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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on November 21, 2025 has been entered.
Detailed Action
This action is in response to the papers filed November 21, 2025.
Amendments
Applicant's response and amendments, filed November 21, 2025, is acknowledged. Applicant has cancelled Claims 2, 6, 9-12, and 14-20, amended Claims 1, 3, and 22-23, and added new claims, Claims 24-33.
Claims 1, 3-5, 7-8, 13, and 21-33 are pending and under examination.
Priority
This application is a 371 of PCT/US2020/61033 filed on November 18, 2020. Applicant’s claim for the benefit of a prior-filed application provisional application 62/952,744 filed on December 23, 2019 and 62/937,468 filed on November 19, 2019 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged.
Information Disclosure Statement
Applicant has filed an Information Disclosure Statement on November 21, 2025 that has been considered.
The signed and initialed PTO Forms 1449 are mailed with this action.
Allowable Subject Matter
1. The following is a statement of reasons for the indication of allowable subject matter:
Claims 1 and 22-23 recite SEQ ID NO:22 or SEQ ID NO:23.
The prior art does not teach or fairly suggest SEQ ID NO:22 and SEQ ID NO:23.
Nucleotides 1-597 of SEQ ID NO:22 are identical to nucleotides 237-833 of SEQ ID NO:23, a portion of which appear to encode a PIN endonuclease domain.
See discussion below per 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, and AIA 35 U.S.C. 103 rejections.
Takeshita et al (Crystal structure of the PIN domain of human telomerase-associated protein EST1A, Proteins 68: 980-989, 2007) and GenBank NP_001269255 (telomerase-binding protein EST1A; January 28, 2019) are considered relevant prior art for having taught a polypeptide comprising an amino acid sequence that is 100% identical to amino acids 2-183 of the amino acid sequence encoded by nucleotides 1-597 of SEQ ID NO:22, as shown below:
QMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAG
GYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLIL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLIL
SCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQ
VG
||
VG
Thus, the PilT N-terminal (PIN) domain encoded by nucleotides 1-597 of SEQ ID NO:22 or nucleotides 237-833 of SEQ ID NO:23 was previously known.
Nucleotides 598-833 of SEQ ID NO:22 encode, in part, the ZNF1 and ZNF2 zinc finger domains.
Nucleotides 598-672 of SEQ ID NO:22 encodes the ZNF1 domain of SEQ ID NO:1.
CATGAATGCCGCGTGTGCGGCGTGACCGAAGTGGGCCTGAGCGCGTATGCGAAACATATT
AGCGGCCAGCTGCAT
SEQ ID NO:1
HECRVCGVTEVGLSAYAKHISGQLH
Nucleotides 688-765 of SEQ ID NO:22 encodes the ZNF2 domain of SEQ ID NO:2.
TATCGCTGCTGGTGGCATGGCTGCAGCCTGATTTTTGGCGTGGTGGATCATCTGAAACAG
CATCTGCTGACCGATCAT
SEQ ID NO:2
YRCWWHGCSLIFGVVDHLKQHLLTDH
Celona et al (available online January 10, 2017; of record in IDS), GenBank AAH25424.1 (mouse ZFP106, 2004; of record), and GenBank AAL40184.1 (human ZFP106, 2001; of record) evidence that the zinc finger domains ZNF1 and ZFN2 were previously known in the art.
Claim Rejections - 35 USC § 112
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.
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.
2. The prior rejections of Claim(s) 12 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, are withdrawn in light of Applicant’s cancellation of the claim.
3. Claim 1, 3-5, 7-8, 13, and 21-33 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.
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 1 recites the broad recitation “a second sequence encoding the PilT N-terminal (PIN) domain” and the claim also recites “of SEQ ID NO:22 or SEQ ID NO:23” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claims 1 and 22-23 recite a nucleic acid encoding a fusion protein.
Nucleotides 1-597 of SEQ ID NO:22 are identical to nucleotides 237-833 of SEQ ID NO:23, each of which appear to encode a PilT N-terminal (PIN) endonuclease domain.
The specification fails to disclose an amino acid sequence, and it’s corresponding SEQ ID NO, for the PilT N-terminal (PIN) domain of SEQ ID NO:22 or SEQ ID NO:23.
A translation of nucleotides 1-597 of SEQ ID NO:22 yields an amino acid sequence of:
MQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQVGSGSETPGTSESATPES
GenBank NP_001269255 (telomerase-binding protein EST1A; January 28, 2019) is considered relevant prior art for having taught a polypeptide comprising an amino acid sequence that is 100% identical to amino acids 2-183 of the amino acid sequence encoded by nucleotides 1-597 of SEQ ID NO:22, as shown below:
QMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAG
GYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLIL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLIL
SCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQ
VG
||
VG
Takeshita et al (Crystal structure of the PIN domain of human telomerase-associated protein EST1A, Proteins 68: 980-989, 2007) is considered relevant prior art for having taught that amino acids 2-183 of the amino acid sequence encoded by nucleotides 1-597 of SEQ ID NO:22, as shown above, are the PilT N-terminal (PIN) domain (e.g. Figure 2a).
The recitation “second sequence encoding the PilT N-terminal (PIN) domain” renders the claim indefinite because while it is clear the fusion protein is to comprise a PilT N-terminal (PIN) domain, it is unclear if the claim is limited to nucleotides 1-597 of SEQ ID NO:22 or nucleotides 237-833 of SEQ ID NO:23, or if the claimed nucleic acid may comprise any nucleic acid sequence that encodes a PilT N-terminal (PIN) domain.
Similarly, it is unclear if the claimed nucleic acid sequence is required to comprise nucleotides 1-6 and/or nucleotides 549-597 of SEQ ID NO:22, and their corresponding amino acids, each of which apparently flank a consensus PilT N-terminal (PIN) domain.
Similarly, it is unclear if the fusion protein encoded by the claimed nucleic acid is to comprise the amino acids 1-2 and/or 184-199 encoded by nucleotides 1-597 of SEQ ID NO:22.
Where applicant acts as his or her own lexicographer to specifically define a term of a claim contrary to its ordinary meaning, the written description must clearly redefine the claim term and set forth the uncommon definition so as to put one reasonably skilled in the art on notice that the applicant intended to so redefine that claim term. Process Control Corp. v. HydReclaim Corp., 190 F.3d 1350, 1357, 52 USPQ2d 1029, 1033 (Fed. Cir. 1999). The phrase “PilT N-terminal (PIN) domain of SEQ ID NO:22 or SEQ ID NO:23” is indefinite because the specification does not clearly redefine the term.
At best, the specification only discloses a nucleotide sequence comprising a promoter operably linked to:
i) a first sequence encoding an amino acid sequence comprising SEQ ID NO:1 or SEQ ID NO:2; and
ii) a second sequence comprising nucleotides 1-597 of SEQ ID NO:22 or nucleotides 237-833 of SEQ ID NO:23, wherein said second sequence encodes a human EST1a PilT N-terminal (PIN) domain.
The instant claims as a whole do not apprise one of ordinary skill in the art of its scope and, therefore, does not serve the notice function required by 35 U.S.C. 112, second paragraph, by providing clear warning to others as to what constitutes infringement of the patent.
Dependent claims are included in the basis of the rejection because they do not correct the primary deficiencies of the independent claims.
4. Claims 22-33 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 22-23 have been amended to be directed to methods of treating a disease or disorder in a human subject, the methods comprising the step of administering by intravenous or intracranial route to said human subject 0.8x10^8 to 1.2x10^15 rAAV9 vector genomes/kg of a nucleic acid vector encoding fusion protein comprising:
i) a zinc finger domain amino acid sequence of SEQ ID NO:1 and/or a zinc finger domain amino acid sequence of SEQ ID NO:2 in combination with as many as 40 structurally and functionally undisclosed zinc finger domains, and
ii) the Pi1T N-terminal (PIN) domain of SEQ ID NO:22 (syn. nucleotides 1-597) or SEQ ID NO:23 (syn. nucleotides 237-833).
The Examiner incorporates herein the above 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, rejection.
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described by their complete structure. 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 complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of making the claimed product, or any combination thereof. The disclosure of a single species is rarely, if ever, sufficient to describe a broad genus, particularly when the specification fails to describe the features of that genus, even in passing. (see In re Shokal 113USPQ283(CCPA1957); Purdue Pharma L.P. vs Faulding Inc. 56 USPQ2nd 1481 (CAFC 2000).
