DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status
This action is written in response to applicant’s correspondence received on 7/17/2023. Claims 1-32 are pending. Claims 4-6, 8, 10-12, 19-20, 22-24, 27, 29, and 31 have been amended. Claims 16-28 have are withdrawn from consideration because they are drawn to a non-elected invention. Claims 1-15 and 29-32 are currently under examination.
Election/Restrictions
Applicant’s election without traverse of invention Group I, which reads on claims 1-15 and 29-32, in the reply filed on 2-6-2026 is acknowledged. Accordingly, claims 16-28 are not presently under examination as they are drawn to a non-elected invention. Furthermore, the Applicant has elected the following species: RNAse with SEQ ID NO: 49, RNAse dimer of SEQ ID NO: 57, NLS species SEQ ID NO: 110, and fusion protein species with SEQ ID NO: 732 and SEQ ID NO: 49. The following rejection is made with these elections taken into consideration.
Drawings
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
Claim Rejections - 35 USC § 112
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.
Claim 30 is 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.
Regarding claim 30, claim 30 recites “the method of claim 23,” however, claim 23 is drawn to a nucleic acid, not a method. It is therefore unclear to which “method” claim 30 is meant to refer, or from what claim claim 30 is meant to depend.
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, 6, and 11-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more.
Regarding claim 1, claim 1 recites a fusion protein comprising a Cas protein and RNAse protein. Per the specification, a “protein” is defined as including a fragment of a protein, fusion protein, and any length of amino acid which is at least two amino acids in length (page 9, fifth paragraph). Thus, a fusion protein, as presently recited, broadly includes a naturally occurring protein which comprises a Cas domain and RNAse domain. As evidenced by Anderson (US 2019/0365781 A1), Cas13a proteins naturally comprise HEPN domains, which are RNAse domains (e.g., paragraph 320). Thus, claim 1 is drawn to a naturally occurring product of nature (Step 2A, prong 1 of the Subject Matter Eligibility Test, MPEP 2106). Furthermore, claim 1 does recite any additional elements which render markedly different characteristics onto the claimed product or integrate the product into a practical application (Step 2A, prong 2). Additionally, claim 1 does not recite any additional elements which would transform the claim into significantly more than the judicial exception (Step 2B). Thus, claim 1 is drawn to naturally occurring products of nature, as such “fusion proteins” can be broadly interpreted to be naturally occurring Cas13a proteins, which comprise RNAse domains (Anderson, paragraph 320).
Regarding claim 6, claim 6 recites the judicial exception of claim 1 (Step 2A, prong 1). Claim 6 recites the additional element that the RNAse is a dimer. However, as taught by Anderson, Cas13a naturally comprises two HEPN domains (i.e., a dimer), where the HEPN domains are nucleases (paragraph 320). Thus, the additional elements recited in claim 6 include naturally occurring characteristics of Cas proteins without markedly different characteristics, where furthermore the elements are not integrated into a practical application (Step 2A, prong 2). Furthermore, claim 6 does not recite additional elements which would transform the claim into significantly more than the judicial exception (Step 2B). Claim 6 is therefore not subject matter eligible.
Regarding claims 11-12, these claims are directed to naturally occurring components of a cell which comprises a Cas13a protein. For instance, Anderson teaches that Cas13 occurs in a natural or “wildtype” form (paragraph 320), where such proteins occur naturally within organisms (paragraph 321). Thus, given that the gene is derived from a naturally occurring organism, it follows that the gene is encoded within a nucleic acid within the genome of the organism (Anderson, paragraphs 320-321, claims 11-12). Thus, the additional elements recited in claims 11-12 are also naturally occurring products of a bacterial cell which encodes Cas13a; claims 11-12 do not recite additional elements which would integrate the exception into a practical application (Step 2A, prong 2) or transform the claim into significantly more than the judicial exception (Step 2B). Claims 11-12 are therefore not subject matter eligible.
Regarding claims 13-15, these claims are drawn to naturally occurring components of the CRISPR/Cas system which is present within the bacterial organisms taught by Anderson (paragraph 321). For instance, Anderson teaches that such CRISPR/Cas Cas13a proteins function with targeting nucleic acid molecules, i.e., crRNA (e.g., paragraph 317-318).
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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, 6, 8, 11-15, and 29-31 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Anderson (US 2019/0365781 A1, published 12/5/2019).
