimidine tract (TOP) element did not reduce transgene expression in the absence of TRAP, demonstrating that in the claimed configuration, the TOP element did not have inherent translation-inhibiting activity, as seen in specification Example 1 and Figures 3 and 8.
However, this is not agreed.
In response to Applicant’s arguments against the references individually, it is noted that the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). 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). Further, the Examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In addition, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
Specifically, regarding Applicant’s argument 1), note that the claims recite a nucleic acid sequence, and as such, the structure of the nucleic acid sequence determines the patentability of the present invention. Determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.” In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted).
Farley was cited for teaching a nucleic acid sequence comprising a nucleotide of interest and a tryptophan RNA-binding attenuation protein (TRAP) binding site (tbs) [Figure 4, 6]; wherein said nucleic acid sequence also comprises a Kozak sequence, wherein said tbs overlaps the Kozak sequence (e.g., “+0” spacer between the tbs and ATG, wherein the 3’ terminal tbs repeat KAGNN (GAGTC) overlaps the core Kozak RNNATG (SEQ ID NO: 125 of the instant application) at a junction sequence of GAGTCATG) [Figure 6, 13A], such that the Kozak sequence generated by the overlap is GGAGTCATGG, wherein the underlined nucleotides indicate the overlap between the tbs and the core Kozak sequence. Although Farley did not teach that the overlapping sequence was designed to be an overlapping tbs-Kozak sequence, the effect of the truncation performed by Farley was to generate an overlapping tbs-Kozak sequence. Therefore, Farley does in fact disclose an overlapping TRAP binding site (tbs) and Kozak sequence.
Further, the GGAGTCATGG Kozak sequence comprised in the +0 spacer construct of Farley comprises the elected RNNATG core Kozak sequence and is similar to the consensus Kozak sequence of GCCRCCATGG and comprises the critical purine (having a G) at position -3 and G at position +4. Additionally, as further evidence of the suitability of this sequence as a bona fide Kozak sequence, Coppola specifically teaches that the GGAGTCATGG sequence agrees reasonably well with the consensus sequence for translation initiation in eukaryotes (i.e., mice) and is present as the functional, native initiator sequence in the murine N-type calcium channel α1 subunit mRNA [Coppola et al. 1994, FEBS Letters, 338, 1-5, column 3 ¶ 7, Figure 1].
Regarding Applicant’s argument 2), as discussed above, Farley explicitly discloses an overlapping tbs-Kozak sequence, and so no modification of Farley is necessary to arrive at the limitation of an overlapping tbs-Kozak sequence. As such, no motivation is required to arrive at the claimed limitation in question.
Regarding Applicant’s argument 3), note that Babitzke was cited for teaching that the B. subtilis ycbK gene, which comprises a natural tbs, comprises the sequence of GAGATG [Figure 2]. Babitzke also teaches that, for the trpP gene, extending the tbs into the coding region results in more effective inhibition of ribosome binding (and thus more effective inhibition of translation), that the tbs of the ycbK gene overlaps the translation initiation region and extends into the coding sequence, and that one might predict that the repeats in the coding sequence may increase the effectiveness of bound TRAP in blocking ribosome binding [column 11 ¶ 1-2, Figure 2]. Babitzke was relied on for teaching the effectiveness of TRAP binding to a site overlapping with the initiation codon specifically, wherein the overlapping sequence comprises GAGATG, and was not relied on for teachings related to the prokaryotic Shine-Delgarno ribosomal recognition sequence. Both prokaryotes and eukaryotes rely on the ATG start codon to initiate translation. The teachings of Babitzke provide motivation for including TRAP binding sites which overlap with the ATG start codon as claimed, and further provide an example of an overlapping tbs-ATG sequence for which TRAP binding is effective for repressing translation by blocking ribosome binding. Therefore, an ordinarily skilled artisan would expect that substitution of the GTCATG taught by Farley with the GAGATG taught by Babitzke would provide effective translational repression by through steric blockage of ribosomal binding.
