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 .
Claim Status
Amendments to the claims filed 02 Aug 2024 and 24 Mar 2025 are acknowledged. Claims 3, 5, 7, 9-11, 13, 15, 20, 24-25, 27, 29-32, 35, 37, and 39-40 are canceled. Claims 1-2, 4, 6, 8, 12, 14, 16-19, 21-23, 26, 28, 33-34, 36, and 38 are amended and pending.
Specification
The abstract of the disclosure does not commence on a separate sheet in accordance with 37 CFR 1.52(b)(4) and 1.72(b). A new abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text.
The title of the invention is not descriptive. A new title is required that is clearly indicative of the invention to which the claims are directed.
Claim Objections
Claims 12, 18-19, and 21 are objected to because the claims do not conform to sequence rules requiring the use of "SEQ ID NO:" when reciting a sequence. See 37 CFR 1.821-1.825 and MPEP § 2422.01. Furthermore, SEQ ID NO. are merely identifiers of the sequences, not the sequences themselves. The claims should recite, for example, "the sequence as set forth in SEQ ID NO. 1" rather than "SEQ ID NO. 1" or "...% identity to the sequence as set forth in SEQ ID NO: 1" rather than "...% identity to SEQ ID NO. 1". Appropriate correction is required.
Where the description or claims of a patent application discuss a sequence that is set forth in the Sequence Listing, in accordance with paragraph (c) of this section, reference must be made to the sequence by use of the sequence identifier (§ 1.823(a)(5) ), preceded by "SEQ ID NO:" or the like, in the text of the description or claims, even if the sequence is also embedded in the text of the description or claims of the patent application. 37 CFR 1.821(d).
Claims 8, 12, 16-17, and 28 are objected to because of the following informalities:
Regarding claims 8 (c) and 12 (c), the term "promoter" is misspelled as "promotor".
Regarding claim 8, the labels for parts (a) through (d) are used redundantly. Further regarding claim 17, parts (a) and (b) are used redundantly. Subparts of the claim should be relabeled to use each letter once.
Regarding claim 16 (b), subparts (i) and (ii) each contain unnecessary commas in the recitation "RNA mediated gene editing, is complementary".
Regarding claim 28 (a), a space is missing between words in "claim1".
Regarding claim 34 (a)(ii), the word "enzyme" is redundant. By definition, nucleases are enzymes.
Appropriate correction is required.
Claim Interpretation
The following claim interpretations are made to promote compact prosecution:
Claim 8 (a)(i) through (a)(v) are interpreted as being listed in the alternative, i.e., (i), (ii), (iii), (vi), or (v).
Claim 19 (f)(iii) and (f)(v) and claim 21 (viii) are interpreted to recite " 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 99%, or 100%".
Claim 19 (a) through (f) are interpreted to as being listed in the alternative, i.e., (a), (b), (c), (d), (e), or (f).
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.
Claims 4, 6, 8, 12, 14, 17-19, 21-23, 34, and 36 are rejected under 35 U.S.C. § 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation in the same claim may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 4 recites the broad recitation "at least 2" in parts (a), (b), (c), (d)(iii), and (e)(iii) and the claim also recites "at least 3, at least 4, at least 5, at least 6, at least 7 , at least 8, at least 9, at least 10 or more" in parts (a) and (c), "at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10" in part (b), and
"at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58, at least 59, at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, at least 68, at least 69, at least 70, at least 71, at least 72, at least 73, at least 74, at least 77, at least 76, at least 77, at least 78, at least 79, at least 80, at least 81, at least 82, at least 83, at least 84, at least 88, at least 86, at least 87, at least 88, at least 89, at least 90, at least 91, at least 92, at least 93, at least 94, at least 99, at least 96, at least 97, at least 98, at least 99, or more",
in parts (d)(iii) and (e)(iii), which are narrower statements of the ranges or limitations. Claim 4 further recites the broad limitation "between 5 and 95" in parts (d)(ii) and (e)(ii), and the claim also recites between "10 and 90, 15 and 85, 20 and 80, 25 and 75, 30 and 70, 35 and 65, 40 and 60, 45 and 55", which are narrower statements of the ranges or limitations.
Furthermore in the present instance, claim 12 recites the broad recitation "at least 80%" in parts (a)(ii), (b)(ii), and (c)(ii), and the claim also recites "or optionally at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%" in part (a) subpart (ii) and "at least 80%" parts (a) subpart (ii), (b) subpart (ii), and the claim also recites " or optionally at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more" in part (b) subpart (ii) and (c) subpart (ii), which are the narrower statements of the ranges or limitations.
Furthermore in the present instance, claim 18 recites the broad recitation "at least 80%" in part (x), and the claim also recites " at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more sequence identity to SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, and/or SEQ ID NO: 21; or that has a sequence that is SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, or SEQ ID NO: 21", which is the narrower statement of the range or limitation.
Furthermore in the present instance, claim 19 recites the broad recitations " at least 80%, " in parts (f)(iii) and (f)(v), and the claim also recites " at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more", which are narrower statements of the ranges or limitations. Claim 22 is included in this rejection as it depends from claim 19 and does not resolve the issue.
Furthermore in the present instance, claim 21 recites the broad recitation "at least 80%", and the claim also recites " at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more", which is the narrower statement of the range or limitation.
The claims are considered indefinite because there is a question or doubt as to whether the features introduced by such narrower language are (a) merely exemplary of the remainder of the claims and therefore not required, or (b) required features of the claims.