Regarding claim 1, Anderson teaches Cas proteins which are fused with RNAse proteins (paragraph 320). Note that the present specification defines a “protein” and “polypeptide” or “peptide” to mean the same thing, where the specification teaches that a protein is any such amino acid sequence comprising two amino acids, and furthermore the terms can mean a biological active fragment (page 9, fifth paragraph). Thus, the Cas13a proteins which comprise two HEPN RNAse domains taught by Anderson reasonably read on the instantly recited fusion proteins comprising Cas and a RNAse, as such a fusion protein can be broadly interpreted to mean the Cas13a protein fused with two HEPN RNAse domains (i.e., biologically active fragments or amino acid sequences of at least two amino acids) taught by Anderson (paragraph 320).
Regarding claim 2, Anderson teaches that the Cas can be a dCas13 (e.g., paragraph 23).
Regarding claim 6, Anderson teaches that the RNAse can be a Cas13a which comprises two HEPN RNAse domains (i.e., a dimer, paragraph 320).
Regarding claim 8, Anderson teaches that the effector domains, which comprise nucleases, of their proteins can comprise nuclear localization signals (NLS, e.g., paragraph 424).
Regarding claims 11-12, Anderson teaches that the components of their system may be encoded in a nucleic acid and be comprised in a composition (e.g., paragraph 329).
Regarding claims 13-14, Anderson teaches that their systems can comprise Cas13a along with targeting nucleic acid molecules such as crRNA (e.g., paragraph 267).
Regarding claim 15, Anderson teaches that targeting nucleic acids can comprise DNA (e.g., see paragraph 266, final 6 lines).
Regarding claims 29-30, Anderson teaches that their methods involve complexing Cas effector proteins with guide nucleic acid sequences to target polynucleotides (e.g., paragraph 331). Anderson teaches that the method can involve using Cas13a to edit or target an RNA transcript (paragraph 327). As discussed above in the rejection of claim 1, Cas13a as taught by Anderson comprises a Cas protein fused with an RNAse. Anderson teaches that their methods can be performed in a subject either in vitro or in vivo (e.g., paragraph 329). Note that for the sake of this 102 rejection, claim 30 is being interpreted to depend from claim 29 (see 112(b) rejection, above).
Regarding claim 31, Anderson teaches the limitations of claim 31 with regards to the components involved in the method are addressed in the rejection of claims 29-30, above. Furthermore, Anderson teaches that their methods involve the introduction of such components to a subject in order to treat a disease (e.g., see paragraphs 518 and 329).
Additional 102 Rejection
Claims 1-2, 5-6, 8, 11-15, and 29-32 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hsu (US 2019/0062724 A1, published 2/28/2019). The rejection is further evidenced by Anderson (US 2019/0365781 A1, published 12/5/2019).
As an initial matter, this additional 102 rejection is made using the interpretation that claim 1 is directed to a Cas protein which does not naturally comprise an RNAse domain but has an additional fusion of an RNAse domain. Such a product is known in the art, as taught by Hsu as illustrated below.
Regarding claim 1, Hsu teaches fusion proteins comprising a Cas protein and an RNAse:
“the Cas13d protein has a native HEPN domain(s) or is fused to
an appropriate effector domain bearing RNase activity, the
RNA can be cut,” (paragraph 437).
Thus, Hsu teaches Cas13 proteins fused to RNAse proteins (paragraph 437).
Regarding claim 2, Hsu teaches dCas13 (e.g., paragraphs 520-522).
Regarding claim 5, Hsu teaches that the Cas13 protein can be further fused with a PIN RNAse (paragraph 383).
Regarding claim 6, Hsu teaches that the Cas13 protein can comprise multiple RNAse domains (paragraph 383). Furthermore, Hsu teaches that Cas13 comprises HEPN “domains,” plural, which reasonably includes at least two (paragraph 437 and paragraph 383). As evidenced by Anderson, HEPN domains are RNAse domains (Anderson, paragraph 320). Thus, the Cas13 proteins taught by Hsu comprise RNAse dimers, as they comprise multiple HEPN domains, and furthermore can comprise multiple additional RNAses which, being fused to the Cas13 protein, are reasonably interpreted to be dimers (paragraph 383).
Regarding claim 8, Hsu teaches that the Cas13 protein can comprise an NLS (e.g., paragraph 382).
