Prim rDETAILED 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 with traverse of claims 1-7, 9-14, 16, 18-21, and 53-66 (Group I) in the reply filed on 04/08/2026 is acknowledged. The traversal is on the ground(s) that Group II (claims 22-52) properly depends from and incorporates the subject matter of claim 1. In response, this is found persuasive, and Groups I and II are hereby rejoined.
Therefore, because a claimed invention previously withdrawn from consideration under 37 CFR 1.142 has been rejoined, the restriction requirement between Group I and Group II as set forth in the Office action mailed on 02/10/2026 is hereby withdrawn. In view of the withdrawal of the restriction requirement as to the rejoined inventions, applicant(s) are advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application.
Once the restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
The Examiner further acknowledges the species election in the reply filed 04/08/2026. Regarding the ribozyme sequence and ligation sequence, the Examiner acknowledges that the sequences work in tandem and therefore necessitate a search of two sequences. Accordingly, both SEQ ID NOs: 1354 and 1355 have been searched for the ribozyme sequence, and both SEQ ID NOs: 1356 and 1357 have been searched for the ligation sequence.
Regarding the elected IRES sequence, the Examiner notes that while Applicant elected SEQ ID NO: 1358, this sequence is not recited at the claims indicated in the requirement for the election of species. The claims recite SEQ ID NOs: 1-1328.
Accordingly, claims 1-7, 9-14, 16, and 18-66 are pending and under consideration.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. The earliest effective filing date to which the instant application is entitled is 01/11/2021.
Information Disclosure Statement
Receipt of information disclosure statements on 07/11/2023, 07/26/2023, and 02/24/2025 is acknowledged. The signed and initialed PTO-1449‘s have been mailed with this action.
Drawings
The drawings filed 07/11/2023 are acceptable.
Claim Objections
Claims 2, 5, 6, 14, 16, 22, 23, 27, 38, 39, 43, 53, 55, and 56 are objected to because of the following informalities:
Claim 6 recites in part “the primer sequence of the first engineered RNA element is different from the primer sequence from the second engineered RNA element” (bolded emphasis added), which is not internally consistent. For purposes of internal consistency, it would be remedial to recite, for example “the primer sequence of the first engineered RNA element is different from the primer sequence of the second engineered RNA element (bolded emphasis added). This is merely an example set forth by the Examiner and is not intended to be limiting.
Claim 14 recites in part “the first RNA promoter and/or the second RNA promoter is a polymerase III promoter” (bolded emphasis added), which does not comport with standard grammatical and/or linguistic conventions. The recitation of and/or necessarily encompasses embodiments wherein both promoters are included and embodiments wherein only one promoter is included. Accordingly, the language must reflect this duality. Therefore, in order to comport with standard grammatical and/or linguistic conventions, it would be remedial to recite, for example, “the first RNA promoter and/or the second RNA promoter is/are a polymerase III promoter” (bolded emphasis added). This is merely an example set forth by the Examiner and is not intended to be limiting.
Similarly, claim 16 recites in part “the first perturbation element and/or the second perturbation element is a sgRNA utilized in a CRISPR knockout screen” (bolded and underlined emphasis added). As noted above, the recitation of and/or necessarily encompasses embodiments wherein both perturbation elements are included and embodiments wherein only one perturbation element is included. Accordingly, the language must reflect this duality. Therefore, in order to comport with standard grammatical and/or linguistic conventions, it would be remedial to recite, for example, “the first perturbation element and/or the second perturbation element is/are…” (bolded emphasis added). This is merely an example set forth by the Examiner and is not intended to be limiting. With regard to the underlined “a,” the Examiner notes that although sgRNA is spelled such that is begins with consonant “s,” said consonant is pronounced with an initial vowel sound, meaning it is more properly preceded by “an” rather than “a.” Accordingly, it would be remedial to recite “an sgRNA utilized in a CRISPR knockout screen” (bolded and underlined emphasis added).
Claims 22 and 38 recite in part “the ribozyme activated RNA-construct(s) is linearized,” which does not comport with standard grammatical and/or linguistic conventions. The recitation of “construct(s)” necessarily encompasses embodiments wherein there is only one construct and also embodiments wherein there are multiple constructs. Accordingly, the language must reflect this duality. Therefore, in order to comport with standard grammatical and/or linguistic conventions, it would be remedial to recite, for example, “the ribozyme activated RNA-construct(s) is/are linearized.” This is merely an example set forth by the Examiner and is not intended to be limiting.
Additionally, claims 22 and 38 both recite in part “wherein the ribozyme activated RNA-construct(s) is[/are] linearized and comprises: a 5’ ribozyme…and a 3’ ribozyme sequence” (bolded emphasis added). For purposes of internal consistency, it would be remedial to recite either a ribozyme or a ribozyme sequence at the 5’ and 3’ positions.
Claims 23 and 39 recite in part “the linear ribozyme activated RNA-construct(s) lacks a polymerase binding region” (bolded emphasis added). As set forth above, the recitation of “construct(s)” necessarily encompasses embodiments wherein there is only one construct and also embodiments wherein there are multiple constructs. Accordingly, the language must reflect this duality. Therefore, in order to comport with standard grammatical and/or linguistic conventions, it would be remedial to recite, for example, “the linear ribozyme activated RNA-construct(s) lack(s) a polymerase binding region” (bolded emphasis added). This is merely an example set forth by the Examiner and is not intended to be limiting.
Claims 27 and 43 both recite in part “wherein the IRES comprises any one of the sequences of SEQ ID NO: 1-1328” (bolded emphasis added), which does not properly invoke a plural recitation of SEQ ID NOs. It would be remedial to recite “wherein the IRES comprises any one of the sequences of SEQ ID NOs: 1-1328” (bolded emphasis added).
Claim 53 recites in part “wherein the aptazyme-based riboswitches when not bound to target ligands destabilize the ribozyme activated RNA-construct(s) leading to decreased expression of the at least polypeptide of interest, and wherein the aptazyme-based riboswitches when bound to target ligands stabilize the ribozyme activated RNA-construct(s) leading to increased expression of the at least polypeptide of interest,” which does not comport with standard grammatical and/or linguistic conventions. It appears that Applicant has unintentionally incorporated a typographical error meant to recite “the at least one polypeptide of interest” (bolded emphasis added). It would be remedial to amend the instant claim language to correct this typographical error, as set forth above.
Claims 55 and 56 both recite in part “the ribozyme activated RNA-construct(s)of claim…” (bolded emphasis added), which omits a space separating “RNA-construct(s)” and “of,” as is required by standard grammatical and/or linguistic conventions. It would be remedial to amend the instant claim language to properly include a space separating “RNA-construct(s)” and “of,” thereby comporting with standard grammatical and/or linguistic conventions.
With further specific regard to claims 2, 5, and 6, each of these claims is drawn to a set of ribozyme activated RNA constructs, wherein said constructs comprise a “primer region.” While the claim term “primer region” is not strictly indefinite, it is not a standard term of the art, and the instant specification is silent as to any particular intended definition thereof. To a person of ordinary skill in the art, a “primer region” may reasonably be interpreted as a region comprising a primer sequence itself or as a region comprising a primer binding site. Based on the examples disclosed in the instant specification, the instantly claimed “primer regions” are utilized for performing RT-PCR (paragraphs [0019], [0023], and [00119]). Thus, for purposes of clarity, it would be remedial to clearly recite whether the instantly claimed “primer region” encompasses a primer binding site, as in the examples disclosed in the instant specification.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 35-37 and 47-49 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 35 and 47, 36 and 48, and 37 and 49 are respectively drawn to a set of ribozyme sequences, a set of ligation sequences, and an IRES sequence, wherein each element is defined by having at least 85% identity to recited SEQ ID NOs. The rejected claims thus comprise a set of sequences that encompass a large number of variable residues, all variations of which must encode functional ribozymes, functional ligation sequence, or functional IRES sequences.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof. The specification describes SEQ ID NOs: 1354 and 1355, which correspond to the instantly claimed ribozyme sequences, SEQ ID NOs: 1356 and 1357, which correspond to the instantly claimed ligation sequences, and SEQ ID NO: 1358, which corresponds to the instantly claimed IRES sequence. The instant specification also discloses that the IRES sequence may correspond to instant SEQ ID NOs: 1-1328 (Figure 19). However, no description is provided of sequences having at least 85% sequence identity to the instantly claimed sequences corresponding to a set of ribozyme sequences, a set of ligation sequences, and an IRES sequence, as set forth above.
Even if one accepts that the examples described in the specification meet the claim limitations of the rejected claims with regard to structure and function, the examples are only representative of the instantly claimed sequences. The results are not necessarily predictive of sequences encompassing up to 15% sequence variation from the instantly claimed sequences, wherein said sequences encode a functional set of ribozyme sequences, a set of ligation sequences, or an IRES sequence, as set forth above. Thus, it is impossible for one to extrapolate from the examples described herein those sequences that would necessarily meet the structural/functional characteristics of the rejected claims.
The prior art does not appear to offset the deficiencies of the instant specification in that it does not describe a set of sequences encompassing up to 15% sequence variation from the instantly claimed sequences, wherein said sequences encode a functional set of ribozyme sequences, a set of ligation sequences, or an IRES sequence, as set forth above. Furthermore, as is known to those of ordinary skill in the art, the variation encompassed by at least 85% sequence identity necessarily impacts a large number of residues, wherein said residues may be synonymously or non-synonymously mutated (reviewed in Hunt et al., 2014). Non-synonymous mutations are typically tolerated at a lower rate than their synonymous counterparts, as non-synonymous mutations alter protein sequence (reviewed in Hunt et al., 2014). The instant claim set and the instant specification are both silent as to whether the instantly claimed 85% sequence identity is restricted to synonymous mutations and therefore it must be considered that the instantly claimed 85% sequence identity is not restricted to synonymous mutations and therefore encompasses both synonymous and non-synonymous mutations.
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 35-37 and 47-49.