Claim 4 recites limitations under parts (a), (b), and/or (c), and/or (d), (e). The inconsistent use of "and/or" between the claim parts between the claim parts renders the claim indefinite because it is unclear which claim limitations are required or listed in the alternative and thus, the metes and bounds of the claim are unclear. To promote compact prosecution, claim 4 is interpreted to list parts as (a), (b), (c), (d), and/or (e).
Claim 6 part (c) recites limitations under parts (i) through (ix) without use of "and", "or", or "and/or" between the claim subparts, which renders the claim indefinite because it is unclear which claim limitations are required or listed in the alternative and thus, the metes and bounds of the claim are unclear. Furthermore, it is unclear whether the recitation on p. 8,
"and wherein the array operator is located upstream (5') of the first nucleic acid sequence region that encodes a nucleic acid that is capable of directing RNA mediated gene regulation or RNA mediated gene editing within each array sub-module, so as to regulate transcription of each sub-module; and
wherein the first array sub-module is located upstream (5') to the second array sub-module so that the array operator of the second array sub-module is positioned 3' to the final nucleic acid region that encodes a nucleic acid that is capable of directing RNA mediated gene regulation or RNA mediated gene editing of the first array sub-module;
or
wherein the array operator is located upstream (3') of the last nucleic acid region that encodes a nucleic acid that is capable of directing RNA mediated gene regulation or RNA mediated gene editing within each array sub-module, so as to regulate transcription of each sub-module; and
wherein the first array sub-module is located upstream (5') to the second array sub-module so that the array operator of the first array sub-module is positioned 5' to the first nucleic acid region that encodes a nucleic acid that is capable of directing RNA mediated gene regulation or RNA mediated gene editing of the second array sub-module",
is a required element of part (d) or is required by the claim as a whole. To promote compact prosecution, the recitation is interpreted as only being required under claim 6 (d). Furthermore, the recitation on p. 8 does not use claim sub-numbering and makes inconsistent use of "and" and "or" between clauses, and therefore it is unclear which clauses are required parts of part (d) and which are listed in the alternative.
Claim 8 recites limitations under parts (a) and/or (b) or (c) in the first part of the claim on pp. 8-10 and under parts (a) or (b), (c) or (d) or (e). The use of "or" and "and/or" between the claim parts renders the claim indefinite because it is unclear which claim limitations are required or listed in the alternative and thus, the metes and bounds of the claim are unclear. To promote compact prosecution, claim 8 is interpreted list the first parts (a) through (c) and the second parts (a) through (e) as listed in the alternative, i.e., (a) or (b) or (c) or (a) or (b) or (c) or (d) or (e).
Claim 8 recites the limitations "the first repressor protein" and "the second repressor protein" on page 10, line 11. There is insufficient antecedent basis for this limitation in the claim.
Claims 8, 17, 19, 22-23, and 34 are rejected on the basis that the claims contain improper Markush groupings of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is a closed group of alternatives, i.e., the selection is made from a group "consisting of", rather than "comprising" or "including", the alternative members. See MPEP § 2173.05(h). In the present instance, the following recitations are indefinite because the use of comprising language is open-ended and does not exclude additional, unrecited elements:
Regarding claim 8, the recitation, "the inducing agent is selected from the group comprising or consisting of: tetracycline (Tc); anhydrotetracycline (aTc); and Doxycycline; optionally wherein the inducer molecule is anhydrotetracycline (aTc)", (emphasis added) in claim 8 (c)(vi) is indefinite.
Regarding claim 17, the recitation, "wherein the polypeptide is selected from the group comprising or consisting of: Cas9 or Cas9-like polypeptide; dCas9 or dCas9-like polypeptide, Cas12a; dCas12a;Cas12b; dCas12b; Cas13a; dCasl3a; Cas13b; dCasl3b; LbCpf1; dLbCpf1; AsCpf1; dAsCpf1; or dFnCpf1; or FnCpf1; or a fusion protein thereof", (emphasis added) in claim 17 (b) is indefinite.
Regarding claim 19, the recitations, "the first regulatory polypeptide is selected from the group comprising or consisting of: Cas9 or Cas9-like polypeptide; dCas9 or dCas9-like polypeptide; Cas12a; dCas12a; Cas12b; dCas12b; Cas13a; dCas13a; Cas13b; dCas13b; LbCpf1; dLbCpf1; AsCpf1; dAsCpf1; or dFnCpf1; or FnCpf1; or a fusion protein thereof" in part (b), "wherein the second regulatory polypeptide is selected from the group comprising or consisting of: Cas9 or Cas9-like polypeptide; dCas9 or dCas9-like polypeptide; Cas12a; dCas12a; Cas12b; dCas12b; Cas13a; dCas13a; Cas13b; dCas13b; LbCpf1; dLbCpf1; AsCpf1; dAsCpf1; or dFnCpf1; or FnCpf1; or a fusion protein thereof" in part (d), "the activator domain is selected from the group comprising or consisting of: VP, VP16, VP64, GAL4 and B42" in part (f)(i)(A), "the repressor domain is selected from the group comprising or consisting of: KRAB-like effectors (optional Mxi1), RD1152, RD11, RD5, and/or RD2" in part (f)(i)(B), "the first regulatory polypeptide is selected from the group comprising or consisting of a Cas9-Mxi1 or Cas9-like-Mxi1 polypeptide; a dCas9-Mxi1 or dCas9-likeMxi1 polypeptide; Cas12a-Mxi1; dCas12a-Mxi1; Cas12b-Mxi1; dCas12b-Mxi1; Cas13a-Mxi1; dCas13a-Mxi1; Cas13b-Mxi1; dCas13b-Mxi1; LbCpf1-Mxi1; dLbCpf1-Mxi1; AsCpf1-Mxi1; dAsCpf1-Mxi1; dFnCpf1-Mxi1; or FnCpf1-Mxi1, optionally is a dCas9-Mxi1 polypeptide" in part (f)(ii)(A), and "the second regulatory polypeptide is selected from the group comprising or consisting of a Cas9-VP or Cas9-like-VP polypeptide; a dCas9-VP or dCas9-like-VP polypeptide; Cas12a-VP; dCas12a-VP; Cas12b-VP; dCas12b-VP; Cas13a-VP; dCas13aVP; Cas13b-VP; dCas13b-VP; LbCpf1-VP; dLbCpf1-VP; AsCpf1-VP; dAsCpf1-VP; dFnCpf1-VP; or FnCpf1-VP, optionally is a dCas12a-VP polypeptide " in part (f)(iv) (emphasis added) are indefinite. Claim 22 is included in this rejection as it depends from claim 19 and does not resolve the issue.