Regarding claims 11-12, Hsu teaches the fusion proteins can be encoded in a nucleic acid (e.g., paragraph 340).
Regarding claims 13-14, Hsu teaches that the kits and compositions of their invention can comprise targeting nucleic acids such as crRNA (e.g., paragraph 410).
Regarding claim 15, Hsu teaches that targeting nucleic acids can be DNA oligos (e.g., paragraph 496).
Regarding claim 29, Hsu teaches the components of the system recited in the method of claim 29, including a Cas protein fused with an RNAse (see rejection of claim 1). Hsu further teaches that such a system can be sued to target an RNA:
“If the Cas13d protein has a native HEPN domain(s) or is fused to
an appropriate effector domain bearing RNase activity, the
RNA can be cut,” (paragraph 437).
Hsu further teaches that their methods can be used to degrade target transcript RNA using targeting nucleic acids like gRNA (paragraph 482 and also 488).
Regarding claim 30, Hsu teaches that their targeting methods can be used either in vitro or in vivo (paragraph 436).
Regarding claims 31-32, Hsu teaches that their methods can be used to target viral RNAs to treat disease, where the Cas13 protein and its effector domains of their invention is paired with a targeting nucleic acid/gRNA to target RNA viruses (e.g., paragraph 489). Furthermore, Hsu also teaches that the method can be used to treat Myotonic dystrophy (paragraph 449).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Hsu (US 2019/0062724 A1, published 2/28/2019) as applied to claims 1-2, 5-6, 8, 11-15, and 29-32 in the 102 rejection, above, and further in view of Yeo (WO 2019/204828 A1, published 10/24/2019).
Regarding claim 3, as discussed above, Hsu teaches Cas13 fusion proteins which can be fused to RNAses (e.g., see paragraph 437). In addition, Hsu specifically teaches the Cas13b protein PspCas13b (paragraph 32, 498, 532, and Figure 10A). Thus, Hsu teaches that PspCas13b is a known, functional Cas13b enzyme which can be used with their methods.
Hsu does not explicitly teach that the sequence of PspCas13b is SEQ ID NO: 47 (Applicant’s elected species).
Yeo is a patent document which teaches methods and systems involving Cas effector proteins and RNA targeting (Title, Abstract, and throughout). Yeo and Hsu therefore directly overlap in subject matter and field of endeavor. Furthermore, Yeo teaches the sequence of PspCas13b (SEQ ID NO: 79, see page 161). An alignment of Yeo’s SEQ ID NO: 79 and instant SEQ ID NO: 47 are a 100% match (see page 1 of Yeo). Thus, SEQ ID NO: 47 is the known sequence of PspCas13b, a Cas13 enzyme also taught by Hsu (Hsu paragraphs 32, 498, 532, Figure 10A, and page 161 of Yeo).
It would have been obvious to a person of ordinary skill in the art before the effective filing date to apply the sequence information taught by Yeo with the systems taught by Hsu, and furthermore to use PspCas13b in the systems and methods of Hsu, because such a combination is the simple substitution of one known prior art element for another with predicable results. In the present case, a practitioner would simply exchange the Cas13b enzymes taught by Hsu with Yeo’s PspCas13b sequence. This substitution is especially obvious in light of the fact that Hsu already teaches PspCas13b, where Yeo is simply supplying the sequence. Furthermore, the results are obvious because Hsu not only teaches PspCas13b but also reduces it to practice and shows that it is a functional Cas enzyme (e.g., Figure 10A).
Claims 4 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Hsu (US 2019/0062724 A1, published 2/28/2019) as applied to claims 1-2, 5-6, 8, 11-15, and 29-32 in the 102 rejection, above, and further in view of Posada (WO 2018/005954 A2).
Regarding claim 4, the teachings of Hsu with regards to claims 1-2, 5-6, 8, 11-15, and 29-32 are incorporated herein. Hsu teaches that Cas13 proteins are fused with RNAses, and furthermore teaches that multiple RNAses can be fused to Cas13 including in the form of homodimers (paragraphs 383 and 437). Hsu offers numerous non-limiting examples of RNAses (e.g., paragraph 383).
Hsu does not specifically teach that the RNAse comprises SEQ ID NO: 49.