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 2, 18, 21, 34, 35, 47, 57, and 60 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 and 18 both recite in part “cleavage of the first and second engineered RNA elements by the first and second self-cleaving ribozymes, respectively, provides for a hybridization construct that comprises a region of dsRNA from the commentary sequences being hybridized together” (bolded emphasis added). However, not only do the instant claims not previously recite “commentary sequences,” but furthermore this term is not a term of the art. It appears that Applicant inadvertently incorporated a typographical error meant to recite “complementary,” thereby rendering the scope of the protection sought indefinite. It would be remedial to amend the instant claim such that it properly recites “the complementary sequences,” as recited earlier in the instant claims themselves. For purposes of examination and in the interest of compact prosecution, the Examiner has interpreted the instantly claimed “commentary sequences” to recite “complementary sequences.”
Claim 21 recites the limitation "the cystic fibrosis transmembrane conductance regulator protein, and the dystrophin protein" in lines 3-4. There is insufficient antecedent basis for this limitation in the claim. It would be remedial to amend the instant claim language such that there is sufficient antecedent basis for every claim term.
Claims 35 and 47 recite “the 5’ and 3’ ribozyme sequences,” which lacks sufficient antecedent basis, as claims 35 and 47 (which depend from claims 22 and 38 respectively) recite “a 5’ ribozyme”-not a 5’ ribozyme sequence (see section Claim Objections). It would be remedial to amend the instant claim set such that there is sufficient antecedent basis for each and every claim term.
Claims 34 and 60 contain the trademark/trade name TALEN. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a transcription activator-like effector nuclease and, accordingly, the identification/description is indefinite.
Claim 57 recites “the ribozyme activated RNA-construct(s) of claim 56, wherein the biological response modifier or an immunopotentiating cytokine,” which is not a proper sentence, rendering the claim itself indefinite. For purposes of examination, the Examiner has interpreted instant claim 57 to recite “the ribozyme activated RNA-construct(s) of claim 56, wherein the biological response modifier is an immunopotentiating cytokine,” as is recited at instant claim 31. It would be remedial to amend the instant claim language such that it recites a proper, definite sentence.
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.
Claims 1, 2, and 9-12 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by WO 2018/237372 A1 (hereinafter Cornell; as cited in the IDS filed 07/11/2023; of record).
With regard to claim 1, which recites “a ribozyme activated RNA-construct(s) comprising:
one or more ribozymes; and
one or more RNA coding sequences for at least one polypeptide of interest;
wherein the transcription of the one or more RNA coding sequences for at least one polypeptide of interest is activated by or dependent upon the activity of the one or more ribozymes,” as previously set forth, Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme (abstract; paragraph [0027]), said constructs being useful for enhancing expression of the effector molecule (paragraph [0044]). The effector molecule of the constructs of Cornell is disclosed to be an RNA molecule encoding a therapeutic protein or peptide sequence, wherein the RNA molecule further comprises an IRES to facilitate translation of the same (paragraphs [0060], [0062], and [0098]). The ribozymes of the construct disclosed by Cornell autocatalytically process the transcript, thereby enhancing expression of the effector molecules taught therein (i.e. peptides, as set forth above) (paragraph [0016]). Thus, Cornell discloses each and every limitation of instant claim 1.
With regard to claim 2, which recites “the ribozyme activated RNA-construct(s) of claim 1, further comprising:
a first engineered RNA element comprising an optional primer region, an optional barcode region, an RNA coding sequence for a polypeptide of interest and a complementary sequence to a sequence of a second engineered RNA element, and a first self-cleaving ribozyme;
a second engineered RNA element comprising an optional primer region, an optional barcode region, an RNA coding sequence for a polypeptide of interest and a complementary sequence to a sequence of the first engineered RNA element, and a second self-cleaving ribozyme;
wherein cleavage of the first and second engineered RNA elements by the first and second self-cleaving ribozymes, respectively, provides for a hybridization construct that comprises a region of dsRNA from the com[plementary] sequences being hybridized together,
wherein the hybridization construct can be further ligated by an RNA ligase to form an RNA-fusion construct, and
wherein expression from the RNA-fusion construct produces the at least one polypeptide of interest,” as set forth above, Cornell anticipates the ribozyme activated RNA construct(s) of claim 1. Furthermore, the Examiner notes that the primer region and barcode region are not required by the instant claim. Accordingly, it is considered that Cornell anticipates each and every limitation of claim 2, as Cornell discloses ribozyme activated RNA-constructs wherein said constructs comprise a first and second engineered RNA element, said elements comprising an RNA coding sequence for a polypeptide of interest (abstract; paragraph [0045]), a complementary sequence to each element (Figure 4A), and a self-cleaving ribozyme (paragraph [0020]). As depicted in Figure 4A, ribozyme cleavage of the first and second engineered RNA elements provide for a hybridization construct that is further ligated by an RNA ligase to form an RNA-fusion construct, as instantly claimed. Thus, it is considered that Cornell anticipates each and every limitation of instant claim 2.
With regard to claim 9, which recites “the first and second ribozymes [of the ribozyme activated RNA-construct(s) of claim 2] are Twister ribozymes, Cornell further discloses that the ribozymes utilized therein may be Twister ribozymes (paragraphs [0037] and [0038]). Thus, Cornell anticipates each and every limitation of instant claim 9.
With regard to claim 10, which recites “the first ribozyme [of the ribozyme activated RNA-construct(s) of claim 9] is a P3 Twister ribozyme,” Cornell further discloses that the first ribozyme may be a Twister ribozyme, specifically a P3 Twister ribozyme (paragraph [0037]). Thus, Cornell anticipates each and every limitation of instant claim 10.
With regard to claim 11, which recites “the second ribozyme [of the ribozyme activated RNA-construct(s) of claim 10] is a P1 Twister ribozyme,” Cornell further discloses that the second ribozyme may be a Twister ribozyme, specifically a P1 Twister ribozyme (paragraph [0038]). Thus, Cornell anticipates each and every limitation of instant claim 11.
With regard to claim 12, which recites “the RNA ligase [of the ribozyme activated RNA-construct(s) of claim 2] is RtcB,” Cornell further discloses that the first and second ligation sequences taught therein are substrates for an RNA ligase such as RtcB (paragraph [0043]). Thus, Cornell anticipates each and every limitation of instant claim 12.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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 3-7 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2018/237372 A1 (hereinafter Cornell; as cited in the IDS filed 07/11/2023; of record) as applied to claim 2 above, and further in view of WO 2020/223539 A1 (hereinafter Blainey) and Apte and Daniel, 2009 (hereinafter Apte).
The disclosure of Cornell is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the barcode limitations of instant claims 3 and 4, nor does it teach the primer limitations of instant claims 5 and 7.
With regard to claim 3, which recites “the first engineered RNA element comprises a barcode sequence or a unique molecular identity (UMI) sequence and/or wherein the second engineered RNA element comprises a barcode sequence or a UMI sequence,” as set forth above, Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme (abstract; paragraph [0027]), said constructs being useful for enhancing expression of the effector molecule (paragraph [0044]). However, Cornell does not disclose that said RNA molecules include a barcode sequence, as instantly claimed. This deficiency is cured by Blainey. Blainey discloses methods and compositions for barcoding nucleic acid libraries and cell populations, said compositions comprising a barcoding construct comprising a trans-splicing element such as a ribozyme, a barcode sequence, and a sequence encoding a perturbation element operably linked to a promoter (abstract; paragraph [0007]). These compositions facilitate the generation of a barcoded nucleic acid library (paragraph [0009]). Thus, it is considered that Blainey discloses each and every additional limitation of instant claim 3.
With regard to claim 4, which recites “the barcode sequence or the UMI sequence of the first engineered element [of the ribozyme activated RNA-construct(s) of claim 3] has a different sequence than the barcode region or the UMI sequence from the second engineered RNA element,” as set forth above, Blainey discloses methods and compositions for barcoding nucleic acid libraries and cell populations (abstract). Blainey further discloses that in some embodiments, each member of the barcoded library generated via the methods taught therein comprises a common barcode sequence (paragraph [0010]) such that when there a plurality of libraries is generated, each library comprises a different barcode to identify the library (paragraph [0058]), meaning Blainey discloses that different editing constructs must comprise different barcode sequences, as instantly claimed. Thus, it is considered that Blainey discloses each and every additional limitation of instant claim 4.
With regard to claim 5, which recites “the first engineered RNA element [of the ribozyme activated RNA-construct(s) of claim 2] comprises a primer sequence, and/or wherein the second engineered RNA element comprises a primer sequence,” as set forth above, Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme (abstract; paragraph [0027]), said constructs being useful for enhancing expression of the effector molecule (paragraph [0044]). However, Cornell does not disclose that said RNA molecules include a primer sequence, as instantly claimed. This deficiency is cured by Blainey. Blainey discloses methods and compositions for barcoding nucleic acid libraries and cell populations, said compositions comprising a barcoding construct comprising a trans-splicing element such as a ribozyme, a barcode sequence, and a sequence encoding a perturbation element operably linked to a promoter (abstract; paragraph [0007]). Blainey further discloses that the constructs taught therein may comprise a reverse transcription primer binding site to regulate or control reverse transcription and further that said constructs may comprise one or more sequencing primer binding sites (paragraphs [0007] and [0081]). As set forth above, the instantly claimed “primer sequence[s]” are considered to refer to primer binding sequences/sites, as supported by the instant specification. Thus, it is considered that Blainey discloses each and every additional limitation of instant claim 5.
With regard to claim 6, which recites “the primer sequence of the first engineered RNA element [of the ribozyme activated RNA-construct(s) of claim 5] is different from the primer sequence from the second engineered RNA element,” as set forth above, Blainey discloses that the ribozyme-containing barcoding constructs taught therein may comprise a reverse transcription primer binding site to regulate or control reverse transcription and further that said constructs may comprise one or more sequencing primer binding sites (paragraphs [0007] and [0081]). While Blainey does not explicitly disclose that each primer binding site is different, one of ordinary skill in the art would be aware that analysis of individual sequences requires individual primer design, as primers are intended to amplify a specific nucleic acid segment without non-specific byproducts (reviewed in Apte: see Introduction). Apte further teaches that multiplex PCR uses one template and several sets of primers for the simultaneous amplification of multiple target sequences, thereby allowing more efficient use of each nucleic acid sample (reviewed in Apte: see MULTIPLEX PCR PRIMER DESIGN). Thus, it is considered that Blainey and Apte collectively disclose each and every additional limitation of instant claim 6.