Regarding Applicant’s argument 4), Zhu was cited for teaching that the sequence of instant SEQ ID NO: 26 (CTTTTTCGCAAC) is the terminal oligopyrimidine tract (TOP) from the EF1α mRNA 5’UTR which is required for translational control of EF1a transcripts, such that it facilitates the translational repression of the transcript following rapamycin treatment and binding of a repressor protein La to the TOP sequence [abstract, column 2 ¶ 1, column 16 ¶ 2, Figure 1A]. Additionally, Schlatter was cited for teaching that TOP elements adopt a specific secondary structure that prevents ribosome binding and translation initiation of mRNAs, and the use of a TOP sequence for the conditional control of transgene expression from a vector in mammalian cells, wherein a TOP sequence is inserted between a promoter and a transgene coding region [abstract]. Schlatter also teaches that this system has proved to provide unprecedented precision in controlling translation in stable transgenic mammalian cell lines [column 18 ¶ 2]. Therefore, given the teachings of Zhu that the EF1α TOP comprises the sequence of instant SEQ ID NO: 26 and the teachings of Schlatter to use TOP sequences as translation control elements to control the expression of transgenes, an ordinarily skilled artisan at the time of filing the instant application would have been motivated to include the EF1α TOP leader sequence within the 5’ UTR (e.g., between a promoter and a start codon) of transgene to allow translational control of the transgene expression, including increasing the repression of the gene by blocking ribosomal binding to the transcript.
With respect to Applicant’s assertion that the present inventors surprisingly found that the sequence encoding the terminal oligopyrimidine tract (TOP) element did not reduce transgene expression in the absence of TRAP, demonstrating that in the claimed configuration, the TOP element did not have inherent translation-inhibiting activity, as seen in specification Example 1 and Figures 3 and 8; note that Figure 3 shows repression by TRAP-tbs for full native promoters (including the EF1alpha promoter according to instant SEQ ID NO: 134) with their native 5’UTR leader sequences as well as truncated promoters with the “Improved Leader L33” [page 15 line 1-13, Figure 3]. The “Improved Leader L33” corresponds to the sequence of instant SEQ ID NO: 25 (identical to SEQ ID NO: 139), which comprises the sequence of SEQ ID NO: 26 (also identical to SEQ ID NO: 140) and therefore encodes the EF1alpha TOP element [Table 1]. Applicant has compared the presence of the full native EF1alpha promoter + 5’UTR sequence to a truncated EF1alpha promoter + the “Improved Leader L33” and shown that the construct having the “Improved Leader L33” exhibited a slightly higher expression level than the construct comprising the native sequence. However, the data presented in Figure 3 does not provide a control lacking a leader sequence, having only the elected leader of SEQ ID NO: 26, nor otherwise differing by only the presence of the “Improved Leader L33” or elected leader sequence.
Applicant suggests that the presence of the intron in the native promoters is insignificant since it is spliced out of the mRNA, and does not address the potential impact of the intron on expression levels. The data presented in Figure 3 was generated by transfecting the constructs comprising the indicated promoters and leader sequences upstream of the tbs-Kozak sequence operably linked to a GFP coding sequence in HEK293T cells [page 149 lines 8-17]. The GFP expression was then measured by flow cytometry as a GFP Expression Score (%GFP positive cells x mean fluorescence intensity), without normalization for the transcription levels of the construct. Therefore, Applicant’s assumption that the presence of an intron is not impacting the data has not been validated.
Note also that for the other promoters tested, the data in Figure 3 show that the “Improved Leader L33” has similar- sometimes slightly higher and sometimes slightly lower- GFP expression levels compared to the respective native promoters.
As such, Applicant has not shown that the “Improved Leader L33” nor the elected leader sequence “surprisingly” do not repress expression, particularly given that the TOP element is present in both the native EF1alpha leader sequence and the “Improved Leader L33” and that transcriptional levels have not been accounted for.