The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.). See also In re Morris, 127 F.3d 1048, 1054-55, 44 USPQ2d 1023, 1027-28 (Fed. Cir. 1997).
The functional properties of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold are dependent upon many different variable parameters, including, but not limited to:
the structure/function of the zinc finger fusion protein encoded by the nucleic acid vector [parameter 1];
the disease/disorder/condition to be treated [parameter 2]; and
the phenotypic response to be achieved [parameter 3].
Parameter 1
The claims encompass an enormously vast genus of zinc finger fusion proteins comprising the zinc finger domain amino acid sequence of SEQ ID NO:1 and/or the zinc finger domain amino acid sequence of SEQ ID NO:2 in combination with as many as 40 structurally and functionally undisclosed zinc finger domains, representing an enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins that are to have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat.
Parameter 2
The claims are broad for reasonably encompassing an enormous genus of etiologically and pathologically distinct hexanucleotide repeat-associated diseases/disorders recited at a high level of generality, including, but not limited to, CNS diseases such as frontotemporal dementia (FTD) or amyotrophic lateral sclerosis (ALS).
Paulson (Chapter 9- Repeat Expansion Diseases, Handbook of Clinical Neurology 147: 105-123, 2018) is considered relevant prior art for having taught that there are more than 40 known diseases caused by expansion of simple sequence repeats, including, but not limited to myotonic dystrophy, Huntington’s disease, polyglutamine disorders, Friedrich ataxia, spinocerebellar ataxias, myoclonic epilepsy, other neurocognitive disorders, other neuromuscular disorders, and fragile X syndrome.
Parameter 3
The specification discloses that treating encompasses a reduction in the number, frequency, severity, or duration of one or more symptoms of a disease/disorder and/or results in a decrease in the development or worsening of one or more symptoms of a disease/disorder (pgs 8-9, joining para).
The specification discloses the zinc finger fusion protein may comprise 6 or more zinc finger domains (e.g. pg 10, lines 30-31).
Sera (U.S. 2003/0134350; of record) is considered relevant prior art for having disclosed the zinc finger protein comprise a zinc finger domain of about 32 amino acids (e.g. [0003]; X3-Cys-X4-Cys-X12-His-X5-His-X4) that recognizes a 4-nucleotide target sequence, wherein said zinc finger protein may comprise as many as 40 zinc finger domains (“x”, below), thereby recognizing a target nucleotide sequence of about 160 nucleotides (e.g. [0024, 28]).
Thus, the claims encompass zinc finger protein embodiments including, but not limited to, exemplary variants shown below:
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(2x10^36)^2 = about 4x10^72 structurally undisclosed zinc finger proteins comprising a combination of 2 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^4 = about 8x10^144 structurally undisclosed zinc finger proteins comprising a combination of 4 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^6 = about 1x10^217 s structurally undisclosed zinc finger proteins comprising a combination of 6 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^8 = about 1x10^289 structurally undisclosed zinc finger proteins comprising a combination of 8 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^10 = about 2x10^361 structurally undisclosed zinc finger proteins comprising a combination of 10 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^12 = about 2x10^433 structurally undisclosed zinc finger proteins comprising a combination of 12 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^14 = about 3x10^505 structurally undisclosed zinc finger proteins comprising a combination of 14 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
((2x10^36)^16 = about 3x10^757 structurally undisclosed zinc finger proteins comprising a combination of 16 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^20 = about 4x10^721 structurally undisclosed zinc finger proteins comprising a combination of 20 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^30 = about 6x10^1081 structurally undisclosed zinc finger proteins comprising a combination of 30 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(2x10^36)^40 = about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^4 = 256 structurally undisclosed 4 nucleotide long RNA target sequences. about 4x10^72 structurally undisclosed zinc finger proteins comprising a combination of 2 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^8 = about 6x10^4 structurally undisclosed 8 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 8x10^144 structurally undisclosed zinc finger proteins comprising a combination of 4 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^24 = about 3x10^14 structurally undisclosed 24 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 1x10^217 structurally undisclosed zinc finger proteins comprising a combination of 6 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^32 = about 2x10^19 structurally undisclosed 32 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 1x10^289 structurally undisclosed zinc finger proteins comprising a combination of 8 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^40 = about 1x10^24 structurally undisclosed 40 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 2x10^361 structurally undisclosed zinc finger proteins comprising a combination of 10 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^48 = about 8x10^28 structurally undisclosed 48 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 2x10^433 structurally undisclosed zinc finger proteins comprising a combination of 12 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^56 = about 5x10^33 structurally undisclosed 56 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 3x10^505 structurally undisclosed zinc finger proteins comprising a combination of 14 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^64 = about 3x10^38 structurally undisclosed 64 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 3x10^757 structurally undisclosed zinc finger proteins comprising a combination of 16 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^80 = about 1x10^48 structurally undisclosed 80 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 4x10^721 structurally undisclosed zinc finger proteins comprising a combination of 20 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^120 = about 2x10^72 structurally undisclosed 120 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 6x10^1081 structurally undisclosed zinc finger proteins comprising a combination of 30 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
4^160 = about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences that are to be bound by the enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding a RNA target sequence.
(www.calculator.net/exponent-calculator.html; last visited April 16, 2025; of record)
The claims fail to recite, and the specification fails to disclose, a structure/function nexus between the amino acid sequence(s) of each zinc finger, and combinations and/or subcombinations thereof, respectively, of the enormously vast genus of zinc finger proteins comprising SEQ ID NO:1 and/or SEQ ID NO:2 in combination with about 8x10^1441 structurally undisclosed zinc finger domains that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences and the corresponding target nucleic acid sequence(s) recognized by each zinc finger, and combinations and/or subcombinations thereof, respectively, for example.
Pruett et al (Comparison of Zinc Finger Nucleases for Use in Gene Targeting in Mammalian Cells, Molecular Therapy 16(4): 707-717, 2008; of record) is considered relevant prior art for having taught that although conceptually ZFPs can be made to recognize new target sequences by mixing and matching individual fingers with known recognition sites (syn. modular assembly), this approach has limitations because it does not take into account the potential interactions between fingers in DNA-binding interactions, which are important in determining target sequence affinity and specificity (e.g. pgs 707-708, joining para). One study reporting that ZFNs made by modular-assembly had only a 50% success rate, and they were never able to target a natural site. Clearly, there are deficiencies in the published methods of making ZFNs for targeting mammalian cells. (pg 708, col. 1).
Gupta et al (Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases, Nucleic Acids Research 39(1): 381-392, 2011; of record) is considered relevant prior art for having taught that many ZFPs display dose-dependent toxicity due to undesired off-target effects (e.g. Abstract). For each ZFP, the number of binding sites within a genome is primarily dictated by the number and quality of the incorporated zinc fingers (e.g. pg 382, col. 1).
Instant claims recite the ZFPs at a high level of generality, with varying numbers of zinc fingers, and no required minimal degree of specificity and/or binding affinity.
Gupta et al also taught that the number of functional target sites is also defined by the composition and length of the linker joining the ZFP and nuclease domain, which determines the required spacing between ZFP half-sites for activity (e.g. pg 382, col. 1).
Instant claims recite the ZFPs at a high level of generality, including the linker.
Handel et al (Zinc-Finger Nuclease Based Genome Surgery: It’s All About Specificity, Current Gene Therapy 11: 28-37, 2011; of record) is considered relevant prior art for having taught that a key issue in the successful biotechnological and therapeutic applications of ZFPs is undeniably the specificity of the nucleases, which is closely linked to ZFP activity and ZFP-associated toxicity (e.g. pg 28, col. 2). The prior art has shown that the DNA binding specificity is a major factor governing ZFP activity and that specificity is inversely correlated with ZFP-associated toxicity (syn. off-target effects). ZFP subunits that do not contain a DNA-binding domain with sufficient affinity to the recognition site will either not find the DNA target at all or bind and cleave many similar sequences in the genome and therefore cause toxicity (pg 29). Determination of the in vivo specificity is quite challenging (pgs 29-30). While modular assembly strategy is appealing due to its straightforwardness, the price for this simplicity is the relatively low success frequency (below 10%) in terms of generating ZFPs that work in the context of a complex genome, and there is some concern about the specificities of such ZFPs. One reason for the low success rate may be that the zinc fingers in a multi-finger array are not truly modular, as individual zinc fingers in an array show positive and negative cooperativity in DNA binding (e.g. pg 33, col. 2). Irrespective of the platform used to assemble the zinc finger arrays, a burning issue with regard to specificity of ZFPs is the question about the optimal number of zinc finger motifs per ZFP subunit (e.g pg 34, col. 1). Also, one should ask ‘what is the optimal affinity of a ZFP subunit?’ Undoubtedly, zinc finger arrays with little affinity will either bind DNA in a non-specific fashion, or not at all. The prior art taught an example whereby the activity of the three-finger ZFP E3 was barely detectable, while the six-finger ZFN E6 was only half as active as the corresponding ZFN E4 and E5 with four and five fingers, respectively (e.g. pg 34, col. 1). High affinity to the target site does not always translate into high specificity.