With regard to claim 7, which recites “the first and second complementary sequences [of the ribozyme activated RNA-construct(s) of claim 2] are from 30 to 60 bp in length,” as set forth above, Figure 4A of Cornell depicts the annealing of complementary sequences from the first and second elements of the construct taught therein. While Cornell is silent as to the length of this complementarity, varying the length of constructs for purposes of optimizing their function(s) is routinely practiced in the field. Per MPEP § 2144.05(II)(A), it is not inventive to optimize prior art conditions through routine experimentation. Accordingly, while Cornell does not disclose the length of complementarity, one of ordinary skill in the art would reasonably be expected to practice routine experimentation to optimize said length, meaning optimization of the length of complementarity cannot be considered to be inventive.
Given that Cornell discloses RNA molecules useful for enhancing effector molecule expression comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme, that Blainey discloses ribozyme-based barcoding constructs comprising identifying barcodes to generate barcoded library as well as primer binding sites for controlling reverse transcription or sequencing thereof, and that Apte discloses that different sequence targets require different primer design, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the construct of Cornell such that it comprises identifying barcode(s) and primer binding sites as disclosed in Blainey to predictably generate an RNA construct capable of generating a barcoded library and capable of being sequenced and/or reverse transcribed. One would have been motivated to make such a modification in order to receive the expected benefit of generating a construct capable of generating a barcoded library and capable of being sequenced and/or reverse transcribed.
Furthermore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to practice routine experimentation to optimize the length of the first and second complementary sequences of the RNA constructs taught therein to predictably generate a ribozyme-containing RNA construct most effective at producing the effector molecule taught therein. One would have been motivated to make such a modification in order to receive the expected benefit of generating a construct effective at producing the effector molecule of said construct.
Claims 13, 14, and 16 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2018/237372 A1 (hereinafter Cornell; as cited in the IDS filed 07/11/2023; of record) as applied to claim 2 above, and further in view of WO 2020/223539 A1 (hereinafter Blainey).
The disclosure of Cornell is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the perturbation element(s) of instant claims 13 and 16. Cornell does teach the promoter of instant claim 14, as set forth below.
With regard to claim 13, which recites “a vector or plasmid comprises the first engineered element [of the ribozyme activated RNA-construct(s) of claim 2], wherein the first engineered element is located downstream of a first RNA promoter and a first perturbation element; and/or wherein a vector or plasmid comprises the second engineered element, wherein the second engineered element is located downstream of a second RNA promoter and a second perturbation element,” as set forth above, Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme (abstract; paragraph [0027]), said constructs being useful for enhancing expression of the effector molecule (paragraph [0044]). Cornell further discloses that said RNA constructs may be packaged within a plasmid (paragraph [0089]), as instantly claimed. However, Cornell is silent as to the instantly claimed perturbation element. Per the instant specification, a perturbation element may be an sgRNA (paragraph [0012]). In view of this definition, the disclosure of Blainey is considered to teach the instantly claimed perturbation element. As set forth above, Blainey discloses methods and compositions for barcoding nucleic acid libraries and cell populations, said compositions comprising a barcoding construct comprising a trans-splicing element such as a ribozyme, a barcode sequence, and a sequence encoding a perturbation element operably linked to a promoter (abstract; paragraph [0007]). Said perturbation elements may be guide RNAs utilized for a Cas knockout screen (paragraph [0092]). Thus, it is considered that Blainey discloses each and every additional limitation of instant claim 13.
With regard to claim 14, which recites “the first RNA promoter and/or the second RNA promoter [of the ribozyme activated RNA-construct(s) of claim 13] is a polymerase III promoter,” Cornell discloses that expression of the constructs taught therein may be driven by an RNA polymerase III promoter (paragraph [0068]). Thus, it is considered that Cornell discloses each and every additional limitation of instant claim 13.
With regard to claim 16, which recites “the first perturbation element and/or the second perturbation element is a[n] sgRNA utilized in a CRISPR knockout screen,” as set forth above, Blainey discloses compositions for barcoding nucleic acid libraries and cell populations, wherein said compositions comprise a ribozyme and a sequence encoding a perturbation element such as a guide RNA utilized for a Cas knockout screen (abstract; paragraphs [0007] and [0092]). Thus, it is considered that Blainey discloses each and every additional limitation of instant claim 16.
Given that Cornell discloses RNA molecules useful for enhancing effector molecule expression, and that Blainey discloses constructs comprising ribozymes encoding a perturbation element such as a guide RNA for use in a CRISPR knockout screen, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the molecules disclosed in Cornell to further encode a perturbation element such as a guide RNA for use in a CRISPR knockout screen (as disclosed in Blainey) in addition to the effector molecule disclosed in Cornell to predictably generate an RNA construct capable of expressing both an effector molecule and a perturbation element, wherein said effector molecule and perturbation element are oriented such that both are efficiently expressed based on routine experimentation/optimization (see MPEP § 2144.05(II)). One would have been motivated to make such a modification in order to receive the expected benefit of generating an RNA construct capable of expressing both an effector molecule and a perturbation element for use in a CRISPR knockout screen.
Claims 18-21 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2018/237372 A1 (hereinafter Cornell; as cited in the IDS filed 07/11/2023; of record) as applied to claim 2 above, and further in view of Mustafina et al., 2019 (hereinafter Mustafina), WO 2021/158964 A1 (effectively filed 02/07/2020; hereinafter Anderson; as cited in the IDS filed 02/24/2025), Parra et al., 2011 (hereinafter Parra) and Gellekink et al., 2006 (hereinafter Gellekink).
The disclosure of Cornell is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the structural limitations of instant claim 18, the intron of instant claim 19, or the coding sequences of instant claim 20 and 21.
With regard to claim 18, which recites “the ribozyme activated RNA-construct(s) of claim 1, comprising:
a first engineered RNA element comprising an RNA coding sequence for a polypeptide of interest, an intron sequence, a complementary sequence to a sequence of a second engineered RNA element and a 3’ aptamer, and a first self-cleaving ribozyme, and wherein the 3’ aptamer interacts with a first self-cleaving ribozyme to stabilize it;
a second engineered RNA element comprising an RNA coding sequence for a polypeptide of interest, an intron sequence, a complementary sequence to a sequence of the first engineered RNA element, and a 3’ aptamer, wherein the second engineered RNA template is tethered to a second self-cleaving ribozyme, and wherein the 3’ aptamer interacts with a second self-cleaving ribozyme to stabilize it;
wherein cleavage of the first and second engineered RNA elements by the first and second self-cleaving ribozymes, respectively, provides for a hybridization construct that comprises a region of dsRNA from the [complementary] sequences being hybridized together, and
wherein the hybridization construct can be further ligated by an RNA ligase and the intron sequences removed by a spliceosome to form an RNA-fusion construct,
wherein expression from the RNA-fusion construct produces the at least one polypeptide of interest,” as set forth above, Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme (abstract; paragraph [0027]), said constructs being useful for enhancing expression of the effector molecule (paragraph [0044]) such as an aptamer (paragraph [0016]. Cornell further discloses that said constructs comprise a first and second engineered RNA element, wherein the first and second engineered RNA elements have complementarity to each other (Figure 4A). Additionally, Cornell discloses that the RNA construct depicted in Figure 4A relates to a self-processed vector wherein self-cleaving ribozymes flank the ends of the circularized insert that contains an RNA aptamer sequence (paragraph [0020]). However, Cornell is silent as to the interaction of the aptamer(s) taught therein with said self-cleaving ribozyme(s). This deficiency is cured by Mustafina, which discloses the development of ON riboswitches comprising an aptamer fused to a ribozyme (i.e. an aptazyme) in tandem such that the aptamer changes conformation upon binding of a ligand, thereby disrupting the ribozyme fold and facilitating protein translation (Figure 1). In the absence of ligand binding, the aptamer assumes a conformation that maintains the ribozyme fold, thereby disrupting protein translation (Figure 1). Thus, Mustafina discloses aptamers that interact with the self-cleaving ribozyme to stabilize it and govern protein production, as is instantly claimed.
Additionally, Anderson discloses that protein expression from the ribozyme constructs taught therein may be enhanced by splicing of splice donor and splice acceptor sites (i.e. an intron) by spliceosome machinery (page 33, lines 2-4), as is instantly claimed. While Anderson does not disclose the inclusion of a second engineered RNA element comprising an intron, as set forth above Cornell discloses a ribozyme-based construct comprising two engineered RNA elements. One of ordinary skill in the art would have thus been motivated to modify the elements of Cornell per the teachings of Anderson in order to predictably produce a ribozyme-based construct capable of producing an effector molecule at enhanced levels, as taught in Anderson and set forth in greater detail below. Thus, it is considered that Cornell, Mustafina, and Anderson collectively disclose each and every limitation of instant claim 18.
With regard to claim 19, which recites “the intron sequence [of the ribozyme activated RNA-construct(s) of claim 18] is derived from dihydrofolate reductase,” as set forth above, Anderson discloses that protein expression from the constructs taught therein may be enhanced by splicing of splice donor and splice acceptor sites (i.e. an intron) by spliceosome machinery (page 33, lines 2-4). This is consistent with accepted principles in the field, namely intron-mediated enhancement, which states that introns increase the expression of the gene (even a heterologous gene) that they are contained in (Parra: abstract). Additionally, it is known in the field that enhancing introns tend to be longer (Parra: Enhancing introns tend to be longer). As depicted in Figure 1 of Gellekink, the introns of DHFR are long, ranging from 347 bp to 11379 bp in humans. Thus, one of ordinary skill in the art would reasonably expect that the longer introns of DHFR would predictably enhance the expression of the desired gene within the construct. Thus, it is considered that Parra and Gellekink collectively disclose each and every additional limitation of instant claim 19.
With regard to claim 20, which recites “the RNA coding sequences for a polypeptide of interest [of the ribozyme activated RNA-construct(s) of claim 18] are adjacent to each of the intron sequences,” as set forth above, Anderson discloses ribozyme-based constructs for the production of proteins or fusion proteins of interest (abstract), wherein said constructs comprise a sequence encoding a protein of interest adjacent to an intron (page 5, lines 3-7). As set forth above, while Anderson does not disclose the inclusion of a second engineered RNA element comprising an intron, as set forth above Cornell discloses a ribozyme-based construct comprising two engineered RNA elements. One of ordinary skill in the art would have thus been motivated to modify the elements of Cornell per the teachings of Anderson (i.e. with the encoding sequence adjacent to an intron) in order to predictably produce a ribozyme-based construct capable of producing an effector molecule at enhanced levels, as taught in Anderson and set forth in greater detail below. Thus, it is considered that Anderson and Cornell collectively disclose each and every additional limitation of instant claim 20.