Regarding claim 22, the recitation "wherein the promoter is selected from the group comprising or consisting of: REV1, PSP2, HTB2, RAD27, or POP6" in part (d)(ii) (emphasis added) is indefinite.
Regarding claim 23, the recitations "wherein the first activator protein is selected from the group comprising or consisting of: rtTA-VP and rtTA-Gal4" in part (i)(b) and " wherein the promoter is selected from the group comprising or consisting of: REV1, PSP2, HTB2, RAD27, or POP6" in part (v) (emphasis added) are indefinite.
Regarding claim 34, the recitation "the inducer molecule is i) selected from the group comprising or consisting of: tetracycline (Tc); anhydrotetracycline (aTc); Doxycycline" in part (b) (emphasis added) is indefinite.
Claim 12 recites the limitations "the first activator protein", "the first repressor protein", and "the second repressor protein" in parts (d), (e), and (f), respectively. There is insufficient antecedent basis for these limitations in the claim.
Claim 12 recites limitations under parts (a) or (b) or (c) or (d), (e), or (f). The inconsistent use of "or" between the claim parts renders the claim indefinite because it is unclear which claim limitations are required or listed in the alternative and thus, the metes and bounds of the claim are unclear. To promote compact prosecution, claim 12 is interpreted list the first parts (a) through (f) as listed in the alternative, i.e., (a) or (b) or (c) or (d) or (e) or (f).
The phrases “strong promoter” and "strong Pol III promoter" recited in claim 14 parts (a)(ii) and (b)(ii), respectively, and "a weak promoter or a medium-strength promoter" recited in claim 22 (d)(ii) and claim 23 (v) are relative phrases that render the claim indefinite. As noted in the specification, the terms "weak, "medium-strength", and "strong" are terms of art used to describe promoter strength (p. 22 lines 15-16 and p. 39 lines 11-13). Further as noted in the specification, methods to measure promoter strength are well known in the art (p. 22 line 26 - p. 23 line 2). However, promoter strength is a continuous variable, not categorical. The claims, specification, and the art do not provide a clear delineation between weak and medium-strength promoters or between medium-strength and strong promoters. The metes and bounds of the claim are unclear because a skilled artisan would be unable to delineate between a weak and medium-strength and a medium-strength and strong promoter.
Claim 19 recites limitations under parts (a), (b), (c), (d), or (e), (f). The inconsistent use of "or" between the claim parts renders the claim indefinite because it is unclear which claim limitations are required or listed in the alternative and thus, the metes and bounds of the claim are unclear. To promote compact prosecution, claim 19 is interpreted list the first parts (a) through (f) as listed in the alternative, i.e., (a) or (b) or (c) or (d) or (e) or (f).
Claim 21 recites limitations under parts (a), (b) with use of "and", "or", or "and/or" between claim parts. Furthermore, claim 21 (b) recites limitations under subparts (i), (ii), (iii), (iv), or (v), (vi), (vii), (viii). The inconsistent or lack of use of "and", "or", or "and/or" renders the claim indefinite because it is unclear which claim limitations are required or listed in the alternative and thus, the metes and bounds of the claim are unclear. To promote compact prosecution, claim 21 is interpreted list the first parts (a) and (b) as listed in the alternative, i.e., (a) or (b). Claim 21 (b) is interpreted to list subparts (i) through (viii) as listed in the alternative.
Claim 22 recites limitations under parts (a), (b), and (c), (d). The use of "and" between the claim parts is inconsistent and therefore, it is unclear whether claim limitations are required or listed in the alternative. Because part (d) recites all of the same elements as part (c) and adds limitation and to promote compact prosecution, claim 22 is interpreted to require parts (a) and (b) and to additionally require one of (c) or (d).
Claim 23 recites limitations under parts (i), (ii), or (iii), (iv), or (v). The inconsistent of use "or", between claim parts renders the claim indefinite because it is unclear which claim limitations are required or listed in the alternative and thus, the metes and bounds of the claim are unclear. To promote compact prosecution, claim 23 is interpreted list the first parts (i) through (v) as listed in the alternative, i.e., (i) or (ii) or (iii) or (iv) or (v).
Claim 36 recites use of the method of claim 33, but since the claim does not set forth any steps involved in the process of using the method to produce at least one organic molecule, it is unclear what method or process is intended by the inventor or joint inventors. A claim is indefinite where it merely recites a use without any active, positive steps delimiting how this use is actually practiced. See MPEP § 2173.05(q).