Juarez et al (Breaking through an epigenetic wall: Re-activation of Oct4 by KRAB-containing designer zinc finger transcription factors Epigenetics 8(2): 164-176, 2013; of record) is considered relevant prior art for having taught a designer fusion protein comprising a ZFP, whereby the potency of the ZFP was dependent on the cell type, and the genomic microenvironment critically influences the regulatory outcome, be it transcriptional repression or transcriptional activation, of the KRAB-ZFPs (e.g. pg 165, col. 2).
Those of ordinary skill in the art immediately recognize that each zinc finger domain recognizes its own target nucleic acid sequence.
Instant specification fails to disclose that the zinc finger domain comprising the amino acid sequence of SEQ ID NO:1 is dispositive for, and controlling over, all the other 40 zinc finger domains (1/40th), and their corresponding nucleic acid target sequences, present in the enormously vast genus zinc finger fusion proteins encompassed by the claims.
Instant specification fails to disclose that the zinc finger domain comprising the amino acid sequence of SEQ ID NO:2 is dispositive for, and controlling over, all the other 40 zinc finger domains (1/40th), and their corresponding nucleic acid target sequences, present in the enormously vast genus zinc finger fusion proteins encompassed by the claims.
Instant specification fails to disclose that the zinc finger domain comprising the amino acid sequences of SEQ ID NO:1 and SEQ ID NO:2 is dispositive for, and controlling over, all the other 38 zinc finger domains (1/20th), and their corresponding nucleic acid target sequences, present in the enormously vast genus zinc finger fusion proteins encompassed by the claims.
Thus, simply appending the fusion proteins comprising the combinations of as many as 40 structurally and functionally undisclosed zinc finger domains having the enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger domain amino acid sequences to a zinc finger domain comprising the amino acid sequence of SEQ ID NO:1 (1/40th of the ZFP), is not, in and of itself dispositive for and the controlling structural element over all of the remaining enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of as many as 40 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences when said enormous vast genus of zinc finger fusion proteins will necessarily and predictably have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold.
Similarly, simply appending the fusion proteins comprising the combinations of as many as 40 structurally and functionally undisclosed zinc finger domains having the enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger domain amino acid sequences to a zinc finger domain comprising the amino acid sequence of SEQ ID NO:2 (1/40th of the ZFP), is not, in and of itself dispositive for and the controlling structural element over all of the remaining enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of as many as 40 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences when said enormous vast genus of zinc finger fusion proteins will necessarily and predictably have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold.
Similarly, simply appending the fusion proteins comprising the combinations of as many as 40 structurally and functionally undisclosed zinc finger domains having the enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger domain amino acid sequences to a zinc finger domain comprising the amino acid sequence of SEQ ID NO:1 and a zinc finger domain comprising the amino acid sequence of SEQ ID NO:2 (1/40th of the ZFP), is not, in and of itself dispositive for and the controlling structural element over all of the remaining enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of as many as 40 structurally and functionally undisclosed zinc finger domains that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences when said enormous vast genus of zinc finger fusion proteins will necessarily and predictably have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold.
As discussed above, the claims encompass zinc finger protein embodiments including, but not limited to, exemplary variants shown below:
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Rather, Applicant’s working examples are directed to the zinc finger fusion protein-encoding nucleic acid SEQ ID NO’s: 11-16 and 18-23, each of which encode zinc finger fusion proteins comprising not more than the zinc finger domain amino acid sequence of SEQ ID NO:1 and/or the zinc finger domain amino acid sequence of SEQ ID NO:2, as shown below:
1;
2;
1, 2; and
2, 1.
Example 3 discloses that, in vitro, the ZNF1 construct showed no reduction in (CUG)105 levels. Rather the ZNF2 construct and the ZNF2+ZNF1 construct results in a reduction of (CUG)105 levels (e.g. Figure 4B).
Example 4, while contemplating administration of AAV9-ZNF1 1x10^10 vector genomes/kg by intracranial injection to a human subject is merely prophetic. Furthermore, instant claims are vastly broader in scope to the prophetic example.
Example 5 is directed to in vitro organoid culture. While the Example indicates efficacy for a scAAV9-ZNF1 construct (e.g. Figure 8b), the example fails to disclose the dosage of said scAAV9-ZNF1 construct administered to the organoid culture in order to achieve such an effect. Thus, the Example fails to provide the corresponding dosage of the vector that is to be administered in vivo to a human subject via intravenous or intracranial routes. Furthermore, instant claims are vastly broader in scope to the scAAV9-ZNF1 organoid example.
United States Court of Appeals for the Federal Circuit, Regents of the University of Minnesota v. Gilead Sciences, Inc (Case 21-2168; decided March 6, 2023).
Written description of a broad genus requires description not only of the outer limits of the genus but also of either a representative number of members of the genus or structural features common to the members of the genus, in either case with enough precision that a relevant artisan can visualize or recognize the members of the genus. See Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1350−52 (Fed. Cir. 2010) (en banc). A broad outline of a genus’s perimeter is insufficient. See id.
The claims fail to recite, and the specification fails to disclose, a first rAAV9 vector encoding a first zinc finger fusion protein comprising the zinc finger domain amino acid sequence of SEQ ID NO:1 and/or the zinc finger domain amino acid sequence of SEQ ID NO:2 in combination with as many as 40 structurally and functionally undisclosed zinc finger domains, representing an enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins that are to have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule [parameter 1] that, upon administration via intravenous or intracranial route at a dosage of 0.8x10^8 to 1.2x10^15 vector genomes/kg will necessarily and predictably have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold, and thereby necessarily and predictably able to prevent [parameter 3] a first disease/disorder/condition, e.g. dementia [parameter 2], in a human subject in need, as opposed to a second rAAV9 vector encoding a first zinc finger fusion protein comprising the zinc finger domain amino acid sequence of SEQ ID NO:1 and/or the zinc finger domain amino acid sequence of SEQ ID NO:2 in combination with as many as 40 structurally and functionally undisclosed zinc finger domains, representing an enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins that are to have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule [parameter 1] that, upon administration via intravenous or intracranial route at a dosage of 0.8x10^8 to 1.2x10^15 vector genomes/kg will necessarily and predictably have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold, and thereby necessarily and predictably able to retard the duration of [parameter 3] a second disease/disorder/condition, e.g. ALS [parameter 2], in a human subject in need, for example.
As discussed above, Pruett et al taught that although conceptually ZFPs can be made to recognize new target sequences by mixing and matching individual fingers with known recognition sites (syn. modular assembly), this approach has limitations because it does not take into account the potential interactions between fingers in DNA-binding interactions, which are important in determining target sequence affinity and specificity (e.g. pgs 707-708, joining para). One study reporting that ZFNs made by modular-assembly had only a 50% success rate, and they were never able to target a natural site. Clearly, there are deficiencies in the published methods of making ZFNs for targeting mammalian cells. (pg 708, col. 1).
Gupta et al taught that many ZFPs display dose-dependent toxicity due to undesired off-target effects (e.g. Abstract). For each ZFP, the number of binding sites within a genome is primarily dictated by the number and quality of the incorporated zinc fingers (e.g. pg 382, col. 1).
Instant claims recite the ZFPs at a high level of generality, with varying numbers of zinc fingers, and no required minimal degree of specificity and/or binding affinity.
Gupta et al also taught that the number of functional target sites is also defined by the composition and length of the linker joining the ZFP and nuclease domain, which determines the required spacing between ZFP half-sites for activity (e.g. pg 382, col. 1).
Instant claims recite the ZFPs at a high level of generality, including the linker.