With regard to claim 21, which recites “the RNA coding sequences for a polypeptide of interest [of the ribozyme activated RNA-construct(s) of claim 18] encode a polypeptide/protein selected from insulin, clotting factor IX, the cystic fibrosis transmembrane conductance regulator protein, and the dystrophin protein,” as set forth above, Anderson discloses ribozyme-based constructs for the production of proteins or fusion proteins of interest (abstract), wherein said constructs comprise a sequence encoding a protein of interest adjacent to an intron (page 5, lines 3-7). Anderson further discloses that the protein of interest encoded therein may be therapeutic protein cargo, such as dystrophin or Cystic fibrosis transmembrane conductance regulator (page 5, lines 8-9; page 29, lines 30-31). Thus, it is considered that Anderson discloses each and every additional limitation of instant claim 21.
Given that Cornell discloses RNA molecules useful for enhancing effector molecule expression, that Mustafina discloses aptazyme-based constructs wherein an aptamer’s conformation based upon ligand binding impacts the linked ribozyme’s structure and activity, thereby controlling protein production, that Anderson discloses ribozyme-based constructs for the production of therapeutic proteins of interest (i.e. dystrophin or Cystic fibrosis transmembrane conductance regulator), said constructs comprising a sequence encoding a protein of interest adjacent to an intron, and that Parra discloses that the inclusion of longer introns (such as those of human DHFR per Gellekink) enhances protein production, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the constructs of Cornell to encode therapeutic proteins such as dystrophin (as disclosed in Anderson), wherein said constructs further comprise an aptazyme (per Mustafina) and an intron (per Anderson, Parra, and Gellekink) to predictably generate a construct capable of enhancing the expression of the protein encoded therein in a controllable manner. One would have been motivated to make such a modification in order to receive the expected benefit of enhancing the expression of the protein encoded therein in a controllable manner.
Claims 22-37 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2018/237372 A1 (hereinafter Cornell; as cited in the IDS filed 07/11/2023; of record) as applied to claim 1 above, and further in view of WO 2021/158964 A1 (effectively filed 02/07/2020; hereinafter Anderson; as cited in the IDS filed 02/24/2025), US 2022/0251578 A1 (effectively filed 06/25/2020; hereinafter Chang), Luke et al., 2009 (hereinafter Luke), Calabrese et al., 2020 (hereinafter Calabrese), US 2023/0174977 A1 (effectively filed 05/26/2020; hereinafter Packard), and US 2013/0244231 A1 (hereinafter Takahashi).
The disclosure of Cornell is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the pharmaceutical composition limitations of instant claims 22-37.
With regard to claim 22, which recites “a pharmaceutical composition comprising the ribozyme activated RNA-construct(s) of claim 1, wherein the ribozyme activated RNA-construct(s) is linearized and comprises:
a 5’ ribozyme;
a 5’ ligation sequence;
an internal ribosome entry site (IRES) sequence;
an RNA coding sequence for at least one polypeptide of interest;
a 3’ ligation sequence; and
a 3’ ribozyme sequence, and
a pharmaceutically acceptable carrier,” as set forth above, Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme (abstract; paragraph [0027]), said constructs being useful for enhancing expression of the effector molecule (paragraph [0044]). The effector molecule of the constructs of Cornell is disclosed to be an RNA molecule encoding a therapeutic protein or peptide sequence, wherein the RNA molecule further comprises an IRES to facilitate translation of the same (paragraphs [0060], [0062], and [0098]). Additionally, as set forth above, Anderson discloses therapeutic protein expression from ribozyme constructs taught therein (abstract). Anderson further discloses that the constructs taught therein may be delivered in linear form (page 21, lines 6-8). Finally, Anderson discloses pharmaceutical compositions comprising the ribozyme constructs taught therein and one or more pharmaceutically acceptable carriers (page 49, line 27-page 50, line 6). Thus, it is considered that Cornell and Anderson collectively disclose each and every limitation of instant claim 22.
With regard to claim 23, which recites “the linear ribozyme activated RNA-construct(s) [of the pharmaceutical composition of claim 22] lacks a polymerase binding region,” Cornell further discloses embodiments of the constructs taught therein wherein said constructs comprise a polymerase binding region (i.e. a promoter sequence) (paragraph [0012]). Cornell also discloses embodiments that do not comprise a polymerase binding region (i.e. a promoter sequence) (paragraph [0011]). The disclosure of separate embodiments with separate components establishes that in embodiments of the constructs taught in Cornell, said constructs do not comprise a promoter sequence, as instantly claimed. Thus, it is considered that Cornell discloses each and every additional limitation of instant claim 23.
With regard to claim 24, which recites “the 5’ and 3’ ribozymes [of the pharmaceutical composition of claim 22] are selected from the group consisting of a twister ribozyme, a hammerhead ribozyme, a hatchet ribozyme, a hepatitis delta virus ribozyme, a ligase ribozyme, a pistol ribozyme, a twister sister ribozyme, a Vg1 ribozyme, a VS ribozyme, and derivatives of any of the foregoing,” as set forth above, the constructs of Cornell are disclosed to comprise two ribozymes (abstract; paragraph [0027]). Cornell further discloses that suitable self-cleaving ribozymes for use in the constructs taught therein include hepatitis delta virus ribozymes, twister ribozymes, twister sister ribozymes, hatchet ribozymes, pistol ribozymes, and derivative thereof (paragraph [0032]). Thus, it is considered that Cornell discloses each and every additional limitation of instant claim 24.
With regard to claims 25 and 26, which respectively recite “the 5’ and 3’ ligation sequences [of the pharmaceutical composition of claim 22] are substrates of naturally occurring ligases in situ,” wherein “the naturally occurring ligase is RtcB,” as set forth above, the constructs of Cornell are disclosed to comprise two ligation sequences (abstract; paragraph [0027]). Cornell further discloses that these ligation sequences are substrates for an RNA ligase such as RtcB (paragraph [0043]), which is a suitable naturally occurring ligase per paragraphs [0007] and [0008] of the instant specification (as also recited at instant claim 26). Thus, it is considered that Cornell discloses each and every additional limitation of instant claims 25 and 26.
With regard to claim 27, which recites “the IRES [of the pharmaceutical composition of claim 22] comprises any one of the sequences of SEQ ID NO[s]: 1-1328,” as set forth above, the constructs of Cornell are disclosed to comprise an IRES to facilitate translation of the therapeutic protein or peptide sequence contained therein (abstract; paragraphs [0060], [0062], and [0098]). However, Cornell does not disclose the instantly claimed IRES sequences. This deficiency is cured by Chang, which discloses genetic elements driving the translation of circular RNAs (abstract). Chang discloses a number of IRES sequences, including SEQ ID NOs: 1-228 and SEQ ID NOs: 229-17201 (paragraph [0009]). While Chang discloses a large number of IRES sequences, a query of the first 25 claimed IRES sequences matches to 8 of the IRES sequences disclosed in Chang. As shown in the Appendix, instant SEQ ID NOs: 2, 3, 7, 10, 15, 19, 23, and 24 comprise 100% identity to SEQ ID NOs: 525, 1426, 1092, 978, 1054, 3110, 1641, and 2936 of Chang. Given that the instant claim set is drawn to a large number of IRES sequences, wherein a small subset of the claimed IRES sequences yields a high proportion of sequence matches when queried against sequence databases, it is overall considered that the IRES sequences of Chang read on the instantly claimed IRES sequences of instant claim 27.
With regard to claims 28 and 29, which respectively recite “the at least one polypeptide of interest [of the pharmaceutical composition of claim 22] comprises two or more polypeptides of interest separated by a self-cleaving peptide,” “wherein the self-cleaving peptide comprises a 2A- or 2A-like peptide,” as set forth above, the constructs of Cornell are disclosed to comprise a sequence encoding a therapeutic protein or peptide sequence (abstract; paragraphs [0027], [0060], [0062], and [0098]). However, Cornell does not disclose embodiments wherein multiple polypeptides of interest are expressed. This deficiency is cured by Luke, which discloses that the 2A region of FMDV encodes a short sequence that mediates self-processing by a novel translational effect, thereby facilitating the production of discrete translational products from a single open reading frame (abstract). Thus, Luke discloses that a single open reading frame (such as that disclosed in Cornell) can produce multiple translational products. Thus, it is considered that Luke discloses each and every additional limitation of instant claims 28 and 29.
With regard to claims 30-32, which respectively recite “the at least one polypeptide of interest [of the pharmaceutical composition of claim 22] is selected from the group consisting of a prodrug activating enzyme, a biological response modifier, a receptor ligand, an immunoglobulin derived binding polypeptide, a non-immunoglobulin binding polypeptide, an antigenic polypeptide, a genome editing enzyme, and any combination thereof wherein multiple polypeptides are separated by a 2A or 2A-like peptide,” “wherein the biological response modifier is an immunopotentiating cytokine,” “selected from the group consisting of interleukins 1 through 38, interferon, tumor necrosis factor (TNF), and a granulocyte-macrophage-colony stimulating factor (GM-CSF),” as set forth above, the constructs of Cornell are disclosed to comprise a sequence encoding a therapeutic protein or peptide sequence (abstract; paragraphs [0027], [0060], [0062], and [0098]). While Cornell does not explicitly disclose that the therapeutic proteins or peptides taught therein are specifically a biological response modifier such as an immunopotentiating cytokine, this deficiency is cured by Calabrese. Calabrese discloses that administration of interferon to COVID-19 patients may contribute to the management of COVID-19 (abstract; CONCLUSION). Therefore, it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the instant invention to encode therapeutic interferon in the constructs disclosed in Cornell for purposes of treating COVID-19 patients in need thereof (as set forth in greater detail below). Thus, it is considered that Calabrese discloses each and every additional limitation of instant claims 30-32. The Examiner notes that the instant claim language encompasses one or more polypeptides of interest and does not require multiple polypeptides of interest, meaning the recited limitations regarding 2A- or 2A-like peptides are not required by the instant claim language.