Figure 8 is a comparison of the “Improved Leader L33” (“L33”) and the elected leader sequence (referred to as “L12”). Figure 8 does not compare constructs comprising the elected L12 with any constructs lacking the elected leader sequence. Therefore, Figure 8 does not provide any data regarding a lack of repression for the elected leader sequence in the absence of TRAP.
Further, data presented for additional promoters have mixed results, wherein the L33-comprising construct is only very slightly increased or even reduced relative to the respective native promoter, and wherein the variance between the L33-comprising construct and the native construct is comparable to the variance observed between the L33- and L12-comrpising constructs, suggesting that the differences observed are not likely attributable to substantial alterations in the repressibility of the constructs [Figure 3, 8].
Additionally, Schlatter teaches that binding of a trans factor (i.e., CNBP or La) to a TOP element facilitates translation of a TOP element-comprising mRNA, and that absence of CNBP/La results in repression of translation in mammalian cells [column 8 ¶ 3- column 9 ¶ 1, Figure 1]. Schlatter also teaches that CNBP is a highly conserved protein expressed in a variety of tissues which is a key translation regulator of TOP-containing ribosomal protein-encoding mRNAs [column 3 ¶ 2]. Schlatter further teaches that La is present in mammalian cells and is involved in translation enhancement of endogenous mRNAs [column 3 ¶ 3]. Further, Zhu teaches that La protein binding to the TOP element in the EF1A 5’ UTR RNA correlates with TOP mRNA translational repression following rapamycin treatment of cells [abstract, column 3 ¶ 2, column 17 ¶ 4].
Therefore, the expression and activity levels of TOP element binding proteins and specific conditions within the cells will determine the level to which a TOP element is able to facilitate repression of a given transcript. Applicant has not shown any data to indicate that the particular cellular conditions under which GFP expression was assessed were conditions for which TOP element-mediated repression would be expected.
Note also that any evidence of unexpected results must be commensurate in scope with the claimed invention, and that a greater, or greater than additive, effect is not necessarily sufficient to overcome a prima facie case of obviousness because such an effect can either be expected or unexpected MPEP 716.02 (a) and (d). Whether the unexpected results are the result of unexpectedly improved results or a property not taught by the prior art, the "objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support." In other words, the showing of unexpected results must be reviewed to see if the results occur over the entire claimed range. In re Clemens, 622 F.2d 1029, 1036, 206 USPQ 289, 296 (CCPA 1980).
Specifically, Applicant has merely shown that altering a construct from having the full native intron-containing EF1alpha promoter with the native 5’ UTR leader sequence (comprising the elected sequence of SEQ ID NO: 26) to having a truncated EF1alpha promoter with a shorter leader sequence L33 (also comprising the elected leader sequence of SEQ ID NO: 26) slightly increased the GFP expression levels in the absence of co-transfected TRAP in a single cell type under a single set of culture conditions [page 149 lines 8-17, Table 1, Figure 3]. Applicant also showed that a construct comprising the elected L12 leader sequence has a similar expression level to the L33-comprising construct when transfected in the absence of co-transfected TRAP in a single cell type under a single set of culture conditions [Figure 8]. Therefore, Applicant’s evidence is not commensurate in scope with the claimed invention, which recites a nucleic acid sequence not limited to any particular leader sequence in the broadest independent claim. With respect to claim 24 specifically, the invention requires the elected leader sequence, but is not limited to any function of the leader sequence nor to inclusion of the nucleic acid within any particular cells, nor to the expression of the nucleic acid under any particular cellular conditions. Additionally, the claim as written requires the sequence of SEQ ID NO: 26 but does not exclude additional sequences, such as the full EF1alpha 5’ UTR or any other sequences.
Therefore, Applicant’s arguments do not overcome a finding of obviousness over Farley, Babitzke, Zhu, and Schlatter under 35 USC 103, and the rejection is maintained.