Handel et al taught that a key issue in the successful biotechnological and therapeutic applications of ZFPs is undeniably the specificity of the nucleases, which is closely linked to ZFP activity and ZFP-associated toxicity (e.g. pg 28, col. 2). The prior art has shown that the DNA binding specificity is a major factor governing ZFP activity and that specificity is inversely correlated with ZFP-associated toxicity (syn. off-target effects). ZFP subunits that do not contain a DNA-binding domain, in this case, a RNA-binding domain, with sufficient affinity to the recognition site will either not find the DNA [RNA] target at all or bind and cleave many similar sequences in the genome and therefore cause toxicity (pg 29). Determination of the in vivo specificity is quite challenging (pgs 29-30). While modular assembly strategy is appealing due to its straightforwardness, the price for this simplicity is the relatively low success frequency (below 10%) in terms of generating ZFPs that work in the context of a complex genome, and there is some concern about the specificities of such ZFPs. One reason for the low success rate may be that the zinc fingers in a multi-finger array are not truly modular, as individual zinc fingers in an array show positive and negative cooperativity in DNA [RNA] binding (e.g. pg 33, col. 2). Irrespective of the platform used to assemble the zinc finger arrays, a burning issue with regard to specificity of ZFPs is the question about the optimal number of zinc finger motifs per ZFP subunit (e.g pg 34, col. 1). Also, one should ask ‘what is the optimal affinity of a ZFP subunit?’ Undoubtedly, zinc finger arrays with little affinity will either bind DNA [RNA] in a non-specific fashion, or not at all. The prior art taught an example whereby the activity of the three-finger ZFP E3 was barely detectable, while the six-finger ZFN E6 was only half as active as the corresponding ZFN E4 and E5 with four and five fingers, respectively (e.g. pg 34, col. 1). High affinity to the target site does not always translate into high specificity.
Juarez et al taught a designer fusion protein comprising a ZFP, whereby the potency of the ZFP was dependent on the cell type, and the genomic microenvironment critically influences the regulatory outcome (e.g. pg 165, col. 2).
Cooper-Knock et al (Sequestration of multiple RNA recognition motif-containing proteins by C9orf72 repeat expansions, Brain 137: 2040-2051, 2014; of record) is considered relevant prior art for having taught that the C9orf72 RNA comprising multiple hexanucleotide repeat expansions naturally forms toxic RNA foci, and binds and sequesters various RNA processing proteins (Abstract; Figure 1b, 1d), which is causal for ALS and/or FTD disease/disorder. The repeat expansion RNA can form G-quadruplexes (e.g. pg 2043, col. 1) and can bind as many as 59 different proteins (e.g. Figure 2e).
Thus, the ordinary artisan would immediately recognize that in order to be therapeutically effective, the instantly recited enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains and comprising the zinc finger domain of SEQ ID NO:1 and/or the a the zinc finger domain of SEQ ID NO:2 that are to have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule must be present in each corresponding target cell in an amount to out-compete and/or prohibit formation of the naturally-occurring, already present, toxic RNA foci comprising as many as 59 different proteins, in order to necessarily and predictably achieve a real-world, clinically meaningful therapeutic effect, including, but not limited to, a reduction in the number, frequency, severity, or duration of one or more symptoms of as many as 40 different diseases/disorders and/or results in a decrease in the development or worsening of one or more symptoms of as many as 40 different diseases/disorders.
The claims fail to recite, and the instant specification fails to disclose, the minimally necessary and sufficient amount of enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains and comprising the zinc finger domain of SEQ ID NO:1 and/or the zinc finger domain of SEQ ID NO:2 that are to have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule must be present in each corresponding target cell in an amount to out-compete and/or prohibit formation of the naturally-occurring, already present, toxic RNA foci thereby necessarily and predictably achieve a real-world, clinically meaningful therapeutic effect, including, but not limited to, a reduction in the number, frequency, severity, or duration of one or more symptoms of as many as 40 different diseases/disorders and/or results in a decrease in the development or worsening of one or more symptoms of as many as 40 different diseases/disorders.
In Amgen, Inc., v. Sanofi (U.S. Supreme Court, No. 21-757 (2023))
“Amgen seeks to monopolize an entire class of things defined by their function”.
“The record reflects that this class of antibodies does not include just the 26 that Amgen has described by their amino acid sequence, but a “vast” number of additional antibodies that it has not.”
“It freely admits that it seeks to claim for itself an entire universe of antibodies.”
In the instant case, the record reflects that the claimed class of the ZFP fusion proteins reasonably encompass an enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains comprising the zinc finger domain of SEQ ID NO:1 and/or the zinc finger domain of SEQ ID NO:2 that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold.
“They leave a scientist forced to engage in painstaking experimentation to see what works. 159 U.S., at 475.
This is not enablement. More nearly, it is “a hunting license”. Brenner v. Manson, 383 U.S. 519, 536 (1966).
“Amgen has failed to enable all that it has claimed, even allowing for a reasonable degree of experimentation”.
While the “roadmap” would produce functional combinations, it would not enable others to make and use the functional combinations; it would instead leave them to “random trial-and-error discovery”.
“Amgen offers persons skilled in the art little more than advice to engage in “trial and error”.
“The more a party claims for itself the more it must enable.”
“Section 112 of the Patent Act reflects Congress’s judg-ment that if an inventor claims a lot, but enables only a lit-tle, the public does not receive its benefit of the bargain. For more than 150 years, this Court has enforced the stat-utory enablement requirement according to its terms. If the Court had not done so in Incandescent Lamp, it might have been writing decisions like Holland Furniture in the dark. Today’s case may involve a new technology, but the legal principle is the same.
Applicant’s working examples are directed to three species of a zinc finger protein comprising one or two zinc finger domains, wherein the first zinc finger domain comprises the amino acid sequence of SEQ ID NO:1 and/or the second zinc finger domain comprises the amino acid sequence of SEQ ID NO:2 (e.g. Figure 1; Znf1, Znf2, or Znf1+Znf2).
Instant claims and specification fail to make up for the deficiencies of the global scientific community.
Applicant is essentially requiring the ordinary artisans to discover for themselves that which they have failed to disclose.
Thus, for the reasons outlined above, it is concluded that the claims do not meet the requirements for written description under 35 U.S.C. 112, first paragraph.
See further discussion below in the 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, enablement rejection.
MPEP 2163 - 35 U.S.C. 112(a) and the first paragraph of pre-AIA 35 U.S.C. 112 require that the “specification shall contain a written description of the invention ....” This requirement is separate and distinct from the enablement requirement. Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010) (en banc)
Dependent claims are included in the basis of the rejection because they do not correct the primary deficiencies of the independent claims.
Response to Arguments
Applicant argues that the amendments to Claim 1 render the prior rejection moot.
Applicant’s argument(s) has been fully considered, but is not persuasive. Applicant’s amendments to independent Claims 17-18 and 22-23 do nothing to address the enormously vast genus of nucleic acid vectors, including but not limited to, plasmids, artificial chromosomes, viral vectors such as adenoviruses, lentiviruses, retroviruses, AAVs comprising at least 125 different AAV capsid serotypes, bacteriophages, cosmids, yeast artificial chromosomes, and bacterial artificial chromosomes, and transposons encoding the enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains comprising the zinc finger domain of SEQ ID NO:1 and/or the zinc finger domain of SEQ ID NO:2, such as:
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that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences, thereby necessarily and predictably decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold.
5. Claims 22-33 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The Examiner incorporates herein the above 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, written description rejection.
While determining whether a specification is enabling, one considers whether the claimed invention provides sufficient guidance to make and use the claimed invention. If not, whether an artisan would have required undue experimentation to make and use the claimed invention and whether working examples have been provided. When determining whether a specification meets the enablement requirements, some of the factors that need to be analyzed are: the breadth of the claims, the nature of the invention, the state of the prior art, the level of one of ordinary skill, the level of predictability in the art, the amount of direction provided by the inventor, the existence of working examples, and whether the quantity of any necessary experimentation to make or use the invention based on the content of the disclosure is “undue” (In re Wands, 858 F.2d 731, 737, 8 USPQ2ds 1400, 1404 (Fed. Cir. 1988)). Furthermore, USPTO does not have laboratory facilities to test if an invention will function as claimed when working examples are not disclosed in the specification. Therefore, enablement issues are raised and discussed based on the state of knowledge pertinent to an art at the time of the invention. And thus, skepticism raised in the enablement rejections are those raised in the art by artisans of expertise.