With regard to claim 33, which recites “the 2A- or 2A-like peptide [of the pharmaceutical composition of claim 29] further comprises a GSG linker moiety,” as set forth above, Luke discloses that a single open reading frame (such as that disclosed in Cornell) can produce multiple translational products. Luke further discloses that cleavage efficiency of 2A-linked constructs is improved by placing a GSG linker between the N-terminal protein and the 2A-peptide (page 243, paragraph 2). Thus, it is considered that Luke discloses each and every additional limitation of instant claim 33.
With regard to claim 34, which recites “the genome editing enzyme [of the pharmaceutical composition of claim 30] is selected from the group consisting of a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), an engineered meganuclease and an RNA-guided DNA endonuclease (Cas) polypeptide,” as set forth above, the constructs of Cornell are disclosed to comprise a sequence encoding a therapeutic protein or peptide sequence (abstract; paragraphs [0027], [0060], [0062], and [0098]). Cornell does not disclose that the constructs taught therein may encode a genome editing enzyme. This deficiency is cured by Anderson. As set forth above, Anderson discloses therapeutic protein expression from ribozyme constructs taught therein (abstract). One such therapeutic protein is disclosed to be Cas9 (page 5, lines 8-9), which is a Cas polypeptide as instantly claimed. Thus, it is considered that Anderson discloses each and every additional limitation of instant claim 34.
With regard to claim 35, which recites “the 5’ and 3’ ribozyme sequences [of the pharmaceutical composition of claim 22] are independently selected from a sequence that is at least 85-100% identical to…” SEQ ID NO: 1354 or SEQ ID NO: 1355, as set forth above, the constructs of Cornell are disclosed to comprise two ribozymes (abstract; paragraph [0027]). However, Cornell is silent as to the sequences of said ribozymes. This deficiency is cured by Packard. Per the instant claim language, the 5’ and 3’ ribozymes are independently selected from SEQ ID NOs: 1354 or 1355; accordingly, both the 5’ and 3’ ribozymes may comprise the same sequence. Packard discloses SEQ ID NO: 14, which is a ribozyme sequence that is 100% identical to instant SEQ ID NO: 1354 (see Appendix). Thus, it is considered that Packard discloses each and every additional limitation of instant claim 35.
With regard to claim 36, which recites “the 5’ and 3’ ligation sequences [of the pharmaceutical composition of claim 22] are independently selected from a sequence that is at least 85-100% identical to…” SEQ ID NO: 1356 or SEQ ID NO: 1357, as set forth above, the constructs of Cornell are disclosed to comprise two ligation sequences (abstract; paragraph [0027]). However, Cornell is silent as to the sequences of said ligation sequences. This deficiency is cured by Packard. Per the instant claim language, the 5’ and 3’ ligation sequences are independently selected from SEQ ID NOs: 1356 or 1355; accordingly, both the 5’ and 3’ ligation sequences may comprise the same sequence. Packard discloses SEQ ID NO: 10, which is a ligation sequence that is 100% identical to instant SEQ ID NO: 1356 (see Appendix). Thus, it is considered that Packard discloses each and every additional limitation of instant claim 36.
With regard to claim 37, which recites “the IRES sequence [of the pharmaceutical composition of claim 22] is at least 85-100% identical to…” SEQ ID NO: 1358, as set forth above, the constructs of Cornell are disclosed to comprise an IRES to facilitate translation of the therapeutic protein or peptide sequence contained therein (abstract; paragraphs [0060], [0062], and [0098]). However, Cornell does not disclose the instantly claimed IRES sequence. This deficiency is cured by Takahashi. Takahashi discloses SEQ ID NO: 9, which comprises an IRES sequence that is 96.3% identical to instant SEQ ID NO: 1358 (see Appendix). Thus, it is considered that Takahashi discloses each and every additional limitation of instant claim 37.
Therefore, given that:
Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, a second ribozyme, and an IRES, said constructs being useful for enhancing expression of the effector molecule, wherein said ribozyme may be a Twister ribozyme, a twister sister ribozyme, a pistol ribozyme, or another self-cleaving ribozyme and wherein said ligation sequences are substrates for naturally-occurring RtcB;
Anderson discloses therapeutic ribozyme constructs (that may be delivered in linear form) and pharmaceutical compositions comprising the same, wherein said therapeutic ribozyme constructs may encode a Cas polypeptide;
Chang discloses numerous IRES sequences corresponding to those of the instant invention;
Luke discloses that the 2A region of FMDV encodes a short sequence that mediates self-processing by a novel translational effect, thereby facilitating the production of discrete translational products from a single open reading frame, wherein inclusion of a GSG linker improves the cleavage efficiency thereof;
Calabrese discloses that administration of interferon can be beneficial in the treatment of COVID-19;
Packard discloses useful ribozyme sequences and ligation sequences corresponding to those of the instant invention; and
Takahashi discloses an IRES sequence comprising 96.3% identity to instant SEQ ID NO: 1358,
it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the constructs of Cornell to encode multiple products from a single open reading frame (as disclosed in Luke), including interferon to treat disease (as disclosed in Calabrese) and/or Cas9 to provide gene editing machinery (as disclosed in Anderson), utilizing the sequences disclosed in Chang, Packard, and Takahashi to predictably drive expression of multiple protein products from the ribozyme constructs taught therein. One would have been motivated to make such a modification in order to receive the expected benefit of driving expression of multiple protein products from the ribozyme constructs taught therein.
Claims 38-52 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2018/237372 A1 (hereinafter Cornell; as cited in the IDS filed 07/11/2023; of record) as applied to claim 1 above, and further in view of WO 2021/158964 A1 (effectively filed 02/07/2020; hereinafter Anderson; as cited in the IDS filed 02/24/2025), Baden et al., 2020 (hereinafter Baden), US 2022/0251578 A1 (effectively filed 06/25/2020; hereinafter Chang), Luke et al., 2009 (hereinafter Luke), US 2023/0174977 A1 (effectively filed 05/26/2020; hereinafter Packard), US 2013/0244231 A1 (hereinafter Takahashi), and WO 2020/255055 A1 (hereinafter Horton)
The disclosure of Cornell is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the vaccine composition limitations of instant claims 38-52.
With regard to claim 38, which recites “a vbaccine composition comprising the ribozyme activated RNA-construct(s) of claim 1, wherein the ribozyme activated RNA-construct(s) is linearized and comprises:
a 5’ ribozyme;
a 5’ ligation sequence;
an internal ribosome entry site (IRES) sequence;
an RNA coding sequence for at least one antigenic polypeptide;
a 3’ ligation sequence; and
a 3’ ribozyme sequence, and
a pharmaceutically acceptable carrier,” as set forth above, Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme (abstract; paragraph [0027]), said constructs being useful for enhancing expression of the effector molecule (paragraph [0044]). The effector molecule of the constructs of Cornell is disclosed to be an RNA molecule encoding a therapeutic protein or peptide sequence, wherein the RNA molecule further comprises an IRES to facilitate translation of the same (paragraphs [0060], [0062], and [0098]). Additionally, as set forth above, Anderson discloses therapeutic protein expression from ribozyme constructs taught therein (abstract). Anderson further discloses that the constructs taught therein may be delivered in linear form (page 21, lines 6-8). Finally, Anderson discloses pharmaceutical compositions comprising the ribozyme constructs taught therein and one or more pharmaceutically acceptable carriers (page 49, line 27-page 50, line 6).
While neither Cornell nor Anderson disclose that the ribozyme-based constructs taught therein may be utilized as vaccine compositions, this deficiency is cured by Baden, which discloses that the COVID-19 vaccine provides an encoded full-length spike protein (i.e. an antigenic protein), thereby protecting individuals from contracting severe COVID-19 (abstract). While the spike protein disclosed in Baden is provided as mRNA (abstract), it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the instant application to provide the same antigenic protein as part of a ribozyme composition, as disclosed in both Cornell and Anderson. Thus, it is considered that Cornell, Anderson, and Baden collectively disclose each and every limitation of instant claim 38.
With regard to claim 39, which recites “the linearized ribozyme activated RNA-construct(s) [of the vaccine composition of claim 38] lacks a polymerase binding region,” Cornell further discloses embodiments of the constructs taught therein wherein said constructs comprise a polymerase binding region (i.e. a promoter sequence) (paragraph [0012]). Cornell also discloses embodiments that do not comprise a polymerase binding region (i.e. a promoter sequence) (paragraph [0011]). The disclosure of separate embodiments with separate components establishes that in embodiments of the constructs taught in Cornell, said constructs do not comprise a promoter sequence, as instantly claimed. Thus, it is considered that Cornell discloses each and every additional limitation of instant claim 39.
With regard to claim 40, which recites “the 5’ and 3’ ribozymes [of the vaccine composition of claim 38] are selected from the group consisting of a twister ribozyme, a hammerhead ribozyme, a hatchet ribozyme, a hepatitis delta virus ribozyme, a ligase ribozyme, a pistol ribozyme, a twister sister ribozyme, a Vg1 ribozyme, a VS ribozyme, and derivatives of any of the foregoing,” as set forth above, the constructs of Cornell are disclosed to comprise two ribozymes (abstract; paragraph [0027]). Cornell further discloses that suitable self-cleaving ribozymes for use in the constructs taught therein include hepatitis delta virus ribozymes, twister ribozymes, twister sister ribozymes, hatchet ribozymes, pistol ribozymes, and derivative thereof (paragraph [0032]). Thus, it is considered that Cornell discloses each and every additional limitation of instant claim 40.
With regard to claims 41 and 42, which respectively recite “the 5’ and 3’ ligation sequences [of the vaccine composition of claim 38] are substrates of naturally occurring ligases in situ,” wherein “the naturally occurring ligase is RtcB,” as set forth above, the constructs of Cornell are disclosed to comprise two ligation sequences (abstract; paragraph [0027]). Cornell further discloses that these ligation sequences are substrates for an RNA ligase such as RtcB (paragraph [0043]), which is a suitable naturally occurring ligase per paragraphs [0007] and [0008] of the instant specification (as also recited at instant claim 26). Thus, it is considered that Cornell discloses each and every additional limitation of instant claims 41 and 42.