Claim Rejections - 35 USC § 101
35 U.S.C. § 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-2, 4, 6, 8, 16-19, 21-23, 28, 33-34, 36 and 38 are rejected under 35 U.S.C. § 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claims recite a nucleic acid construct comprising components of CRISPR/Cas (clustered, regularly interspaced short palindromic repeats/CRISPR-associated proteins) systems found in bacteria species. This judicial exception is not integrated into a practical application because the claims do not recite any additional element that distinguishes the claimed nucleic acid from natural CRISPR/Cas systems. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims only recite elements found naturally in bacterial CRISPR/Cas systems.
Deltcheva (E. Deltcheva, et al., Nature, 2011) teaches analysis of the CRISPR01 operon within the S. pyogenes genome, which comprises all of the elements of the claimed nucleic acid construct.
Regarding claims 1 and 38, Deltcheva teaches analysis of the CRISPR01 operon within the S. pyogenes genome (nucleic acid construct), which comprises an endogenous promoter (promoter module comprising at least one promoter operator of a first sequence) and a gene-editing array module comprising six CRISPR RNAs (crRNAs, polycistronic array of nucleic acids capable of directing RNA-mediated gene editing) (pp. 602-604 and Fig. 1). The gene editing array is transcribed as a pre-crRNA (single polycistronic transcript) from the single endogenous promoter (operably linked to the promoter module), which is cleaved at spacers located between the individual crRNAs to produce mature crRNAs capable of directing gene editing (pp. 602-603 and Fig. 1). No definition is provided in the specification for "array operator". Therefore, under broadest reasonable interpretation, the array operator is interpreted to mean any composition within or that associates with the gene regulation or gene editing array and results in a change in a second protein or nucleic acid sequence. The spacers are considered to be array operators of a second sequence as the spacers are located within the array module and as cleavage of the spacers allows for mature, individual crRNA to direct editing of the host genome (second sequence) (pp. 602-603 and Fig. 1).
Regarding claim 2, the sequence of the endogenous promoter and the spacers are different (part (iv)) (pp. 602-603 and Fig. 1).
Regarding claim 4, the gene-editing array of CRISPR01 comprises six crRNA, each flanked by spacers (each sub-module comprises at least 2 array operators of a second sequence, part (b), between 2 and 100 array sub-modules, part (d)(i), between 5 and 95 array-sub-modules, part (d)(ii), and at least 2 array sub-modules, part (d)(iii)) (pp. 602-603 and Fig. 1).
Regarding claim 6, the gene-editing array of CRISPR01 comprises spacers (array operators of a second sequence) located upstream and downstream of each crRNA (parts (a) and (b)) (pp. 602-603 and Fig. 1).
Regarding claim 8, expression of the gene-editing array of CRISPR01 is driven by an endogenous promoter (pp. 602-603 and Fig. 1). Because the sequence is expressed, the ability of the promoter to bind to an activator protein is considered inherent (capable of binding to a first activator protein, part (a)(i)).
Regarding claim 16, the crRNA are complementary to regions of the host genome comprising invading phages or plasmids (nucleic acid region capable of directing RNA mediated gene editing is complementary to a target nucleic acid region, part (a)) (p. 602).
Regarding claim 17, the crRNA associate with RNase III and Csn1 for maturation, which allows for the crRNA to direct editing genes of invading phages or plasmids (each are independently capable of associated with a regulatory polypeptide, wherein said polypeptide is capable of regulating a gene, part (a)) (pp. 602-605 and Fig. 3-4). No limiting definition is provided for what the inventor regards as a Cas9-like protein. Therefore, Csn1 is regarded as a Cas9-like polypeptide because both Csn1 and Cas9 are Cas proteins (part (b)) (p. 602).. Furthermore, the activity of Csn1 and RNase III are required for crRNA maturation, which is required for RNA-mediated gene editing of target sequences; therefore, Csn1 and RNase III are regarded as polypeptides capable of regulating a gene (parts (a) and (b)) (pp. 604-605).
Regarding claim 18, the spacers in the gene editing array of CRISPR01 comprise cleavage sites for RNase III (an endoribonuclease cleavage site, part (ii) (p. 605 and Fig. 4). The spacers have no further known function (transcriptionally inert, part (i)) (pp. 602-603 and Fig. 1).
Regarding claim 19, CRISPR01 comprises a sequence encoding for Csn1 (first nucleotide region encoding a first regulatory polypeptide, part (a), a Cas9-like polypeptide, part (b) (pp. 602-603 and Fig. 1). CRISPR01 further comprises sequences encoding for Cas1 and Cas2 (second nucleotide region encoding a second regulatory polypeptide, part (c), a Cas9-like polypeptide, part (d)) (Fig. 1).
Regarding claim 21, the S. pyogenes genome (nucleic acid construct) comprises a sequence encoding RNase III, which cleaves the spacers within the pre-crRNA (polypeptide that is capable of cleaving the cleavage site present in the array module when in RNA form, part (a), an endoribonuclease, part (b)(i)) (pp. 602 and 604-605 and Fig. 4).
Regarding claim 22, transcription of Csn1, Cas1, and Cas2 are driven by a single endogenous promoter and transcription of RNase III is driven by the rnc gene promoter (parts (a) through (c) (pp. 602-603 and Fig. 1).