Double Patenting
The rejection of claims 1-17, 19-24, 32-38, and 40-41 on the ground of nonstatutory double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 10,544,429, hereafter referred to as the ‘429 patent, in view of Babitzke [2004, Current Opinion in Microbiology, 7, 132-139]; is withdrawn over cancelled claims 4 and 19-20; maintained over amended, previously presented, and original claims 1-3, 5-17, 21-24, 32-38, and 40-41; and newly applied to new claims 93-94. Applicant's amendments to the claims and arguments have been fully considered but have not been found persuasive in overcoming the rejection for reasons of record as discussed in detail below.
The limitations newly introduced into independent claim 1 were previously rejected with respect to cancelled claims 4 and 19-20. Applicant has not introduced new limitations which would alter the scope of the claims to overcome the rejection of record.
Applicant argues that the ‘429 patent claims do not recite a nucleic acid sequence comprising a tbs that overlaps a Kozak sequence, nor is there any disclosure that would render such a nucleic acid sequence obvious; and that the disclosure of Babitzke is irrelevant to the present invention because the nucleic acid sequence discussed in Babitzke is a bacterial sequence and does not comprise a Kozak sequence;
However, this is not agreed.
The application from which the ‘429 patent was issued was published as Farley [US20160333373A1], which serves as the base reference for the rejection under 35 USC 103 above.
The ‘429 patent claim 8 recites a method of increasing viral vector titers in a eukaryotic vector production cell, thereby indicating that eukaryotic genes are specifically encompassed species of the nucleotide of interest, and therefore the accompanying control sequences must also be suitable for eukaryotic expression. Note that at the time of filing, Kozak sequences are well-known elements contributing to eukaryotic translation; and the ‘429 patent disclosure (Farley) provides extensive teachings of Kozak sequences in conjunction with the tbs sites [0075, 0576, 0598, 0603, Figure 13, 14]. Therefore, a nucleic acid comprising both a tbs and a Kozak sequence for translation of a nucleotide of interest is an obvious species for the vector genome claimed by the ‘429 patent claims.
Additionally, the ‘429 patent disclosure (Farley) teaches a nucleic acid sequence comprising a nucleotide of interest and a tryptophan RNA-binding attenuation protein (TRAP) binding site (tbs) [Figure 4, 6]; wherein said nucleic acid sequence also comprises a Kozak sequence, wherein said tbs overlaps the Kozak sequence [e.g., “+0” spacer between the tbs and ATG, wherein the 3’ terminal tbs repeat KAGNN (GAGTC) overlaps the core Kozak RNNATG (SEQ ID NO: 125 of the instant application) at a junction sequence of GAGTCATG] [Figure 6, 13A], such that the Kozak sequence generated by the overlap is GGAGTCATGG, wherein the underlined nucleotides indicate the overlap between the tbs and the core Kozak sequence. Although ‘429 patent disclosure did not teach that the overlapping sequence was designed to be an overlapping tbs-Kozak sequence, the effect of the truncation performed by Farley was to generate an overlapping tbs-Kozak sequence. Therefore, ‘429 patent disclosure does in fact disclose an overlapping TRAP binding site (tbs) and Kozak sequence.
Further, the GGAGTCATGG Kozak sequence comprised in the +0 spacer construct of the ‘429 patent disclosure comprises the elected RNNATG sequence and is similar to the consensus Kozak sequence of GCCRCCATGG and comprises the critical purine (having a G) at position -3 and G at position +4. Additionally, as further evidence of the suitability of this sequence as a bona fide Kozak sequence, Coppola specifically teaches that the GGAGTCATGG sequence agrees reasonably well with the consensus sequence for translation initiation in eukaryotes (i.e., mice) and is present as the functional, native initiator sequence in the murine N-type calcium channel α1 subunit mRNA [Coppola et al. 1994, FEBS Letters, 338, 1-5, column 3 ¶ 7, Figure 1].