With regard to claim 43, which recites “the IRES [of the vaccine composition of claim 38] comprises any one of the sequences of SEQ ID NO[s]: 1-1328,” as set forth above, the constructs of Cornell are disclosed to comprise an IRES to facilitate translation of the therapeutic protein or peptide sequence contained therein (abstract; paragraphs [0060], [0062], and [0098]). However, Cornell does not disclose the instantly claimed IRES sequences. This deficiency is cured by Chang, which discloses genetic elements driving the translation of circular RNAs (abstract). Chang discloses a number of IRES sequences, including SEQ ID NOs: 1-228 and SEQ ID NOs: 229-17201 (paragraph [0009]. While Chang discloses a large number of IRES sequences, a query of the first 25 claimed IRES sequences matches to 8 of the IRES sequences disclosed in Chang. As shown in the Appendix, instant SEQ ID NOs: 2, 3, 7, 10, 15, 19, 23, and 24 comprise 100% identity to SEQ ID NOs: 525, 1426, 1092, 978, 1054, 3110, 1641, and 2936 of Chang. Given that the instant claim set is drawn to a large number of IRES sequences, wherein a small subset of the claimed IRES sequences yields a high proportion of sequence matches when queried against sequence databases, it is overall considered that the IRES sequences of Chang read on the instantly claimed IRES sequences of instant claim 43.
With regard to claims 44-46, which respectively recite “the at least one antigenic polypeptide [of the vaccine composition of claim 38] comprises two or more antigenic polypeptides separated by a self-cleaving peptide,” “wherein the self-cleaving peptide comprises a 2A- or 2A-like peptide,” “wherein the 2A- or 2A-like peptide further comprises a GSG linker moiety,” as set forth above, the constructs of Cornell are disclosed to comprise a sequence encoding a therapeutic protein or peptide sequence (abstract; paragraphs [0027], [0060], [0062], and [0098]). However, Cornell does not disclose embodiments wherein multiple polypeptides of interest are expressed. This deficiency is cured by Luke, which discloses that the 2A region of FMDV encodes a short sequence that mediates self-processing by a novel translational effect, thereby facilitating the production of discrete translational products from a single open reading frame (abstract). Thus, Luke discloses that a single open reading frame (such as that disclosed in Cornell) can produce multiple translational products. Luke further discloses that cleavage efficiency of 2A-linked constructs is improved by placing a GSG linker between the N-terminal protein and the 2A-peptide (page 243, paragraph 2). Thus, it is considered that Luke discloses each and every additional limitation of instant claims 44-46.
With regard to claim 47, which recites “the 5’ and 3’ ribozyme sequences [of the vaccine composition of claim 38] are independently selected from a sequence that is at least 85-100% identical to…” SEQ ID NO: 1354 or SEQ ID NO: 1355, as set forth above, the constructs of Cornell are disclosed to comprise two ribozymes (abstract; paragraph [0027]). However, Cornell is silent as to the sequences of said ribozymes. This deficiency is cured by Packard. Per the instant claim language, the 5’ and 3’ ribozymes are independently selected from SEQ ID NOs: 1354 or 1355; accordingly, both the 5’ and 3’ ribozymes may comprise the same sequence. Packard discloses SEQ ID NO: 14, which is a ribozyme sequence that is 100% identical to instant SEQ ID NO: 1354 (see Appendix). Thus, it is considered that Packard discloses each and every additional limitation of instant claim 47.
With regard to claim 48, which recites “the 5’ and 3’ ligation sequences [of the pharmaceutical composition of claim 22] are independently selected from a sequence that is at least 85-100% identical to…” SEQ ID NO: 1356 or SEQ ID NO: 1357, as set forth above, the constructs of Cornell are disclosed to comprise two ligation sequences (abstract; paragraph [0027]). However, Cornell is silent as to the sequences of said ligation sequences. This deficiency is cured by Packard. Per the instant claim language, the 5’ and 3’ ligation sequences are independently selected from SEQ ID NOs: 1356 or 1355; accordingly, both the 5’ and 3’ ligation sequences may comprise the same sequence. Packard discloses SEQ ID NO: 10, which is a ligation sequence that is 100% identical to instant SEQ ID NO: 1356 (see Appendix). Thus, it is considered that Packard discloses each and every additional limitation of instant claim 48.
With regard to claim 49, which recites “the IRES sequence [of the pharmaceutical composition of claim 22] is at least 85-100% identical to…” SEQ ID NO: 1358, as set forth above, the constructs of Cornell are disclosed to comprise an IRES to facilitate translation of the therapeutic protein or peptide sequence contained therein (abstract; paragraphs [0060], [0062], and [0098]). However, Cornell does not disclose the instantly claimed IRES sequence. This deficiency is cured by Takahashi. Takahashi discloses SEQ ID NO: 9, which comprises an IRES sequence that is 96.3% identical to instant SEQ ID NO: 1358 (see Appendix). Thus, it is considered that Takahashi discloses each and every additional limitation of instant claim 49.
With regard to claim 50, which recites “the antigenic polypeptide [of the vaccine composition of claim 38] comprises a SARS-CoV-2 spike protein,” as set forth above, Baden, which discloses that the COVID-19 vaccine provides an encoded full-length spike protein (i.e. an antigenic protein), thereby protecting individuals from contracting severe COVID-19 (abstract). While the spike protein disclosed in Baden is provided as mRNA (abstract), it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the instant application to provide the same antigenic protein as part of a ribozyme composition, as disclosed in both Cornell and Anderson. Thus, it is considered that Baden discloses each and every additional limitation of instant claim 50.
With regard to claims 51 and 52, which respectively recite “the at least one polypeptide of interest or antigenic polypeptide [of the vaccine composition of claim 38] is contained within a self-amplifying RNA construct,” “wherein the self-amplifying RNA construct comprises an alphavirus or a Paramyxovirus,” as set forth above, Cornell, Anderson, and Baden collectively disclose the vaccine composition of instant claim 38. However, none of the cited art discloses that said vaccine composition comprises a self-amplifying RNA construct, as instantly claimed. This deficiency is cured by Horton. Horton discloses vaccines comprising self-replicating RNA molecules (abstract). These vaccines comprising self-replicating RNA molecules are disclosed to provide therapeutic immunity, meaning that the vaccinated subject is able to control an infection with the pathogenic agent against which the vaccination was done (page 3, lines 3-20; page 83, lines 5-8). Horton further discloses that the self-replicating RNA molecules taught therein are derived from an alphavirus replicon (page 5, lines 1-3). Thus, it is considered that Horton discloses each and every additional limitation of instant claims 51 and 52.
Therefore, given that:
Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, a second ribozyme, and an IRES, said constructs being useful for enhancing expression of the effector molecule, wherein said ribozyme may be a Twister ribozyme, a twister sister ribozyme, a pistol ribozyme, or another self-cleaving ribozyme and wherein said ligation sequences are substrates for naturally-occurring RtcB;
Anderson discloses therapeutic ribozyme constructs (that may be delivered in linear form) and pharmaceutical compositions comprising the same, wherein said therapeutic ribozyme constructs may encode a Cas polypeptide;
Baden discloses a vaccine composition comprising an mRNA encoding a SARS-CoV-2 spike protein to protect individuals from contracting severe COVID-19;
Chang discloses numerous IRES sequences corresponding to those of the instant invention;
Luke discloses that the 2A region of FMDV encodes a short sequence that mediates self-processing by a novel translational effect, thereby facilitating the production of discrete translational products from a single open reading frame, wherein inclusion of a GSG linker improves the cleavage efficiency thereof;
Packard discloses useful ribozyme sequences and ligation sequences corresponding to those of the instant invention;
Takahashi discloses an IRES sequence comprising 96.3% identity to instant SEQ ID NO: 1358; and
Horton discloses vaccines comprising self-amplifying RNA constructs derived from alphaviruses that provide therapeutic immunity to vaccinated subjects,
it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the constructs of Cornell to encode multiple products from a single open reading frame (as disclosed in Luke), including a SARS-CoV-2 spike protein (as disclosed in Baden), within a self-replicating RNA molecule of a vaccine (as disclosed in Horton) to provide therapeutic immunity (as disclosed in Horton), utilizing the sequences disclosed in Chang, Packard, and Takahashi to predictably drive expression of multiple protein products from the ribozyme constructs taught therein. One would have been motivated to make such a modification in order to receive the expected benefit of driving expression of multiple protein products from the ribozyme constructs taught therein for purposes of providing therapeutic immunity.
Claims 53-66 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2018/237372 A1 (hereinafter Cornell; as cited in the IDS filed 07/11/2023; of record) as applied to claim 1 above, and further in view of Mustafina et al., 2019 (hereinafter Mustafina), WO 2021/158964 A1 (effectively filed 02/07/2020; hereinafter Anderson; as cited in the IDS filed 02/24/2025), Luke et al., 2009 (hereinafter Luke), Calabrese et al., 2020 (hereinafter Calabrese), Arimbasseri et al., 2013 (hereinafter Arimbasseri), Azzoni et al., 2007 (hereinafter Azzoni), and WO 2020/223539 A1 (hereinafter Blainey).
The disclosure of Cornell is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the additional limitations of instant claims 53-66.
With regard to claim 53, which recites “the ribozyme activated RNA-construct(s) of claim 1, wherein the ribozyme activated RNA-construct(s) comprises:
one or more promoter sequences;
one or more RNA coding sequences for at least one polypeptide of interest;
one or more ribozymes, wherein the one or more ribozymes are aptazyme-based riboswitches;
a 3’ UTR sequence comprising the aptazyme-based riboswitches; and
a poly(A) sequence;
wherein the aptazyme-based riboswitches when not bound to target ligands destabilize the ribozyme activated RNA-construct(s) leading to decreased expression of the at least [one] polypeptide of interest, and
wherein the aptazyme-based riboswitches when bound to target ligands stabilize the ribozyme activated RNA-construct(s) leading to increased expression of the at least [one] polypeptide of interest,” as set forth above, Cornell discloses the ribozyme activated RNA-construct(s) of instant claim 1. Furthermore, as set forth above, the constructs of Cornell comprise a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, a second ribozyme, and a promoter sequence (abstract; paragraph [0012]).