Regarding claim 23, CRISPR01 comprises sequences encoding for Cas1 and Cas2 proteins (Fig. 1). Note that no limiting definition is provided in the specification for "activator protein" or for "repressor protein". Therefore, any protein that drives gene editing and/or regulation activity of the nucleic acid construct is regarded as an activator protein. Likewise, any protein that limits gene editing and/or regulation of the nucleic acid construct is regarded as a repressor protein. As taught by Nuñez (J.K. Nuñez, et al., Nat Struc Mol Biol, 2014), Cas1 activity is required for CRISPR/Cas-based gene editing in bacterial species (activator protein, part (i)(a)) (pp. 528 and 532). However, in the absence of Cas2, Cas1 endonuclease activity is not limited to CRISPR loci; thus, Cas2 acts as a brake on Cas1 (repressor protein, part (ii)(a) (pp. 528 and 532-533).
Regarding claim 28, CRISPR01 is located in the genome of S. pyogenes and is expressed as a single transcript from an endogenous promoter (a cell comprising the nucleic acid construct, part (a), and a single polycistronic nucleic acid transcript, part (c)) (p. 602-603 and Fig. 1).
Regarding claim 33, S. pyogenes CRISPR/Cas activity is induced by invasion of a phages or foreign plasmid (inducer molecule) (contacting the cell with an inducer molecule, part (a), maintaining the cell in culture conditions suitable for expression of the array module, part (b)).
Regarding claim 34, S. pyogenes CRISPR/Cas activity requires expression of RNase III, which cleaves the spacer sites in the pre-crRNA (contacting the cell with a nuclease capable of cleaving the cleavage site when in RNA form, parts (a)(i) and (a)(ii)) (pp. 602-604 and Fig. 1 and 4).
Regarding claim 36, S. pyogenes CRISPR/Cas activity results in expression of tracrRNA (trans-activating CRISPR RNA), Cas1, Cas2, Csn1, RNase III, and multiple crRNA (producing at least one organic molecule) (p. 602).
The Office published the guidance document entitled 2014 Interim Guidance on Patent Subject Matter Eligibility (Interim Eligibility Guidance), published 16 Dec 2014. Step 2A was revised to include two prongs (Federal Register / Vol. 84, No. 4 / 07 Jan 2019).
Analysis is as follows:
Step 1: Is the claim drawn to one of the statutory categories of invention?
Step 1: The claim is directed to a composition of matter (a nucleic acid construct).
Step 1: Yes.
Step 2A, Prong One: Is the claim drawn to a judicial exception (a law of nature, a natural product/phenomenon, or an abstract idea)?
Step 2A, Prong One: The composition of matter (a nucleic acid construct) is directed to a natural product. The claim recites a composition that is not markedly different from bacterial CRISPR/Cas systems, such as the one in S. pyogenes described by Deltcheva.
Step 2A, Prong One: Yes.
Step 2A, Prong Two: Does the claim recite additional elements that integrate the judicial exception into practical application of the exception?
Step 2A, Prong Two: This exception is not integrated into practical application because the claims do not recite additional elements that integrate the judicial exception into practical application. The claims merely recite known features of bacterial CRISPR/Cas systems.
Step 2A, Prong Two: No.
Step 2B: Does the claim recite additional elements that individually or in combination amount to significantly more than the judicial exception (i.e., whether the additional elements provide an inventive concept)?
Step 2B: The claims merely recite known features of bacterial CRISPR/Cas systems. There are no additional elements in the claims that could amount to significantly more.
Step 2B: No.
The markedly different characteristics analysis performed in Step 2A, Prong One is a comparison of the nature-based product limitation to its naturally occurring counterpart in its natural state. Markedly different characteristics can be expressed as the product’s structure, function, and/or other properties. Product of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart. See MPEP § 2106.04(b)(II). If the claim recites a nature-based product limitation that does not exhibit markedly different characteristics, the claim is directed to a product of nature exception, and the claim will require further analysis to determine eligibility based on whether additional elements add significantly more to the exception. In accordance with this analysis, a nucleic acid construct, for example, is eligible when there is a resultant change in characteristics sufficient to show a marked difference from naturally occurring bacterial CRISPR/Cas systems. It is concluded here that the claimed nucleic acid construct is not markedly different from its naturally occurring counterpart, the S. pyogenes genome, as the claim does not recite structural limitations that distinguish the nucleic acid construct composition from the composition of the S. pyogenes genome.
The Supreme Court has identified several considerations for determining whether a claim with additional elements amounts to significantly more than the judicial exception itself. Limitations that may qualify as significantly more when recited in a claim with a judicial exception include: improvements to another technology or technical field; improvements to the functioning of the computer itself; applying the judicial exception with, or by use of, a particular machine; effecting a transformation or reduction of a particular article to a different state or thing; adding a specific limitation other than what is well-understood, routine and conventional in the field, or adding unconventional steps that confine the claim to a particular useful application; or other meaningful limitations beyond generally linking the use of the judicial exception to a particular technological environment.
Limitations that were found not to be enough to qualify as significantly more when recited in a claim with a judicial exception include: adding the words ‘apply it’ (or an equivalent) with the judicial exception; mere instructions to implement an abstract idea on a computer; simply appending well-understood, routine and conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception; adding insignificant extra-solution activity to the judicial exception; or generally linking the use of the judicial exception to a particular technological environment or field of use.