Considering the mode of administration, the specification simply requires administration of the nucleic acid vectors to the subject by any means. The art has demonstrated through numerous publications, delivery of nucleic acid vectors in vivo is highly unpredictable for successful human therapy.
At issue in general are organ barriers, failure to persist, side-effects in other organs, T-cell responses, virus neutralizing antibodies, humoral immunity, normal tropism of the vector to other organs and more. The challenge is to maintain the efficiency of delivery and expression while minimizing any pathogenicity of the virus from which the vector was derived. The inability to develop an adequate means of overcoming obstacles such as humoral; responses and refractory cells limits the successful means by which the nucleic acid can be administered. The physiological art is recognized as unpredictable. (MPEP 2164.03.) In cases involving predictable factors, such as mechanical or electrical elements, a single embodiment provides broad enablement in the sense that, once imagined, other embodiments can be made without difficulty and their performance characteristics predicted by resort to known scientific laws. In cases involving unpredictable factors, such as most chemical reactions and physiological activity, the scope of enablement obviously varies inversely with the degree of unpredictability of the factors involved. In this case, the nucleic acid is broadly stated as being administered to a patient. The lack of guidance exacerbates the highly unpredictable field of gene therapy and the method of delivery of polynucleotides is highly unpredictable to date. Gene delivery has been a persistent problem for gene therapy protocols and the route of delivery itself presents an obstacle to be overcome for the application of the vector therapeutically.
Reliance on animal models is not predictive of clinical outcome. This has been complicated by the inability to extrapolate delivery methods in animals with those in humans or higher animals.
Mingozzi and High (Immune responses to AAV vectors: overcoming barriers to successful gene therapy, Blood 122(1): 23-36, 2013) demonstrate that the human findings are not recapitulated from the animal studies (page 26, col 2, “it seemed logical that one could model the human immune response in these animals, but multiple attempts to do so have also failed”). Hence, lessons learned from small animals such as the mice studies could not recapitulate the ability to deliver adequately in humans.
Kattenhorn et al (Adeno-Associated Virus Gene Therapy for Liver Disease, Human Gene Therapy 27(12): 947-961, November 28, 2016) taught concerns for translation lead to extensive analysis of the effects on clinical use. The use of AAV after initial promising results went on hiatus (pg 947, col. 2, “clinical hiatus in the field”) as the animal models were deficient (pg 953, col. 2, “Although animal models predicted many aspects of the human immune response…, they largely failed to predict responses to AAV capsid”; “Work done in nonhuman primates has not met with any additional success”). This emphasizes that the challenge in humans is to maintain the efficiency of delivery and expression while minimizing any pathogenicity of the virus from which the vector was derived. Eventually, the use of AAV is serotype-dependent (e.g. pg 950, col. 1), organ and concentration dependent. The inability to develop an adequate means of overcoming humoral responses, neutralizing antibody, inactivation of transgene expression, shedding and refractory cells limits the successful means by which the nucleic acid can be administered.
The claims fail to recite, and the specification fails to disclose, a first rAAV9 vector encoding a first zinc finger fusion protein comprising the zinc finger domain amino acid sequence of SEQ ID NO:1 and/or the zinc finger domain amino acid sequence of SEQ ID NO:2 in combination with as many as 40 structurally and functionally undisclosed zinc finger domains, representing an enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins that are to have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule [parameter 1] that, upon administration via intravenous or intracranial route at a dosage of 0.8x10^8 to 1.2x10^15 vector genomes/kg will necessarily and predictably have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold, and thereby necessarily and predictably able to prevent [parameter 3] a first disease/disorder/condition, e.g. dementia [parameter 2], in a human subject in need, as opposed to a second rAAV9 vector encoding a first zinc finger fusion protein comprising the zinc finger domain amino acid sequence of SEQ ID NO:1 and/or the zinc finger domain amino acid sequence of SEQ ID NO:2 in combination with as many as 40 structurally and functionally undisclosed zinc finger domains, representing an enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins that are to have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule [parameter 1] that, upon administration via intravenous or intracranial route at a dosage of 0.8x10^8 to 1.2x10^15 vector genomes/kg will necessarily and predictably have the functional property of binding a G4C2 or C4G2 hexanucleotide motif in an RNA molecule, thereby decreasing the expression level of an RNA comprising a G4C2 or C4G2 hexanucleotide repeat by at least 2-fold, and thereby necessarily and predictably able to retard the duration of [parameter 3] a second disease/disorder/condition, e.g. ALS [parameter 2], in a human subject in need, for example.
The specification fails to make up for deficiencies of the global scientific community, and thus the ordinary artisans must determine for themselves that which Applicant fails to disclose.
The Quantity of Any Necessary Experimentation to Make or Use the Invention
It is generally recognized in the art that biological compounds often react unpredictably under different circumstances (Nationwide Chem. Corp. v. Wright, 458 F. supp. 828, 839, 192 USPQ95, 105(M.D. Fla. 1976); Affd 584 F.2d 714, 200 USPQ257 (5th Cir. 1978); In re Fischer, 427 F.2d 833, 839, 166 USPQ 10, 24(CCPA 1970)). The relative skill of the artisan and the unpredictability of the pharmaceutical art are very high. Where the physiological activity of a chemical or biological compound is considered to be an unpredictable art (Note that in cases involving physiological activity such as the instant case, "the scope of enablement obviously varies inversely with the degree of unpredictability of the factors involved" (See In re Fischer, 427 F.2d 833, 839, 166 USPQ 10, 24(CCPA 1970))), the skilled artisan would have not known how to formulate a pharmaceutical composition comprising:
the enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains comprising the zinc finger domain of SEQ ID NO:1 and/or the zinc finger domain of SEQ ID NO:2 that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences, thereby necessarily and predictably decreasing G4C2 or C4G2 hexanucleotide repeats in the CNS by at least 2-fold;
the enormous genus of unrecited and undisclosed nucleic acid vectors of the broad genus of structurally and functionally different nucleic acid vectors encoding the enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains comprising the zinc finger domain of SEQ ID NO:1 and/or the zinc finger domain of SEQ ID NO:2 that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences, thereby necessarily and predictably decreasing G4C2 or C4G2 hexanucleotide repeats in the CNS by at least 2-fold, respectively,
so as to necessarily and predictably achieve a real-world, clinically meaningful therapeutic result treating a subject in need thereof for the broad genus of at least 40 etiologically and pathologically distinct repeat expansion-associated disorders, including G4C2 or C4G2 hexanucleotide repeat expansion-associated disorders, thereby necessarily and predictably achieving a reduction in the number, frequency, severity, or duration of one or more symptoms of a disease/disorder and/or results in a decrease in the development or worsening of one or more symptoms of a disease/disorder and/or a decrease the level of RNA comprising a G4C2 or C4G2 hexanucleotide repeat motif by as little as 2-fold, or as much as 150-fold.
The courts have stated that reasonable correlation must exist between scope of exclusive right to patent application and scope of enablement set forth in patent application. 27 USPQ2d 1662 Exparte Maizel. In the instant case, in view of the lack of guidance, working examples, breadth of the claims, the level of skill in the art and state of the art at the time of the claimed invention was made, it would have required undue experimentation to make and/or use the invention as claimed.
If little is known in the prior art about the nature of the invention and the art is unpredictable, the specification would need more detail as to how to make and use the invention in order to be enabling. See, e.g., Chiron Corp. v. Genentech Inc., 363 F.3d 1247, 1254, 70 USPQ2d 1321, 1326 (Fed. Cir. 2004) ("Nascent technology, however, must be enabled with a 'specific and useful teaching.' The law requires an enabling disclosure for nascent technology because a person of ordinary skill in the art has little or no knowledge independent from the patentee's instruction. Thus, the public's end of the bargain struck by the patent system is a full enabling disclosure of the claimed technology." (citations omitted)).
As In re Gardner, Roe and Willey, 427 F.2d 786,789 (C.C.P.A. 1970), the skilled artisan might eventually find out how to use the invention after “a great deal of work”. In the case of In re Gardner, Roe and Willey, the invention was a compound which the inventor claimed to have antidepressant activity, but was not enabled because the inventor failed to disclose how to use the invention based on insufficient disclosure of effective drug dosage. The court held that “the law requires that the disclosure in the application shall inform them how to use, not how to find out how to use for themselves”.