However, Cornell does not disclose the instantly claimed aptazyme-based riboswitches. This deficiency is cured by Mustafina. As depicted in Figure 1, Mustafina discloses mammalian riboswitch systems based on aptamer-ribozyme fusion architecture, wherein the aptazyme-based riboswitch is located in the 3’ UTR of the protein of interest (i.e. EGFP) and is followed by a poly(A) sequence. As previously set forth, the aptazymes disclosed in Mustafina function by fusing an aptamer to a ribozyme such that the aptamer changes conformation upon binding of a ligand, thereby disrupting the ribozyme fold and facilitating protein translation (Figure 1). In the absence of ligand binding, the aptamer assumes a conformation that maintains the ribozyme fold, thereby disrupting protein translation (Figure 1), as instantly claimed. Thus, it is considered that Cornell and Mustafina disclose each and every additional limitation of instant claim 53.
With regard to claim 54, which recites “the aptazyme-based riboswitches [of the ribozyme activated RNA-construct(s) of claim 53] are hammerhead aptazymes,” as set forth above, Mustafina discloses the features of the instantly claimed aptazymes. Mustafina further discloses that suitable aptazymes comprise an aptamer connected to a hammerhead ribozyme (page 19, column 2, paragraph 1; page 23, column 2, paragraph 3; page 24, column 1, paragraph 2). Thus, it is considered that Mustafina discloses each and every additional limitation of instant claim 54.
With regard to claim 55, which recites “the target ligands [of the ribozyme activated RNA-construct(s) of claim 53] are selected from tetracycline, theophylline, and guanine,” as set forth above, Mustafina discloses the features of the instantly claimed aptazymes. Mustafina further discloses that ligands suitable for controlling the aptazymes taught therein include guanine (abstract; Figure 3). Thus, it is considered that Mustafina discloses each and every additional limitation of instant claim 55.
With regard to claims 56-58, which respectively recite “the at least one polypeptide of interest [of the ribozyme activated RNA-construct(s) of claim 53] is selected from the group consisting of a prodrug activating enzyme, a biological response modifier, a receptor ligand, an immunoglobulin derived binding polypeptide, a non-immunoglobulin binding polypeptide, an antigenic polypeptide, a genome editing enzyme, and any combination thereof wherein multiple polypeptides are separated by a 2A or 2A-like peptide,” “wherein the biological response modifier is an immunopotentiating cytokine,” “selected from the group consisting of interleukins 1 through 38, interferon, tumor necrosis factor (TNF), and a granulocyte-macrophage-colony stimulating factor (GM-CSF),” as set forth above, the constructs of Cornell are disclosed to comprise a sequence encoding a therapeutic protein or peptide sequence (abstract; paragraphs [0027], [0060], [0062], and [0098]). While Cornell does not explicitly disclose that the therapeutic proteins or peptides taught therein are specifically a biological response modifier such as an immunopotentiating cytokine, this deficiency is cured by Calabrese. Calabrese discloses that administration of interferon to COVID-19 patients may contribute to the management of COVID-19 (abstract; CONCLUSION). Therefore, it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the instant invention to encode therapeutic interferon in the constructs disclosed in Cornell for purposes of treating COVID-19 patients in need thereof (as set forth in greater detail below). Thus, it is considered that Calabrese discloses each and every additional limitation of instant claims 56-58. The Examiner notes that the instant claim language encompasses one or more polypeptides of interest and does not require multiple polypeptides of interest, meaning the recited limitations regarding 2A- or 2A-like peptides are not required by the instant claim language.
With regard to claim 59, which recites “the 2A- or 2A-like peptide [of the ribozyme activated RNA-construct(s) of claim 56] further comprises a GSG linker moiety,” as set forth above, the language of instant claim 56 encompasses one or more polypeptides of interest and does not require multiple polypeptides of interest, meaning the recited limitations regarding 2A- or 2A-like peptides are not required by the instant claim language. However, if someone of ordinary skill in the art were to design the ribozyme activated RNA-construct such that it encodes multiple polypeptides of interest, Luke discloses that the 2A region of FMDV encodes a short sequence that mediates self-processing by a novel translational effect, thereby facilitating the production of discrete translational products from a single open reading frame (abstract). Thus, Luke discloses that a single open reading frame (such as that disclosed in Cornell) can produce multiple translational products. Luke further discloses that cleavage efficiency of 2A-linked constructs is improved by placing a GSG linker between the N-terminal protein and the 2A-peptide (page 243, paragraph 2). Thus, it is considered that Luke discloses each and every additional limitation of instant claim 59.
With regard to claim 60, which recites “the genome editing enzyme [of the ribozyme activated RNA-construct(s) of claim 56] is selected from the group consisting of a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), an engineered meganuclease, and an RNA-guided DNA endonuclease (Cas) polypeptide,” as set forth above, the constructs of Cornell are disclosed to comprise a sequence encoding a therapeutic protein or peptide sequence (abstract; paragraphs [0027], [0060], [0062], and [0098]). Cornell does not disclose that the constructs taught therein may encode a genome editing enzyme. This deficiency is cured by Anderson. As set forth above, Anderson discloses therapeutic protein expression from ribozyme constructs taught therein (abstract). One such therapeutic protein is disclosed to be Cas9 (page 5, lines 8-9), which is a Cas polypeptide as instantly claimed. Thus, it is considered that Anderson discloses each and every additional limitation of instant claim 60.
With regard to claim 61, which recites “the one or more promoter sequences [of the ribozyme activated RNA-construct(s) of claim 53] are polymerase II (pol-II) promoter sequences,” as set forth above, Cornell discloses that expression of the constructs taught therein may be driven by an RNA polymerase III promoter (paragraph [0068]). However, Cornell is silent as to the instantly claimed polymerase II promoter. This deficiency is cured by Arimbasseri, which discloses that polymerase II is more useful for encoding protein products than polymerase III, which typically encodes short, non-coding RNA products (page 1, column 1, paragraph 1). Thus, it is considered that Arimbasseri discloses each and every additional limitation of instant claim 61.
With regard to claim 62, which recites “the one or more promoter sequences [of the ribozyme activated RNA-construct(s) of claim 53] have a sequence(s) for EF1α, hU6, SV40, CMV, a RSV, NEUROD2 and/or TBX20,” as set forth above, Cornell discloses that expression of the constructs taught therein may be driven by an RNA polymerase III promoter (paragraph [0068]). However, Cornell is silent as to the instantly claimed promoters. This deficiency is cured by Anderson, which discloses that a suitable promoter for the ribozyme constructs taught therein includes the CMV promoter sequence, which is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto (page 46, lines 26-29). Anderson further discloses that other suitable promoters include the EF1α promoter and the SV40 promoter (page 46, lines 29-31). Thus, it is considered that Anderson discloses each and every additional limitation of instant claim 62.
With regard to claim 63, which recites “the poly(A) sequence [of the ribozyme activated RNA-construct(s) of claim 53] is a bGH poly(A) sequence,” while Mustafina discloses that the aptazyme constructs taught therein comprise a poly(A) sequence (Figure 1), Mustafina is silent as to said poly(A) sequence being a bGH poly(A) sequence. However, this deficiency is cured by Azzoni. Azzoni discloses that bGH poly(A) is most efficient for transfection and subsequent transgene production (Figure 9). Thus, it is considered that Azzoni discloses each and every additional limitation of instant claim 63.
With regard to claim 64, which recites “a plasmid or capsid comprising the ribozyme activated RNA-construct(s) of claim 53,” as set forth above, Cornell and Mustafina disclose each and every limitation of instant claim 53. Additionally, Cornell further discloses that the constructs taught therein may be supplied via a plasmid vector (paragraphs [0062] and [0063]) or via a viral vector (paragraphs [0062] and [0064]). Thus, it is considered that Cornell discloses each and every additional limitation of instant claim 64.
With regard to claim 65, which recites “the plasmid or capsid is an AAV-based plasmid or capsid,” as set forth above, Cornell discloses that the constructs taught therein may be supplied via a viral vector (paragraphs [0062] and [0064]) such as an AAV vector (paragraph [0064]). Thus, it is considered that Cornell discloses each and every additional limitation of instant claim 65.
With regard to claim 66, which recites “the plasmid or capsid of claim 64, wherein the plasmid expresses a Cas9 protein and a gRNA,” as set forth above, the constructs of Cornell are disclosed to comprise a sequence encoding a therapeutic protein or peptide sequence (abstract; paragraphs [0027], [0060], [0062], and [0098]). Additionally, Luke discloses that the 2A region of FMDV encodes a short sequence that mediates self-processing by a novel translational effect, thereby facilitating the production of discrete translational products from a single open reading frame (abstract). Thus, Luke discloses that a single open reading frame (such as that disclosed in Cornell) can produce multiple translational products. Finally, as set forth above, Blainey discloses ribozyme-based production of gRNA sequences (paragraph [0041]), while Anderson discloses ribozyme-based production of Cas9 (page 5, lines 8-9). Therefore, it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the instant invention to modify the constructs of Cornell such that they encode multiple products (as per Luke), such as a gRNA and Cas9 for genome targeting (as disclosed in Blainey and Anderson). Thus, it is considered that Cornell, Luke, Blainey, and Anderson disclose each and every additional limitation of instant claim 66.
Therefore, given that:
Cornell discloses RNA molecules comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, a second ribozyme, and an IRES, said constructs being useful for enhancing expression of the effector molecule, wherein said constructs are delivered via a plasmid vector or a viral vector;
Mustafina discloses aptazyme constructs wherein said constructs comprise hammerhead aptazymes controlled by guanine;
Anderson discloses therapeutic ribozyme constructs (that may be delivered in linear form) and pharmaceutical compositions comprising the same, wherein said therapeutic ribozyme constructs may encode a Cas polypeptide;
Luke discloses that the 2A region of FMDV encodes a short sequence that mediates self-processing by a novel translational effect, thereby facilitating the production of discrete translational products from a single open reading frame, wherein inclusion of a GSG linker improves the cleavage efficiency thereof;
Calabrese discloses that administration of interferon can be beneficial in the treatment of COVID-19;
Arimbasseri discloses that polymerase II is more useful for encoding protein products than polymerase III, which encodes short, non-coding RNA products;
Azzoni discloses that bGH poly(A) is most efficient for transfection and subsequent transgene production; and
Blainey discloses ribozyme-based production of gRNAs;
it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the constructs of Cornell to encode multiple products from a single open reading frame (as disclosed in Luke), including interferon (as disclosed in Calabrese) or gRNA and a Cas9 (as disclosed in Blainey and Anderson), controlled by an aptazyme (as disclosed in Mustafina) and regulated by a polymerase II promoter (as disclosed in Arimbasseri) and a bGH poly(A) sequence (as disclosed in Azzoni) to predictably drive efficient expression of multiple products from the ribozyme constructs taught therein for therapeutic and/or gene editing purposes. One would have been motivated to make such a modification in order to receive the expected benefit of driving expression of multiple products from the ribozyme constructs taught therein for therapeutic and/or gene editing purposes.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 2, 7, 9-12, 22, 24-26, 29, 38, 41, 42, 40, 45, and 65 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 9, 22, 23, 35, 43, 45, 94, 95, 127, 128, and 130 of copending Application No. 18/835,296 (reference application; corresponds to US 2025/0163454 A1) in view of WO 2018/237372 A1 (hereinafter Cornell; as cited in the IDS filed 07/11/2023; of record), WO 2021/158964 A1 (effectively filed 02/07/2020; hereinafter Anderson; as cited in the IDS filed 02/24/2025), and Baden et al., 2020 (hereinafter Baden).