In the instant case, the limitations of the claims do not impose limits on the scope of the claim such that the nucleic acid construct is markedly different from a naturally occurring product. Accordingly, based on analysis of the claim as a whole, claims 1-2, 4, 6, 8, 16-19, 21-23, 28, 33-34, 36 and 38 do not recite additional elements adding significantly more than the judicial exception and is thus rejected under 35 U.S.C. § 101 because the claimed invention is not directed to patent eligible subject matter.
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.
Claims 1-2, 4, 6, 8, 12, 14, 16-19, 21-23, 26, 28, 33-34, 36 and 38 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Campa (C.C. Campa, et al., Nat Method, 2019, cited in the IDS filed 11 Nov 2024) as evidenced by Gilchrist (D.A. Gilchrist, et al., Genes Dev, 2012).
Regarding claims 1 and 38, Campa discloses a nucleic acid construct comprising an EF1a promoter controlling expression of Cas12a (promoter module comprising at least one promoter operator of a first sequence) and a gene-editing array comprising sequences that encode for five CRISPR guide RNAs (gRNA) (at least one array sub-module comprising at least a first nucleic acid region that encodes for a nucleic acid capable of directing RNA-mediated gene-editing) (Results pp. 888-889 and Fig 2). Transcription of the array module in the nucleic acid construct disclosed by Campa is under the control of the EF1a promoter (the gene-editing array module is operably linked to the promoter module), is transcribed into a single mRNA transcript (gene-editing array module is capable of being transcribed into a single polycistronic nucleic acid transcript from a single promoter), and comprises spacers between the gRNA sequences that are cleaved after transcription by the Cas12a RNAase domain (between each nucleic acid region that encodes a nucleic acid capable of directing RNA mediated RNA mediated gene-editing is a sequence that when in RNA form is an RNA cleavage site and array operator of a second sequence) (Introduction p. 887, Results pp. 888-889, and Fig 2).
No definition is provided in the specification for "array operator". Therefore, under broadest reasonable interpretation, the array operator is interpreted to mean any composition within or that associates with the gene regulation or gene editing array and results in a change in a second protein or nucleic acid sequence. The spacers are considered to be array operators of a second sequence as the spacers are located within the array module and as cleavage of the spacers by Cas12a allows for the gRNA to direct editing of the host genome (second sequence) (Results pp. 888-889).
Regarding claim 2, the sequence of the EF1a (promoter operator of a first sequence) and the spacers between the sequence encoding for gRNA (at least one array operator of a second sequence) in the nucleic acid construct disclosed by Campa are different (part (iv)) (Results pp. 888-889 and Fig 2).
Regarding claim 4, the gene-editing array in the nucleic acid construct disclosed by Campa comprises five array sub-modules, each flanked by spacers (each sub-module comprises at least 2 array operators of a second sequence, part (b), between 2 and 100 array sub-modules, part (d)(i), at least 2 array sub-modules, part (d)(iii)) (Results pp. 888-889 and Fig 2).
Regarding claim 6, the gene-editing array in the nucleic acid construct disclosed by Campa comprises spacers (array operators of a second sequence) located upstream and downstream of each gRNA sequence (parts (a) and (b)) (Results pp. 888-889 and Fig 2).
Regarding claims 8 and 14, EF1a promoter (promoter operator of a first sequence) in the gene-editing array in the nucleic acid construct disclosed by Campa is capable of binding to polymerase II (Pol II, first activator protein, claim 8 (a)(i) and claim 14 (a)(i)) (Introduction p. 887, Results pp. 888-889, and Fig 2). Pol II binds to promoter sequences prior to induction and Pol II transcriptional activity is inducible by numerous stimuli (Gilchrist p.933). Therefore, Pol II is an inducible promoter capable of binding to EF1a in the presence of an inducing agent (claim 8 (a)(ii) and claim 14 (a)(ii)). Campa further discloses in alternative embodiment a nucleic acid construct comprising the same elements and further comprising a U6 promoter controlling expression of the gRNA sequences, which is a polymerase III (Pol III) promoter (claim 14 (b)(i) and (b)(ii)) (Introduction p. 887, Results pp. 888-889, and Fig 2c).
Regarding claim 12, Campa discloses in an alternative embodiment a nucleic acid construct comprising repeats of a TetO sequence (TetO operator, part (a)(i)) upstream of a minCMV promoter controlling expression of Cas12a and a gene editing array comprising gRNA complementary to DNMT1 that is flanked by Cas12a cleavage sites (Results p. 888, Methods p. 894, and Supp Fig. 1). The TetO sequence disclosed by Campa has the sequence tccctatcagtgatagaga, which has 100% sequence identity to the sequence set forth in SEQ ID NO. 1 (parts (a)(ii) and (a)(iii)) (Methods p. 894 and Supplementary Information p. 13).
Regarding claim 16, the gRNA in the gene-editing array in the nucleic acid construct disclosed by Campa are each complementary to a region of the host genome based on Watson-Crick base pairing, including FANCF, EMX1, GRIN2B, VEGFA, and DNMT1 (the nucleic acid region that encodes a nucleic acid that is capable of directing RNA mediated gene regulation or RNA mediated gene editing is complementary to a target nucleic acid region, part (a)) (Introduction p. 887, Results pp. 888-889, and Fig 2).
Regarding claim 17, the gRNA in the gene-editing array in the nucleic acid construct disclosed by Campa are each capable of interacting with Cas12a to direct RNA-mediated gene editing when transcribed into RNA form (parts (a) and (b)) (Results pp. 888-889, and Fig 2).