Posada is a patent document which focuses on RNAse fusion proteins (Title, Abstract, and throughout). Posada and Hsu therefore directly overlap because they both focus on engineered fusion of RNAses. Posada teaches and reduces to practice dimer fusion proteins comprising SEQ ID NO: 4 (see Example 1, page 67). An alignment of Posada’s SEQ ID NO: 4 and instant SEQ ID NO: 49 is shown below:
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488
1282
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As seen above, Posada’s SEQ ID NO: 4 is a 100% match of instant SEQ ID NO: 49. Furthermore, Posada has reduced to practice chimeric RNAse dimers using SEQ ID NO: 4 (example 1, page 67). Furthermore, Posada singles out SEQ ID NO: 4 as a preferred embodiment of an RNAse (e.g., claim 22 of Posada). Thus, Posada teaches that instant SEQ ID NO: 49 is a known RNAse sequence, where furthermore such a sequence has already been reduced to practice as a dimer, where such teachings give a reasonable expectation of success that such an RNAse would retain its function as a fusion protein and/or dimer.
Regarding claim 7, claim 7 recites SEQ ID NO: 57. SEQ ID NO: 57 is simply a dimer (two copies) of SEQ ID NO: 49 (see page 148 of specification, which identifies SEQ ID NO” 57 as a tandem dimer of human RNAse 1, i.e., SEQ ID NO: 49, per page 148 of specification). Thus SEQ ID NO: 57 is simply a homodimer of SEQ ID NO: 49.
It would have been obvious to a person of ordinary skill in the art before the effective filing date to combine the teachings Hsu and Posada, where Hsu teaches Cas13b proteins fused to RNAase dimers including homodimers and heterodimers and Posada teaches instant SEQ ID NO: 49 as a known RNAse that can be fused as a dimer and retains its functionality, as such a combination is the simple combination of known prior art elements with predictable success. In the present case, a practitioner would be combining the known RNAse of Posada to the RNAse fusion Cas proteins taught by Hsu, either individually (claim 4) or as a tandem homodimer (claim 7). Furthermore, such a combination is predictable because Posada has already reduced such dimers to practice and Hsu teaches that Cas fusions can comprise RNAse homodimers or heterodimers.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Hsu (US 2019/0062724 A1, published 2/28/2019) as applied to claims 1-2, 5-6, 8, 11-15, and 29-32 in the 102 rejection, above, and further in view of Voytas (US 6,228,647 B1, issued 5/1/2001).
Regarding claim 9, the teachings of Hsu are discussed above in the rejection of 102 and are incorporated here. Hsu teaches the elements of claim 1, and furthermore teaches that such fusion proteins can comprise nuclear localization signals (NLS).
Hsu does not teach the NLS is SEQ ID NO: 110 (Applicant’s elected species).
Voytas is a patent document which focuses on methods of genetic manipulation at targeted sites, and therefore overlaps in subject matter with Hsu (Title, Abstract, and throughout). Furthermore, Voytas teaches the Ty1 NLS sequence, and specifically identifies the region of Ty1 which is critical for its functionality as an NLS (see Figure 2B, partially reproduced below):
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74
1189
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Voytas teaches that, with regards to Figure 2B reproduced above:
“Lines above Ty1 amino acid residues indicate sequences important for nuclear localization [Kenna et al. (1997); Moore et al. (1997),” (column 4, 5th paragraph).
An alignment of the section of Ty1 underneath the “lines” in Figure 2B with instant SEQ ID NO: 110 is shown below:
NSKKRSLEDNETEIKVSRDTWNTKNMRSLEPPRSKKRIH – Figure 2B, Voytas
NSKKRSLEDNETEIKVSRDTWNTKNMRSLEPPRSKKRIH – SEQ ID NO: 110
As shown above, the NLS signal taught by the region of Voytas to be critical as an NLS is 100% identical to instant SEQ ID NO: 110. Furthermore, Voytas references Kenna and Moore when describing the NLS sequence; thus, instant SEQ ID NO: 110 was an established NLS well-known in the art at the time of filing.
It would have been obvious to a person of ordinary skill in the art to exchange the NLS sequence taught by Hsu with the Ty1 NLS sequence taught by Voytas because such a combination is the simple substitution of one known prior art element for another with predictable results. In the present case, the practitioner would simply exchange the NLS of Hsu for the art-recognized NLS taught by Voytas. Furthermore, the result is predictable because, as taught by Voytas, the Ty1 NLS (i.e., SEQ ID NO: 110) was an art-established NLS which would therefore produce expected results.