The Examiner notes that copending claims 22 and 23 are drawn to a method rather than a product, as in the instant claim set.
Accordingly, MPEP 804 II B 1 states:
The specification can be used as a dictionary to learn the meaning of a term in the patent claim. Toro Co. v. White Consol. Indus., Inc., 199 F.3d 1295, 1299, 53 USPQ2d 1065, 1067 (Fed. Cir. 1999)… Further, those portions of the specification which provide support for the patent claims may also be examined and considered when addressing the issue of whether a claim in the application defines an obvious variation of an invention claimed in the patent. In re Vogel, 422 F.2d 438, 441-42, 164 USPQ 619, 622 (CCPA 1970).
The following rejections are in view of the decision of the Court of Appeals for the Federal Circuit in Pfizer Inc, v Teva pharmaceuticals USA Inc., 86 USPQ2d 1001, at page 1008 (March 2008), which indicates that there is no patentable distinction between claims to a product and a method of using that product disclosed in the specification of the application and that the preclusion of such a double patenting rejection under 35 USC 121 does not apply where the present application is other than a divisional application of the patent application containing such patentably indistinct claims.
Copending claims 1 and 35 are both drawn to a linearized ribozyme activated RNA construct, said constructs respectively comprising a first ligation sequence, an IRES sequence, a polynucleotide sequence of interest encoding a recombinant polypeptide, a 3’ UTR sequence, a poly(A) sequence, and a second ligation sequence, wherein the first and second ligation sequences hybridize to form a stem substrate for an RNA ligase (as recited at copending claim 9); or comprising a first twister ribozyme, a first ligation sequence, an IRES sequence, a polynucleotide sequence of interest encoding a recombinant polypeptide, a 3’ UTR sequence, a poly(A) sequence, a second ligation sequence, and a second twister ribozyme.
Additionally, copending claim 94 is drawn to a ribozyme RNA-construct(s) comprising an optional primer region, an optional barcode region, a first ribozyme domain, a first ligation stem domain, a payload domain, a second ligation stem domain, and a second ribozyme domain, wherein the payload domain comprises an IRES or a P2A peptide coding sequence, a coding sequence of at least one polypeptide and/or nucleic acid of interest, and a 3’ UTR sequence, wherein the transcription of the payload domain is activated by or dependent upon the activity of the one or more ribozymes. Copending claim 95 further recites that the first and second ligation stem domains are from 30 to 60 bp in length.
In comparison, instant claim 1 is drawn to a ribozyme activated RNA-construct(s), said construct(s) comprising one or more ribozymes and one or more RNA coding sequences for at least one polypeptide of interest, wherein the transcription of the one or more RNA coding sequence for at least one polypeptide of interest is activated by or dependent upon the activity of the one or more ribozymes. Thus, instant claim 1 is not patentably distinct from copending claims 1, 35, and 94.
Furthermore, instant claim 2 is drawn to the ribozyme activated RNA-construct(s) of instant claim 1, further comprising an optional primer region and an optional barcode region, wherein cleavage of the first and second engineered RNA elements by self-cleaving ribozymes provides for hybridization of complementary sequences contained therein such that the hybridization construct can be further ligated by an RNA ligase to form an RNA-fusion construct that produces the at least one polypeptide of interest. Thus, instant claim 2 is not patentably distinct from copending claim 94, with the exception of the recited limitation regarding self-cleaving ribozymes. This deficiency is cured by Cornell. As set forth above, Cornell discloses the utility of self-cleaving ribozymes in activating RNA constructs to express a polypeptide of interest (abstract; paragraphs [0020] and [0045]; Figure 4A). Thus, the copending application in view of Cornell is not patentably distinct from instant claim 2.
Instant claim 7 recites that the first and second complementary sequences are from 30 to 60 bp in length, which is identical to the range recited at copending claim 95, as set forth above. Thus, the recitation of instant claim 7 is not patentably distinct from the copending claim 95.
Instant claims 22 and 38 are respectively drawn to a pharmaceutical composition or a vaccine composition comprising the ribozyme activated RNA-construct(s) of instant claim 1 (set forth above), wherein the ribozyme activated RNA-construct(s) is linearized and comprises a 5’ ribozyme, a 5’ ligation sequence, an IRES, an RNA coding sequence for at least one polypeptide of interest, a 3’ ligation sequence, a 3’ ribozyme sequence, and a pharmaceutically acceptable carrier. While copending claims 1, 35, and 94 do not recite a pharmaceutical composition or a vaccine composition comprising these structural features, the copending claims do recite all other structural limitations of instant claims 22 and 38. The deficiencies regarding the instantly claimed pharmaceutical composition or vaccine composition are respectively cured by Anderson and Baden. As set forth above, Anderson discloses pharmaceutical compositions comprising the ribozyme constructs taught therein and one or more pharmaceutically acceptable carriers (page 49, line 27-page 50, line 6), and Baden discloses that the COVID-19 vaccine provides an mRNA-encoded full-length spike protein (i.e. an antigenic protein), thereby protecting individuals from contracting severe COVID-19 (abstract). While the spike protein disclosed in Baden is provided as mRNA (abstract), it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the instant application to provide the same antigenic protein as part of a ribozyme composition, as disclosed in both Cornell and Anderson (as set forth above). Thus, the copending application in view of Cornell, Anderson, and Baden is not patentably distinct from instant claims 22 and 38.
Instant claims 29 and 45 both recite that the constructs claimed therein comprise a 2A- or 2A-like peptide, as recited at copending claim 94. Thus, instant claims 29 and 45 are not patentably distinct from copending claim 94.
Per copending claim 22, an RNA ligase (RtcB per copending claim 23) ligates the first and second ligation sequences, thereby forming the circular RNA construct.
Instant claims 12, 25, 26, 41, and 42 all recite that the RNA ligase utilized therein is naturally-occurring RtcB. Accordingly, instant claim 12 is not patentably distinct from copending claim 22.
Per copending claims 43 and 45, the first and/or second ribozyme of the linearized ribozyme-RNA construct of copending claim 35 is a P1 or a P3 twister ribozyme.
Instant claims 9-11 respectively recite that the first and second ribozymes are Twister ribozymes, specifically a P3 Twister ribozyme and a P1 Twister ribozyme. Thus, instant claims 9-11 are not patentably distinct from copending claims 43 and 45.
Furthermore, instant claims 24 and 40 respectively recite that the pharmaceutical composition or vaccine composition claimed therein comprise a 5’ and 3’ twister ribozyme, as recited at copending claims 43 and 45. Thus, instant claims 24 and 40 are not patentably distinct from copending claims 24 and 40.
Finally, per copending claims 127, 128, and 130, a vector, such as an AAV viral vector, comprises the ribozyme RNA-construct(s) of copending claim 35.
In comparison, instant claim 65 is drawn to an AAV-based plasmid or capsid comprising the instantly claimed ribozyme activated RNA-construct(s). Thus, instant claim 65 is not patentably distinct from copending claims 127, 128, and 130.
Therefore, the instant and copending applications are not patentably distinct from each other, with the exceptions of:
The self-cleaving ribozymes recited at instant claim 2. As set forth above, Cornell discloses the utility of self-cleaving ribozymes in activating RNA constructs to express a polypeptide of interest (abstract; paragraphs [0020] and [0045]; Figure 4A).
Pharmaceutical compositions comprising the instantly claimed constructs. As set forth above, Anderson discloses pharmaceutical compositions comprising the ribozyme constructs taught therein and one or more pharmaceutically acceptable carriers (page 49, line 27-page 50, line 6).
Vaccine compositions comprising the instantly claimed constructs. As set forth above, Baden discloses that the COVID-19 vaccine provides an mRNA-encoded full-length spike protein (i.e. an antigenic protein), thereby protecting individuals from contracting severe COVID-19 (abstract).
Given that the instant and copending applications are not patentably distinct from each other, with the exception of the limitations noted above, and that Cornell discloses the utility of self-cleaving ribozymes in activating RNA constructs to express a polypeptide of interest, such as a COVID-19 spike protein (as disclosed in Baden), while Anderson discloses pharmaceutical compositions comprising ribozyme-activated constructs, it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the instant invention to modify the construct(s) of the copending application to comprise self-cleaving ribozymes (as disclosed in Cornell) to predictably express a polypeptide of interest (such as a COVID-19 spike protein as disclosed in Baden) delivered in a pharmaceutical composition (as disclosed in Anderson) such as a vaccine composition (analogous to the vaccine disclosed in Baden). One would have been motivated to make such a modification in order to receive the expected benefit of expressing a polypeptide of interest (such as a COVID-19 spike protein) from a pharmaceutical composition or a vaccine composition for therapeutic intervention of patients in need thereof.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
Claims 2, 5, 6, 14, 16, 22, 23, 27, 38, 39, 43, 53, 55, and 56 are objected to.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Sarah E Allen whose telephone number is (571)272-0408. The examiner can normally be reached M-F 8-5.
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, Jennifer Dunston can be reached at 571-272-2916. 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.
/SARAH E ALLEN/ Examiner, Art Unit 1637
/J. E. ANGELL/ Primary Examiner, Art Unit 1637
Prosecution Insights