Regarding claim 18 and 21, the cleavage sites in the gene-editing array in the nucleic acid construct disclosed by Campa are cleavable by the RNA endonuclease activity of Cas12a (claim 18 parts (ii), (vii), and (viii) and claim 21 parts (a), (b)(i), (b)(v), and (b)(vi)) (Introduction p. 887, Results pp. 888-889, and Fig 2).
Regarding claims 19 and 23, the nucleic acid construct disclosed by Campa encodes for Cas12a (a first regulatory peptide, claim 19 parts (a) and (b)) (Results pp. 888-889, and Fig 2). Campa further discloses in an alternative embodiment a nucleic acid construct comprising the same elements but with Cas12a substituted for a DNase dead Cas12a (ddCas12a) with a Krüppel associated box (KRAB) domain of the transcriptional repressor ZNF10 (KRAB-like effector) fused to the C-terminus of ddCas12a (wherein the first regulatory peptide is fused to a repressor domain and first repressor protein) and with the gRNA substituted for gRNA directed to RAB51, RAB7, EEA1, and PIK3C3 (claim 19 parts (e) and (f)(i)(B) and claim 23 part (ii)(a)) (Results pp. 889-890 and Fig. 3).
Regarding claim 22, Campa discloses a nucleic acid construct comprising two nucleic acid sequences, the first nucleic acid sequence comprising a EF1a promoter controlling transcription of a sequence encoding siT-Cas12a-[Repr] (first nucleotide region encoding a first regulatory peptide operably linked to a promoter region, part (a)) and a second nucleic acid sequence comprising a EF1a promoter controlling transcription of a sequence encoding siT-Cas12a-[Activ] (second nucleotide region encoding a second regulatory peptide operably linked to a promoter region, part (b)) (Results p. 891 and Fig. 5). Each of siT-Cas12a-[Repr] and siT-Cas12a-[Activ] is capable of cleaving spacers located between gRNA (nucleic acid region encoding a polypeptide capable of cleaving the cleavage site present in the array module when in RNA for mis operably linked to a promoter region, part (c)) (Results p. 891 and Fig. 5).
Regarding claims 26 and 28, Campa discloses transfection of the nucleic acid construct into HEK293T cells using Lipofectamine® as a vector (cell comprising a vector comprising the nucleic acid construct) (Methods p. 894). Campa discloses transcription of the nucleic acid construct in the HEK293T cells under the control of an EF1a promoter (promoter module) and that the transcript comprises sequences encoding for Cas12a (regulatory polypeptide and nuclease capable of cleaving the nucleic acid as the cleavage sites when in RNA form) and multiple gRNA separated by cleavage sites (polycistronic) (parts (a) through (c)) (Introduction p. 887, Results pp. 888-889, and Fig 2).
Regarding claims 33-34 and 36, Campa discloses a method of RNA-mediated gene regulation comprising transfection of HEK293T cells with Lipofectamine® comprising of a nucleic acid construct comprising a DNase dead Cas12a (ddCas12a) with a Krüppel associated box (KRAB) domain of the transcriptional repressor ZNF10 (KRAB-like effector) fused to the C-terminus of ddCas12a under control of a TetO operator and a minCMV promoter and a gRNA array directed to RAB51, RAB7, EEA1, and PIK3C3 (Results pp. 889-890, Methods p. 894, and Fig. 3). Addition of doxycycline (inducer molecule, claim 33 (a) and claim 34 (b)(i)) induces transcription of the nucleic acid construct and ddCas12a-KRAB-gRNA-associated regulation of the transcription of genes corresponding the gRNA array (maintaining the cell in culture conditions suitable for the expression of the array module, claim 33 (b)) (Results pp. 889-890, Methods p. 894, and Fig. 3). The ddCas12a fusion protein retains endoribonuclease activity capable of cleaving the spacer sequences between the gRNA sequences (claim 34 (a)(i) and (a)(ii)) (Results pp. 889-890, Methods p. 894, and Fig. 3). The method results in changes in transcription of RAB51, RAB7, EEA1, and PIK3C3 (process of producing at least one organic molecule) (Fig. 3A).
Claims 1-2, 4, 6, 8, 16-19, 21-23, 28, 33-34, 36 and 38 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Deltcheva (E. Deltcheva, et al., Nature, 2011) and as evidenced by Nuñez (J.K. Nuñez, et al., Nat Struc Mol Biol, 2014).
Regarding claims 1 and 38, Deltcheva teaches analysis of the CRISPR01 operon within the S. pyogenes genome (nucleic acid construct), which comprises an endogenous promoter (promoter module comprising at least one promoter operator of a first sequence) and a gene-editing array module comprising six clustered, regularly interspaced short palindromic repeat (CRISPR) RNAs (crRNAs, polycistronic array of nucleic acids capable of directing RNA-mediated gene editing) (pp. 602-604 and Fig. 1). The gene editing array is transcribed as a pre-crRNA (single polycistronic transcript) from the single endogenous promoter (operably linked to the promoter module), which is cleaved at spacers located between the individual crRNAs to produce mature crRNAs capable of directing gene editing (pp. 602-603 and Fig. 1). No definition is provided in the specification for "array operator". Therefore, under broadest reasonable interpretation, the array operator is interpreted to mean any composition within or that associates with the gene regulation or gene editing array and results in a change in a second protein or nucleic acid sequence. The spacers are considered to be array operators of a second sequence as the spacers are located within the array module and as cleavage of the spacers allows for mature, individual crRNA to direct editing of the host genome (second sequence) (pp. 602-603 and Fig. 1).
Regarding claim 2, the sequence of the endogenous promoter and the spacers are different (part (iv)) (pp. 602-603 and Fig. 1).