In Amgen, Inc., v. Sanofi (U.S. Supreme Court, No. 21-757 (2023))
“Amgen seeks to monopolize an entire class of things defined by their function”.
“The record reflects that this class of antibodies does not include just the 26 that Amgen has described by their amino acid sequence, but a “vast” number of additional antibodies that it has not.”
“It freely admits that it seeks to claim for itself an entire universe of antibodies.”
In the instant case, the record reflects that the claimed class of the ZFP fusion proteins reasonably encompass an enormously vast genus of about 8x10^1441 structurally undisclosed zinc finger proteins comprising a combination of 40 structurally and functionally undisclosed zinc finger domains comprising the zinc finger domain of SEQ ID NO:1 and/or the zinc finger domain of SEQ ID NO:2 that are to have the functional property of binding an enormously vast genus of about 2x10^96 structurally undisclosed 160 nucleotide long RNA target sequences, thereby decreasing the level of RNA comprising a G4C2 or C4G2 hexanucleotide repeat motif by as little as 2-fold, or as much as 150-fold.
Similarly, the record reflects that the claimed class of PIN RNA endonuclease domain fragments reasonably encompasses an enormously vast genus of about 3x10^32 structurally and functionally undisclosed PIN fragments.
“They leave a scientist forced to engage in painstaking experimentation to see what works. 159 U.S., at 475.
This is not enablement. More nearly, it is “a hunting license”. Brenner v. Manson, 383 U.S. 519, 536 (1966).
“Amgen has failed to enable all that it has claimed, even allowing for a reasonable degree of experimentation”.
While the “roadmap” would produce functional combinations, it would not enable others to make and use the functional combinations; it would instead leave them to “random trial-and-error discovery”.
“Amgen offers persons skilled in the art little more than advice to engage in “trial and error”.
“The more a party claims for itself the more it must enable.”
“Section 112 of the Patent Act reflects Congress’s judg-ment that if an inventor claims a lot, but enables only a lit-tle, the public does not receive its benefit of the bargain. For more than 150 years, this Court has enforced the stat-utory enablement requirement according to its terms. If the Court had not done so in Incandescent Lamp, it might have been writing decisions like Holland Furniture in the dark. Today’s case may involve a new technology, but the legal principle is the same.
Applicant’s working examples are directed to three species of a zinc finger protein comprising one or two zinc finger domains, wherein the first zinc finger domain comprises the amino acid sequence of SEQ ID NO:1 and/or the second zinc finger domain comprises the amino acid sequence of SEQ ID NO:2 (e.g. Figure 1; Znf1, Znf2, or Znf1+Znf2).
Instant claims and specification fail to make up for the deficiencies of the global scientific community.
Applicant is essentially requiring the ordinary artisans to discover for themselves that which they have failed to disclose.
Perrin (Make Mouse Studies Work, Nature (507): 423-425, 2014; of record) taught that the series of clinical trials for a potential therapy can cost hundreds of millions of dollars. The human costs are even greater (pg 423, col. 1). For example, while 12 clinical trials were tested for the treatment of ALS, all but one failed in the clinic (pg 423, col. 2). Experiments necessary in preclinical animal models to characterize new drugs or therapeutic compounds are expensive, time-consuming, and will not, in themselves, lead to new treatments. But without this upfront investment, financial resources for clinical trials are being wasted and [human] lives are being lost (pg 424, col. 1). Animal models are highly variable, and require a large number of animals per test group. Before assessing a drug’s efficacy, researchers should investigate what dose animals can tolerate, whether the drug reaches the relevant tissue at the required dose and how quickly the drug is metabolized or degraded by the body. We estimate that it takes about $30,000 and 6–9 months to characterize the toxicity of a molecule and assess whether enough reaches the relevant tissue and has a sufficient half-life at the target to be potentially effective. If those results are promising, then experiments to test whether a drug can extend an animal’s survival are warranted — this will cost about $100,000 per dose and take around 12 months. At least three doses of the molecule should be tested; this will help to establish that any drug responses are real and suggest what a reasonable dosing level might be. Thus, even assuming the model has been adequately characterized, an investment of $330,000 is necessary just to determine whether a single drug has reasonable potential to treat disease in humans. It could take thousands of patients, several years and hundreds of millions of dollars to move a drug through the clinical development process. The investment required in time and funds is far beyond what any one lab should be expected to do. (pg 425, col.s 2-3). The human costs are even greater: patients with progressive terminal illnesses may have just one shot at an unproven but promising treatment. Clinical trials typically require patients to commit to year or more of treatment, during which they are precluded from pursuing other experimental options (pg 423, col.2 1-3).
Greenberg (Gene Therapy for heart failure, Trends in Cardiovascular Medicine 27: 216-222, 2017; of record) is considered relevant prior art for taught that despite success in experimental animal models, translating gene transfer strategies from the laboratory to the clinic remains at an early stage (Abstract). The success of gene therapy depends on a variety of factors that will ultimately determine the level of transgene expression within the targeted cells. These factors include the vector used for delivery, the method and conditions of delivery of the vector to the [target tissue], the dose that is given and interactions between the host and the vector that alter the efficiency of transfection of [target] cells (e.g. pg 217, col. 1). Failure of therapeutic results may arise because the vector DNA levels were at the lower end of the threshold for dose-response curves in pharmacology studies, and/or only a small proportion of target cells were expressing the therapeutic transgene (e.g. pg 220, col. 1). Although the use of AAVs for gene therapy is appealing, additional information about the best strain of AAVs to use in human patients is needed. Experience indicates that there is a need to carefully consider the dose of the gene therapy vector; however, this has proved to be difficult in early phase developmental studies due to the complexity and cost of such studies (e.g. pg 221, col. 1).
Maguire et al (Viral vectors for gene delivery to the inner ear, Hearing Research 394: e107927, 13 pages, doi.org/10.1016/j.heares.2020.107927, 2020; of record) is considered relevant post-filing art for taught that despite the progress with AAV vectors in the inner ear, little is known regarding the mechanism of transduction of specific cells by AAV within the cochlea (e.g. pg 2, col. 2). There are limitations to what experiments in mice can tell us about the true translation potential of a new therapeutic (e.g. pg 8, col. 2), e.g. species-related physiological differences between mice and humans (e.g. pg 9, col. 1). The AAV dosage is a significant factor in achieving transduction of the target cell, as insufficient dosage may achieve no transduction of the target cells (e.g. pg 9, col. 2).
Tobias (Mouse Study Used in Research, Multiple Sclerosis News Today, multiplesclerosisnewstoday.com/news-posts/2023/09/08/lets-not-get-overexcited-about-any-mice-study-used-research/; September 8, 2023; last visited September 27, 2024; of record) is considered relevant art for having taught that, “Mice exaggerate and monkeys lie, some researchers jokingly say. (Or is it the other way around?)” The odds of an experimental treatment making it from mouse or monkey to human are very low. Less than 8% of cancer treatments make it from animal studies into a clinical setting, where they’re tested on people, and only 10% of the medications in those clinical trials make it through to government approval. No wonder some researchers joke about mice and monkeys lying and exaggerating.
MPEP 2163 - 35 U.S.C. 112(a) and the first paragraph of pre-AIA 35 U.S.C. 112 require that the “specification shall contain a written description of the invention ....” This requirement is separate and distinct from the enablement requirement. Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010) (en banc)
Dependent claims are included in the basis of the rejection because they do not correct the primary deficiencies of the independent claims.
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 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 of this title, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
6. The prior rejection of Claims 1, 3-5, 7-8, 11-12, and 16 under AIA 35 U.S.C. 103 as being unpatentable over Celona et al (available online January 10, 2017; of record in IDS) in view of GenBank AAH25424.1 (mouse ZFP106, 2004; of record), GenBank AAL40184.1 (human ZFP106, 2001; of record), Chen et al (available online April 27, 2016; of record) and Sulej et al (2012; of record), Choudhury et al (available online October 23, 2012; of record) and Xu et al (2012; of record) is withdrawn in light of Applicant’s amendment to the independent claim to recite the PIN domain of SEQ ID NO:22 or SEQ ID NO:23, necessitating new grounds of rejection.