Note that Babitzke was cited for teaching that the B. subtilis ycbK gene, which comprises a natural tbs, comprises the sequence of GAGATG, wherein the ATG is the start codon [Figure 2]. Babitzke was also cited for teaching that, for the trpP gene, extending the tbs into the coding region results in more effective inhibition of ribosome binding (and thus more effective inhibition of translation), that the tbs of the ycbK gene overlaps the translation initiation region and extends into the coding sequence, and that one might predict that the repeats in the coding sequence may increase the effectiveness of bound TRAP in blocking ribosome binding [column 11 ¶ 1-2, Figure 2]. Babitzke was relied on for teaching the effectiveness of TRAP binding to a site overlapping with the initiation codon specifically, wherein the overlapping sequence comprises GAGATG, and was not relied on for teachings related to the prokaryotic Shine-Delgarno ribosomal recognition sequence. Both prokaryotes and eukaryotes rely on the ATG start codon to initiate translation. The teachings of Babitzke provide motivation for including TRAP binding sites which overlap with the ATG start codon as claimed, and further provide an example of an overlapping tbs-ATG sequence for which TRAP binding is effective for repressing translation by blocking ribosome binding.
Kozak sequences comprise ATG start sites, and so by overlapping the tbs with the ATG start site of a eukaryotic gene, the tbs necessarily overlaps the Kozak sequence. Therefore, the ’429 patent disclosure in fact teaches a species comprising an overlapping tbs-Kozak sequence and Babitzke provides motivation for doing so. Therefore, the ‘429 patent claims reciting a vector genome comprising a tbs operably liked to a nucleotide of interest, wherein the tbs is capable of interacting with TRAP such that the NOI translation is repressed, encompass and render obvious the claims of the instant application.
Accordingly, Applicant’s arguments do not overcome the nonstatutory double patenting rejection.
The rejection of claims 1-17, 19-24, 32-38, and 40-41 on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of U.S. Patent No. 12,054,735, hereafter referred to as the ‘735 patent, in view of Babitzke [2004, Current Opinion in Microbiology, 7, 132-139]; is withdrawn over cancelled claims 4 and 19-20; maintained over amended, previously presented, and original claims 1-3, 5-17, 21-24, 32-38, and 40-41; and newly applied to new claims 93-94. Applicant's amendments to the claims and arguments have been fully considered but have not been found persuasive in overcoming the rejection for reasons of record as discussed in detail below.
The limitations newly introduced into independent claim 1 were previously rejected with respect to cancelled claims 4 and 19-20. Applicant has not introduced new limitations which would alter the scope of the claims to overcome the rejection of record.
Applicant argues that the ‘735 patent claims do not recite a nucleic acid sequence comprising a tbs that overlaps a Kozak sequence, nor is there any disclosure that would render such a nucleic acid sequence obvious; and that the disclosure of Babitzke is irrelevant to the present invention because the nucleic acid sequence discussed in Babitzke is a bacterial sequence and does not comprise a Kozak sequence;
However, this is not agreed.
The ‘735 patent is a divisional of the ‘429 patent discussed above, and so shares a disclosure with the ‘429 patent. The application from which the ‘429 patent was issued was published as Farley [US20160333373A1], which serves as the base reference for the rejection under 35 USC 103 above.
The ‘735 patent claims 7-10 recite a viral vector comprising the nucleic acid sequence of claim 1, which comprises a tbs operably linked to a nucleotide of interest (NOI) such that the NOI translation is repressed in a viral vector production cell. Claims 9-10 recite viral vectors which transduce eukaryotic cells. Additionally, claim 11 recites a cell transduced by the viral vector of claim 7. Therefore, the ‘735 patent claims themselves indicate that eukaryotic genes are specifically encompassed species of the nucleotide of interest, and as such, the accompanying control sequences must also be suitable for eukaryotic expression. Note that at the time of filing, Kozak sequences are well-known elements contributing to eukaryotic translation; and the ‘735 patent disclosure provides extensive teachings of Kozak sequences in conjunction with the tbs sites [see, for example, 0028, 0494, 0516, 0521, Figure 13, 14]. Therefore, a nucleic acid comprising both a tbs and a Kozak sequence for translation of a nucleotide of interest is an obvious species for the nucleic acid sequence claimed by the ‘735 patent claims.