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Hsu (US 2019/0062724 A1, published 2/28/2019) as applied to claims 1-2, 5-6, 8, 11-15, and 29-32 in the 102 rejection, above, and further in view of Yeo (WO 2019/204828 A1, published 10/24/2019), Posada (WO 2018/005954 A2), Voytas (US 6,228,647 B1, issued 5/1/2001), and Reddy Chichili (Reddy Chichili VP et al. Protein Sci. 2013 Feb;22(2):153-67).
Regarding claim 10, as an initial matter, Applicant has elected SEQ ID NO: 732 and SEQ ID NO: 49. Regarding SEQ ID NO: 732, per the Applicant’s specification, SEQ ID NO: 732 is a sequence which comprises a 3x FLAG tag, Ty1 NLS, and dPspCas13b, followed by a linker and RNAse (in this case, the RNAse is the RNAse SEQ ID NO: 49). As addressed above in the rejections of claims 1-4, the prior art teaches each of these elements with the exception of a linker. For instance, Voytas teaches NLS Ty1 (see rejection of claim 9), Hsu/Yeo teach dPspCas13b (see rejection of claim 3), and Posada teaches the known RNAse sequence of SEQ ID NO: 49 (see rejection of claim 4 and 7, above). In addition, Hsu also teaches FLAG tagging as a method of purification/tagging (e.g., paragraph 387). Thus, each of the components in SEQ ID NO: 732 are taught in the prior art. Thus, SEQ ID NO: 732 in combination with SEQ ID NO: 49 is characterized as a known Cas13b (dCas13b, Hsu/Yeo), which has a routine tag (i.e., FLAG, as taught by Hsu), a known, routine addition of a known NLS (Ty1, Voytas) fused with a known RNAse (Posada), where furthermore the fusion of Cas13b to an RNAse is already a strategy taught by Hsu.
Hsu, Yeo, Voytas, and Posada do not explicitly teach glycine rich linkers such as those in SEQ ID NO: 732.
Reddy Chichili is a review article which teaches linkers used in structural biology to join protein domains (Title, Abstract, and throughout). Reddy Chichili teaches that it is known that glycine and/or serine rich linkers, such as those used in SEQ ID NO: 732, were already known in the art as routine linkers of protein domains (Abstract).
It would have been obvious to a person of ordinary skill in the art before the effective filing date to arrive at fusion protein comprising SEQ ID NOs 732 and 49, as such a fusion protein is the simple combination of known prior art elements to arrive at a predictable result. In the present case, FLAG tagging and the addition of an NLS are routine laboratory practices as taught by Hsu and Voytas. Furthermore, Hsu has already taught the dPspCas13b in SEQ ID NO: 732, and furthermore teaches that such FLAG-tagged, NLS-bearing Cas13b proteins should be fused with RNAses to target RNAs (paragraph 437). SEQ ID NO: 49 is simply a known, functional RNAse which was known to function as a fusion protein. Additionally, linkers such as glycine and serine linkers are also routine in the art, as evidenced by Reddy Chichili’s teachings (e.g., Abstract). Thus, the combination is predictable, where each component is known and is being used for its known use.
Claims 1-15 and 29-32 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.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Regents of the University of California v. Eli Lilly & Co, 119 F.3d at 1568, 43 USPQ2d at 1406.
Regarding independent claims 1, 29, and 31, these claims are broadly drawn to systems and methods which use fusion proteins, where the fusion proteins comprise a Cas protein fused with an RNAse. Thus, the products and methods of claims 1, 29, and 31 are claiming a genus of fusion protein wherein the Cas portion can be any Cas protein and the RNAse can be any RNAse. This claim language is problematic because the Applicant has not shown sufficient species or embodiments which would show possession of this genus of fusion protein, where such a fusion protein is known in the art to comprise uncharacterized and unpredictable Cas and RNAse proteins.
Regarding the guidance provided in the specification, the Applicant has provided examples of a few fusion proteins, where dead PspCas13 was fused to a handful of RNAses (e.g., Figure 1C, and 5C-5D). The results appear to show variability in the functionality of the fusion proteins. Thus, the Applicant has provided two examples in the specification, where the results appear to show unpredictability. This point is highlighted in the specification itself, where the Applicant writes:
“However, some CRISPRases showed little to no activity, which may be due in part to substrate or sequence requirements of the RNases, necessity to homodimerize, requirements for cofactors, such as metal ions or other enzymatic conditions, for example pH, or improper folding. In this regard, among the most potent CRISPRase enzymes at this target site included the fusion to RNase Tl, which functions as a monomer and does not require metal ions for activity,” (page 168, paragraph 3 of the specification).