7. The prior rejection of Claims 13 and 21 under AIA 35 U.S.C. 103 as being unpatentable over Celona et al (available online January 10, 2017; of record in IDS) in view of GenBank AAH25424.1 (mouse ZFP106, 2004; of record), GenBank AAL40184.1 (human ZFP106, 2001; of record), Chen et al (available online April 27, 2016; of record) and Sulej et al (2012; of record), Choudhury et al (available online October 23, 2012; of record) and Xu et al (2012; of record), as applied to Claims 1, 3-5, 7-8, 11-12, and 16 above, and in further view of Allocca et al (2006; of record) and Woo et al (Loss of function CHCHD10 mutations in cytoplasmic TDP-43 accumulation and synaptic integrity, Nature Communications 8: e15558; 15 pages, doi:10.1038/ncomms15558; available online June 6, 2017) is withdrawn for reasons discussed above.
8. Claims 1, 3-5, and 7-8 are rejected under AIA 35 U.S.C. 103 as being unpatentable over Celona et al (available online January 10, 2017; of record in IDS) in view of GenBank AAH25424.1 (mouse ZFP106, 2004; of record), GenBank AAL40184.1 (human ZFP106, 2001; of record), Chen et al (available online April 27, 2016; of record) and Sulej et al (2012; of record), Choudhury et al (available online October 23, 2012; of record), Xu et al (2012; of record), GenBank NP_001269255 (telomerase-binding protein EST1A; January 28, 2019), Takeshita et al (Crystal structure of the PIN domain of human telomerase-associated protein EST1A, Proteins 68: 980-989, 2007), and Gene ID:23293 (ncbi.nlm.nih.gov/nuccore/?term=human+EST1a; last accessed November 26, 2025).
Determining the scope and contents of the prior art, and Ascertaining the differences between the prior art and the claims at issue.
With respect to Claim 1, Celona et al is considered relevant prior art for having taught an isolated nucleic acid molecule encoding mouse ZFP106 (e.g. pg 9, Materials and Methods, Plasmids), and that mutations in the human ZFP106 ortholog is strongly linked to human ALS disease/disorder, suggesting a possible role in human ALS (pg 2).
Celona et al taught that ZFP106 is an RNA-binding protein and able to specifically bind the G4C2 repeats of C9orf72 RNA (pg 2).
Celona et al taught that ZFP106 might be a potential new drug target for treating ALS in humans (e.g. pg 2).
GenBank AAH25424.1 is considered relevant prior art for having taught that the mouse ZFP106 polypeptide comprises an amino acid sequence (upper line) that is 100% identical to instant SEQ ID NO:1 (lower line), as shown below:
HECRVCGVTEVGLSAYAKHISGQLH
|||||||||||||||||||||||||
HECRVCGVTEVGLSAYAKHISGQLH
GenBank AAH25424.1 does not teach wherein the mouse ZFP106 polypeptide comprises the amino acid sequence of SEQ ID NO:2.
GenBank AAL40184.1 is considered relevant prior art for having taught that the human ZFP106 polypeptide comprises an amino acid sequence (upper line) that is 100% identical to instant SEQ ID NO:1 (lower line), as shown below:
HECRVCGVTEVGLSAYAKHISGQLH
|||||||||||||||||||||||||
HECRVCGVTEVGLSAYAKHISGQLH
Said human ZFP106 polypeptide also comprises an amino acid sequence (upper line) that is 100% identical to instant SEQ ID NO:2 (lower line), as shown below:
YRCWWHGCSLIFGVVDHLKQHLLTDH
|||||||||||||||||||||||||
YRCWWHGCSLIFGVVDHLKQHLLTDH
Chen et al is considered relevant prior art for having taught the synthesis of zinc finger fusion proteins comprising at least one zinc finger domain and a reporter protein, e.g. GFP (e.g. Figure 1, fluorescent ZFP), thereby allowing the ordinary artisan to visualize the localization of the ZFP-GFP fusion protein in living cells.
Celona et al and Chen et al do not teach wherein the zinc finger protein is fused to an RNA degrading enzyme, more specifically an RNA endonuclease.
However, prior to the effective filing date of the instantly claimed invention, Sulej et al is considered relevant prior art for having taught a zinc finger protein fused to an RNA degrading enzyme, more specifically an RNA endonuclease, thereby achieving sequence-specific cleavage of RNA. Sulej et al taught that, at least as of 2012, there were no RNAses available for purely sequence-dependent fragmentation of RNA (Abstract); whereas, appending the RNAse to a zinc finger protein provided the RNA sequence-specific cleavage.
Choudhury et al is considered relevant prior art for having taught the design of engineered RNA endonucleases with customized sequence specificities (Title), wherein the engineered RNA endonuclease comprises a heterologous target recognition domain fused to RNA endonuclease includes a PIN RNA endonuclease (e.g. pg 2, col. 1, Results, “we used the PIN domain (PiLT amino terminus) of SMG6, as it has a well-define molecular architecture”).
Xu et al is considered relevant prior art for having taught that a PIN RNA endonuclease naturally comprises a zinc finger domain adjacent to the PIN domain (PiLT amino terminus) (e.g. Figure 1a), whereby the zinc finger domain participates in RNA recognition (e.g. pg 6961, col. 1) and is required for efficient digestion of substrate RNA (e.g. pg 6960, col. 1).
GenBank NP_001269255 is considered relevant prior art for having taught a human EST1a polypeptide, as per Takeshita et al, comprising an amino acid sequence that is 100% identical to amino acids 2-183 of the amino acid sequence encoded by nucleotides 1-597 of SEQ ID NO:22, as shown below:
QMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAG
GYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLIL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLIL
SCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQ
VG
||
VG
Takeshita et al is considered relevant prior art for having taught that amino acids 2-183 of the amino acid sequence encoded by nucleotides 1-597 of SEQ ID NO:22 are the PilT N-terminal (PIN) domain. Takeshita et al taught a PilT N-terminal (PIN) domain sequence alignment using EST1a and SMG6 proteins (e.g. Figure 2a).
Gene ID: 23293 evidences that human EST1a is synonymous for SMG6.
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Resolving the level of ordinary skill in the pertinent art.
People of the ordinary skill in the art will be highly educated individuals such as medical doctors, scientists, or engineers possessing advanced degrees, including M.D.'s and Ph.D.'s. Thus, these people most likely will be knowledgeable and well-read in the relevant literature and have the practical experience in molecular biology and the synthesis of zinc finger fusion proteins. Therefore, the level of ordinary skill in this art is high.
"A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton." KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1397 (2007). "[I]n many cases a person of ordinary skill will be able to fit the teachings of multiple patents together like pieces of a puzzle." Id. Office personnel may also take into account "the inferences and creative steps that a person of ordinary skill in the art would employ." Id. at ___, 82 USPQ2d at 1396.
Considering objective evidence present in the application indicating obviousness or nonobviousness.
The focus when making a determination of obviousness should be on what a person of ordinary skill in the pertinent art would have known at the time of the invention, and on what such a person would have reasonably expected to have been able to do in view of that knowledge. This is so regardless of whether the source of that knowledge and ability was documentary prior art, general knowledge in the art, or common sense. M.P.E.P. §2141.
The rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law. In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988); In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992). See also In re Kotzab, 217 F.3d 1365, 1370, 55 USPQ2d 1313, 1317 (Fed. Cir. 2000) (setting forth test for implicit teachings); In re Eli Lilly & Co., 902 F.2d 943, 14 USPQ2d 1741 (Fed. Cir. 1990) (discussion of reliance on legal precedent); In re Nilssen, 851 F.2d 1401, 1403, 7 USPQ2d 1500, 1502 (Fed. Cir. 1988) (references do not have to explicitly suggest combining teachings); and Ex parte Levengood, 28 USPQ2d 1300 (Bd. Pat. App. & Inter. 1993) (reliance on logic and sound scientific reasoning). See MPEP §2144.
Prior to the effective filing date of the instantly claimed invention, it would have been obvious to one of ordinary skill in the art to modify the ZFP106 protein of Celona et al to further comprise a heterologous polypeptide, e.g. GFP, with a reasonable expectation of success because Celona et al successfully demonstrated fusing ZFP106 to a peptide fusion partner, e.g. FLAG tag, and Chen et al taught that those of ordinary skill in the art had previously recognized and successfully reduced to practice the design and synthesis of ZFP-GFP fusion proteins, thereby allowing the ordinary artisans to visualize the location of their ZFP in living cells.