Additionally, the ‘735 patent disclosure teaches a nucleic acid sequence comprising a nucleotide of interest and a tryptophan RNA-binding attenuation protein (TRAP) binding site (tbs) [Figure 4, 6]; wherein said nucleic acid sequence also comprises a Kozak sequence, wherein said tbs overlaps the Kozak sequence [e.g., “+0” spacer between the tbs and ATG, wherein the 3’ terminal tbs repeat KAGNN (GAGTC) overlaps the core Kozak RNNATG (SEQ ID NO: 125 of the instant application) at a junction sequence of GAGTCATG] [Figure 6, 13A], such that the Kozak sequence generated by the overlap is GGAGTCATGG, wherein the underlined nucleotides indicate the overlap between the tbs and the core Kozak sequence. Although ‘735 patent disclosure did not teach that the overlapping sequence was designed to be an overlapping tbs-Kozak sequence, the effect of the truncation performed by Farley was to generate an overlapping tbs-Kozak sequence. Therefore, ‘735 patent disclosure does in fact disclose an overlapping TRAP binding site (tbs) and Kozak sequence.
Further, the GGAGTCATGG Kozak sequence comprised in the +0 spacer construct of the ‘735 disclosure comprises the elected RNNATG sequence and is similar to the consensus Kozak sequence of GCCRCCATGG and comprises the critical purine (having a G) at position -3 and G at position +4. Additionally, as further evidence of the suitability of this sequence as a bona fide Kozak sequence, Coppola specifically teaches that the GGAGTCATGG sequence agrees reasonably well with the consensus sequence for translation initiation in eukaryotes (i.e., mice) and is present as the functional, native initiator sequence in the murine N-type calcium channel α1 subunit mRNA [Coppola et al. 1994, FEBS Letters, 338, 1-5, column 3 ¶ 7, Figure 1].
Note that Babitzke was cited for teaching that the B. subtilis ycbK gene, which comprises a natural tbs, comprises the sequence of GAGATG, wherein the ATG is the start codon [Figure 2]. Babitzke was also cited for teaching that, for the trpP gene, extending the tbs into the coding region results in more effective inhibition of ribosome binding (and thus more effective inhibition of translation), that the tbs of the ycbK gene overlaps the translation initiation region and extends into the coding sequence, and that one might predict that the repeats in the coding sequence may increase the effectiveness of bound TRAP in blocking ribosome binding [column 11 ¶ 1-2, Figure 2]. Babitzke was relied on for teaching the effectiveness of TRAP binding to a site overlapping with the initiation codon specifically, wherein the overlapping sequence comprises GAGATG, and was not relied on for teachings related to the prokaryotic Shine-Delgarno ribosomal recognition sequence. Both prokaryotes and eukaryotes rely on the ATG start codon to initiate translation. The teachings of Babitzke provide motivation for including TRAP binding sites which overlap with the ATG start codon as claimed, and further provide an example of an overlapping tbs-ATG sequence for which TRAP binding is effective for repressing translation by blocking ribosome binding.
Kozak sequences comprise ATG start sites, and so by overlapping the tbs with the ATG start site of a eukaryotic gene, the tbs necessarily overlaps the Kozak sequence. Therefore, the ’735 patent disclosure in fact teaches a species comprising an overlapping tbs-Kozak sequence and Babitzke provides motivation for doing so. Therefore, the ‘735 patent claims reciting a nucleic acid comprising a tbs operably liked to a nucleotide of interest, wherein the tbs is capable of interacting with TRAP such that the NOI translation is repressed, encompass and render obvious the claims of the instant application.
Accordingly, Applicant’s arguments do not overcome the nonstatutory double patenting rejection.
Conclusion
No claim is allowed.
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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DR. KATIE L. PENNINGTON
Examiner
Art Unit 1634
/KATIE L PENNINGTON/Examiner, Art Unit 1634
Dr. A.M.S. Wehbé
/ANNE MARIE S WEHBE/Primary Examiner, Art Unit 1634
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