Thus, the Applicant acknowledges that their fusion constructs act in unpredictable ways, where not all fusion constructs function (“showed little to no activity,” above), owing to a variety of factors which are specific to the components of the fusion proteins (above). Thus, the Applicant’s specification demonstrates the unpredictability of the claimed genus of fusion protein, where the fusion protein can comprise any Cas protein or any RNase enzyme, as the Applicant has demonstrated that such combinations do not yield predictable results. Furthermore, the Applicant does not provide guidance to demonstrate core structural-functional relationships between the recited components of the fusion proteins to demonstrate possession of functional fusion proteins (i.e., the Applicant does not identify a way to reliably predict what fusion proteins would function).
Furthermore, it is known in the art that both Cas proteins and RNases can behave in unpredictable ways, where such proteins need to be structurally and functionally characterized in order to make predications about their functionality. For instance, Hu (Hu Y et al. Cell Discov. 2022 Oct 11;8(1):107) is a post-filing publication which teaches that:
“by mining bulk metagenomic data (> 10 TB) from various environments, we identified hundreds of orthologs of known and novel Cas13 systems in this study, the latter of which could be classified into five novel subtypes based on protein sequence similarity. Notably, the novel Cas13 systems discovered in this study can be developed into efficient RNA editors and expand the RNA-editing toolbox,” (Abstract).
Thus, Hu teaches that novel Cas13 enzymes with novel sequences are still being discovered. Given that the Applicant has already demonstrated unpredictability and has further acknowledged that not all Cas enzymes work in the recited fusion constructs, the Applicant can not said to have been in possession of the recited genus of fusion proteins. This is particularly true in light of the teachings of Hu, who teaches that novel sequences of Cas13 enzymes are still being discovered; the Applicant was not in possession of these sequences at the time of filing and has no way of predicting if any of the novel Cas13 enzymes of Hu would function in their recited systems and methods.
Regarding the other component of the fusion proteins recited in the independent claims (i.e., RNases), RNases are similarly known to be not fully characterized and unpredictable. For instance, Wu (Wu R et al. Res Sq [Preprint]. 2023 Dec 27:rs.3.rs-3788707) teaches the discovery of a post-filing RNase comprising a “conformation that resembles no other known RNases,” (Abstract). Thus, Wu teaches that novel RNases are still being discovered with unique and uncharacterized properties (Abstract). The Applicant has therefore not characterized the claimed fusion protein, which comprise as one portion of the fusion the genus “RNase” because RNases with unique sequences, structures, and characteristics have been discovered since the submission of the instant application; given that the Applicant has acknowledged that not all Cas/RNase fusion protein function, and offer no way of predicting functionality of such fusion, the Applicant can not be said to have shown possession of the broad genus of fusion protein given that novel RNases with unique structures are still being discovered (Wu, Abstract).
Furthermore, the claimed subject matter is further confounded by the fact that the fusion protein comprises two unpredictable and uncharacterized domains (i.e., a Cas and an RNase). Thus, the complexity and unpredictability of the claimed genus of fusion protein is compounded by the fact that each individual component of the fusion protein is uncharacterized and unpredictable. For instance, the independent claims encompass a fusion of the unpredictable novel Cas13 proteins of Hu with the unpredictable and uncharacterized RNase of Wu, where the Applicant can not said to have been in possession of such a fusion protein and/or identified if such a fusion protein would function.
In addition, regarding the method claims 29 and 31, the Applicant has not tested any methods where the fusion constructs are administered to a subject to target RNA or treat any disease. Thus, the Applicant is claiming an untested, unpredictable genus of fusion protein, where furthermore the unpredictability is compounded by the fact that the Applicant has not reduced to practice or shown that such fusion proteins would function in a subject.
Regarding claims 2, the Applicant narrows the claim language to specifically Cas13 in claim 2. However, the subject matter of claim 2 was not shown to be in possession by the Applicant. With regards to claim 2, as discussed above, Hu teaches that novel, uncharacterized Cas13 proteins are still being discovered; the Applicant was not in possession of the genus of “Cas13. (Hu, Abstract).