Regarding claim 4, the gene-editing array of CRISPR01 comprises six crRNA, each flanked by spacers (each sub-module comprises at least 2 array operators of a second sequence, part (b), between 2 and 100 array sub-modules, part (d)(i), between 5 and 95 array-sub-modules, part (d)(ii), and at least 2 array sub-modules, part (d)(iii)) (pp. 602-603 and Fig. 1).
Regarding claim 6, the gene-editing array of CRISPR01 comprises spacers (array operators of a second sequence) located upstream and downstream of each crRNA (parts (a) and (b)) (pp. 602-603 and Fig. 1).
Regarding claim 8, expression of the gene-editing array of CRISPR01 is driven by an endogenous promoter (pp. 602-603 and Fig. 1). Because the sequence is expressed, the ability of the promoter to bind to an activator protein is considered inherent (capable of binding to a first activator protein, part (a)(i)).
Regarding claim 16, the crRNA of CRISPR01 are complementary to regions of the host genome comprising invading phages or plasmids (nucleic acid region capable of directing RNA mediated gene editing is complementary to a target nucleic acid region, part (a)) (p. 602).
Regarding claim 17, the crRNA of CRISPR01 associate with RNase III and Csn1 for maturation, which allows for the crRNA to direct editing genes of invading phages or plasmids (each are independently capable of associated with a regulatory polypeptide, wherein said polypeptide is capable of regulating a gene, part (a)) (pp. 602-605 and Fig. 3-4). No limiting definition is provided for what the inventor regards as a Cas9-like protein. Therefore, Csn1 is regarded as a Cas9-like polypeptide because both Csn1 and Cas9 are Cas proteins (part (b)) (p. 602).. Furthermore, the activity of Csn1 and RNase III are required for crRNA maturation, which is required for RNA-mediated gene editing of target sequences; therefore, Csn1 and RNase III are regarded as polypeptides capable of regulating a gene (parts (a) and (b)) (pp. 604-605).
Regarding claim 18, the spacers in the gene editing array of CRISPR01 comprise cleavage sites for RNase III (an endoribonuclease cleavage site, part (ii) (p. 605 and Fig. 4). The spacers have no further known function (transcriptionally inert, part (i)) (pp. 602-603 and Fig. 1).
Regarding claim 19, CRISPR01 comprises a sequence encoding for Csn1 (first nucleotide region encoding a first regulatory polypeptide, part (a), a Cas9-like polypeptide, part (b) (pp. 602-603 and Fig. 1). CRISPR01 further comprises sequences encoding for Cas1 and Cas2 (second nucleotide region encoding a second regulatory polypeptide, part (c), a Cas9-like polypeptide, part (d)) (Fig. 1).
Regarding claim 21, the S. pyogenes genome (nucleic acid construct) comprises a sequence encoding RNase III, which cleaves the spacers within the pre-crRNA (polypeptide that is capable of cleaving the cleavage site present in the array module when in RNA form, part (a), an endoribonuclease, part (b)(i)) (pp. 602 and 604-605 and Fig. 4).
Regarding claim 22, transcription of Csn1, Cas1, and Cas2 are driven by a single endogenous promoter and transcription of RNase III is driven by the rnc gene promoter (parts (a) through (c) (pp. 602-603 and Fig. 1).
Regarding claim 23, CRISPR01 comprises sequences encoding for Cas1 and Cas2 proteins (Fig. 1). Note that no limiting definition is provided in the specification for "activator protein" or for "repressor protein". Therefore, any protein that drives gene editing and/or regulation activity of the nucleic acid construct is regarded as an activator protein. Likewise, any protein that limits gene editing and/or regulation of the nucleic acid construct is regarded as a repressor protein. As taught by Nuñez, Cas1 activity is required for CRISPR/Cas-based gene editing in bacterial species (activator protein, part (i)(a)) (pp. 528 and 532). However, in the absence of Cas2, Cas1 endonuclease activity is not limited to CRISPR loci; thus, Cas2 acts as a brake on Cas1 (repressor protein, part (ii)(a) (Nuñez pp. 528 and 532-533).
Regarding claim 28, CRISPR01 is located in the genome of S. pyogenes and is expressed as a single transcript from an endogenous promoter (a cell comprising the nucleic acid construct, part (a), and a single polycistronic nucleic acid transcript, part (c)) (p. 602-603 and Fig. 1).
Regarding claim 33, S. pyogenes CRISPR/Cas activity is induced by invasion of a phages or foreign plasmid (inducer molecule) (contacting the cell with an inducer molecule, part (a), maintaining the cell in culture conditions suitable for expression of the array module, part (b)).
Regarding claim 34, S. pyogenes CRISPR/Cas activity requires expression of RNase III, which cleaves the spacer sites in the pre-crRNA (contacting the cell with a nuclease capable of cleaving the cleavage site when in RNA form, parts (a)(i) and (a)(ii)) (pp. 602-604 and Fig. 1 and 4).
Regarding claim 36, S. pyogenes CRISPR/Cas activity results in expression of tracrRNA (trans-activating CRISPR RNA), Cas1, Cas2, Csn1, RNase III, and multiple crRNA (producing at least one organic molecule) (p. 602).
Conclusion
No claim is allowed.
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Eric B Wright, PhD
Examiner
Art Unit 1632
/Eric B Wright/Examiner, Art Unit 1632
/PETER PARAS JR/Supervisory Patent Examiner, Art Unit 1632
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