Regarding claim 3, claim 3 recites a specific Cas13, such as SEQ ID NO: 47, or a “variant thereof.” The Applicant was not in possession of “variants” of SEQ ID NO: 47, because they have not performed any mutagenesis analysis, or identified any structural-functional relationships between SEQ ID NO: 47 and its function as a Cas13. SEQ ID NO: 47 is identified as dPspCas13b (see specification at page 148). However, Hu 2 (Hu W et al. Nat Struct Mol Biol. 2024 Nov;31(11):1702-1716) teaches that PspCas13 is “poorly characterized” and further teaches that systematic mutational analysis is required in order to fully characterize PspCas13 (Abstract). The Applicant has not performed any structural studies, mutational analysis studies, or any other such studies in order to identify what “variant” of SEQ ID NO: 47 would function as a dCas13. As no structure-function relationship was performed, the Applicant was not in possession of “variants” of SEQ ID NO: 47, as it us unclear and unpredictable what such variants would render functional Cas13 proteins as recited.
Similarly, claim 4 also recites a specific sequence RNase, but also recites the genus of “variant” of said RNase. This claim language is problematic because the Applicant has not identified any variants of RNases which would render the recited functionality; the Applicant has not identified a core structure of the Rnases which is connected with the recited functionality of the protein (i.e., acting as a functional RNase). Furthermore, it is known in the art that variations in RNases can have profound effects on their functionality. For instance, Rohman (Rohman MS et al. FEBS J. 2008 Oct;275(19):4836-49) teaches that:
“Certain mutations in any subunit of human RNase H2 cause Aicardi–Goutie`res syndrome (AGS). AGS is an autosomal recessive genetic disorder that is phenotypically similar to in utero viral infection, leading to severe neurological defects. RNase H2 deficiency may promote the accumulation of RNA⁄DNA hybrids in cells, which may induce the innate immunity. Of these mutations, the Gly37 fi Ser mutation in the catalytic subunit (RNASEH2A) has been shown to greatly reduce enzymatic activity without seriously affecting the stability of the complex. However, it remains to be determined whether other mutations in the accessory proteins (RNASEH2B and RNASEH2C) also reduce enzymatic activity without seriously affecting complex stability. In addition, the reason why the Gly37 Ser mutation in RNASEH2A reduces the enzymatic activity remains to be clarified,” (page 4837, left column, third paragraph).
Rohman therefore teaches that minor mutations in RNases can severely affect their enzymatic functionality, where furthermore it remains to be known/clarified why such mutations reduce enzymatic activity. Thus, it was known in the art that “variants” of RNases can profoundly affect their function (above). The Applicant has not performed any structural or functional analysis on catalytic domains of, for instance, SEQ ID NO: 49, and has therefore not characterized or shown possession of the genus of “variants” of RNases such as the specific sequences recited in claim 4.
Similarly, the Applicant has not shown possession of variants of NLS sequences recited in claim 9. For example, the Applicant is claiming SEQ ID NO: 110, or a “variant’ of SEQ ID NO: 110. This claim language is problematic because it was known in the art that SEQ ID NO: 110 is a critical region for acting as an NLS. For example, Voytas (US 6,228,647 B1) teaches SEQ ID NO: 110 as the Ty1 NLS, and further teaches that the entirety of SEQ ID NO: 110 is critical for the NLS portion of Ty1 (see Figure 2B, where the lines above “Ty1” represent the region critical for NLS functionality per column 4, 5th paragraph of Voytas). The Applicant has not shown that “variants” of SEQ ID NO: 110 function as NLS, or furthermore identified what variants of SEQ ID NO: 110 would retain the functionality of being an NLS. Given that Voytas teaches that the entirety of SEQ ID NO: 110 is important for NLS functionality, the Applicant does not appear to be in possession of “variants” of SEQ ID NO: 110 which would still function as an NLS given that they have not tested any variants or shown which regions of SEQ ID NO: 110 can be mutated or deleted.
Claims 2-15, 30, and 32 depend from claims 1, 29, and 31, respectively, and do not resolve the issues of claim 1. Similarly, the dependent claims also suffer additional 112(a) issues as discussed above. Thus, the Applicant has not shown possession of the invention as presently recited.
Conclusion
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/D.C.R./Examiner, Art Unit 1635
/KIMBERLY CHONG/Primary Examiner, Art Unit 1636