Prior to the effective filing date of the instantly claimed invention, it also would have been obvious to one of ordinary skill in the art to substitute a marker protein, e.g. GFP, in a ZFP106 fusion protein, with a RNA endonuclease domain, more specifically with a PIN RNA endonuclease in a ZFP106 fusion protein, with a reasonable expectation of success because the simple substitution of one known element for another would have yielded predictable results to one of ordinary skill in the art at the time of the invention. M.P.E.P. §2144.07 states "The selection of a known material based on its suitability for its intended use supported a prima facie obviousness determination in Sinclair & Carroll Co. v. Interchemical Corp., 325 U.S. 327, 65 USPQ 297 (1945).” “Reading a list and selecting a known compound to meet known requirements is no more ingenious than selecting the last piece to put in the last opening in a jig-saw puzzle." 325 U.S. at 335, 65 USPQ at 301.).” When substituting equivalents known in the prior art for the same purpose, an express suggestion to substitute one equivalent component or process for another is not necessary to render such substitution obvious. In re Fout, 675 F.2d 297, 213 USPQ 532 (CCPA 1982). M.P.E.P. §2144.06. An artisan would be motivated to substitute a marker protein, e.g. GFP, in a ZFP106 fusion protein, with a RNA endonuclease domain, more specifically with a PIN RNA endonuclease in a ZFP106 fusion protein because:
i) Celona et al taught that C9orf72 repeat-containing RNA forms pathogenic aggregates that sequester RNA binding proteins, leading to altered RNA metabolism in motor neurons (Abstract);
ii) Sulej et al taught that by appending a zinc finger protein to an RNA degrading enzyme, more specifically an RNA endonuclease, the ordinary artisan can thereby achieve sequence-specific cleavage of RNA;
iii) those of ordinary skill in the art had previously successfully reduced to practice the ability to engineer sequence-specific RNA endonuclease fusion proteins comprising a sequence-specific nucleic acid targeting domain fused to a PIN RNA endonuclease domain (Choudhury et al); and
iv) the ordinary artisan previously recognized that a PIN RNA endonuclease naturally comprises a zinc finger domain adjacent to the N-terminal RNA endonuclease domain, wherein said zinc finger domain is involved in RNA recognition (Xu et al).
Xu et al taught that the PIN RNA endonuclease zinc finger does not have substrate specificity (pg 6964, col. 1). However, the ordinary artisan would have reasonably expected that the ZFP106, being sequence-specific for G4C2 hexanucleotide motif, to confer sequence specificity to a PIN RNA endonuclease in such a fusion protein.
Thus, appending the ZFP106 to a PIN RNA endonuclease would reasonably re-capitulate the naturally occurring combination of a zinc finger domain containing polypeptide operably linked to a PIN RNA endonuclease domain, and it logically flows that such a ZFP106-RNA endonuclease fusion protein would be reasonably expected by the ordinary artisan to degrade the pathogenic C9orf72 repeat-containing RNA.
Prior to the effective filing date of the instantly claimed invention, it also would have been obvious to one of ordinary skill in the art to substitute a first PIN domain (Choudhury et al, Xu et al), e.g. a SMG6 PIN domain (Choudhury et al), for second PIN domain, i.e. a human EST1a (syn. human SMG6) PIN domain, per Takeshita et al, with a reasonable expectation of success…with a reasonable expectation of success because the simple substitution of one known element for another would have yielded predictable results to one of ordinary skill in the art at the time of the invention. M.P.E.P. §2144.07 states "The selection of a known material based on its suitability for its intended use supported a prima facie obviousness determination in Sinclair & Carroll Co. v. Interchemical Corp., 325 U.S. 327, 65 USPQ 297 (1945).” “Reading a list and selecting a known compound to meet known requirements is no more ingenious than selecting the last piece to put in the last opening in a jig-saw puzzle." 325 U.S. at 335, 65 USPQ at 301.).” When substituting equivalents known in the prior art for the same purpose, an express suggestion to substitute one equivalent component or process for another is not necessary to render such substitution obvious. In re Fout, 675 F.2d 297, 213 USPQ 532 (CCPA 1982). M.P.E.P. §2144.06.
It is proper to "take account of the inferences and creative steps that a person of ordinary skill in the art would employ." KSR Int'l Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741,82 USPQ2d 1385, 1396 (2007). See also Id. At 1742, 82 USPQ2d 1397 ("A person of ordinary skill is also a person of ordinary creativity, not an automaton.").
It should be noted that the KSR case forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness. See the recent Board decision Ex parte Smith, —USPQ2d—, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396) (available at http: www. uspto.gov/web/offices/dcom/bpai/prec/fd071925 .pdf).
With respect to Claim 3, GenBank AAL40184 taught that the human ZFP106 naturally comprises a first RNA-binding zinc finger domain comprising an amino acid sequence 100% identical to instant SEQ ID NO:1 and a second RNA-binding zinc finger domain comprising an amino acid sequence 100% identical to instant SEQ ID NO:2.
With respect to Claims 4-5 and 7-8, Chen et al taught wherein the zinc finger domains are directly adjacent to each other via a linker sequence (e.g. Figure 1).
The instant specification discloses the linker sequence may be as few as 1 amino acid to 20 amino acids.
The "mere existence of differences between the prior art and an invention does not establish the invention's nonobviousness." Dann v. Johnston, 425 U.S. 219, 230, 189 USPQ 257, 261 (1976). The gap between the prior art and the claimed invention may not be "so great as to render the [claim] nonobvious to one reasonably skilled in the art."Id.
In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990). It is routine procedure to optimize component amounts to arrive at an optimal product that is superior for its intended use, since it has been held where the general conditions of a claim are disclosed in the prior art, discovering the optimum or workable ranges involves only routine skill in the art. Similarly, a prima facie case of obviousness exists where the claimed ranges or amounts do not overlap with the prior art but are close enough that one skilled in the art would have expected them to have the same properties. See M.P.E.P. §2144.05(I).
The specification fails to disclose an element of criticality for the presence and/or absence of a linker being only 1 amino acid to 20 amino acids in length between adjacent zinc finger domains.
The cited prior art meets the criteria set forth in both Graham and KSR, and the teachings of the cited prior art provide the requisite teachings and motivations with a clear, reasonable expectation of success. Thus, the invention as a whole is prima facie obvious.
9. Claims 13 and 21 are rejected under AIA 35 U.S.C. 103 as being unpatentable over Celona et al (available online January 10, 2017; of record in IDS) in view of GenBank AAH25424.1 (mouse ZFP106, 2004; of record), GenBank AAL40184.1 (human ZFP106, 2001; of record), Chen et al (available online April 27, 2016; of record) and Sulej et al (2012; of record), Choudhury et al (available online October 23, 2012; of record), Xu et al (2012; of record), GenBank NP_001269255 (telomerase-binding protein EST1A; January 28, 2019), Takeshita et al (Crystal structure of the PIN domain of human telomerase-associated protein EST1A, Proteins 68: 980-989, 2007), and Gene ID:23293 (ncbi.nlm.nih.gov/nuccore/?term=human+EST1a; last accessed November 26, 2025), as applied to Claims 1, 3-5, and 7-8 above, and in further view of Allocca et al (2006; of record) and Woo et al (Loss of function CHCHD10 mutations in cytoplasmic TDP-43 accumulation and synaptic integrity, Nature Communications 8: e15558; 15 pages, doi:10.1038/ncomms15558; available online June 6, 2017).
Determining the scope and contents of the prior art, and Ascertaining the differences between the prior art and the claims at issue.
Celona et al taught an isolated nucleic acid molecule encoding mouse ZFP106 (e.g. pg 9, Materials and Methods, Plasmids), and that mutations in the human ZFP106 ortholog is strongly linked to human ALS disease/disorder, e.g. pathogenic repeat RNA aggregates in motor neurons (e.g. Abstract, Introduction), suggesting a possible role in human ALS (pg 2).
With respect to Claim 21, Celona et al taught formulating the plasmid with a transfection reagent (e.g. pg 12), and thus reasonably fulfills a pharmaceutical composition. The instant specification discloses transfection is a means of nucleic acid delivery encompassed by the claims (e.g. pg 7, lines 22-25; pg 23, lines 26-30).
Celona et al do not teach wherein the nucleic acid vector is a viral vector, more specifically an AAV9 viral vector.
However, prior to the effective filing date of the instantly claimed invention, and with respect to Claims 13 and 21, Allocca et al is considered relevant prior art for having taught a nucleic acid vector encoding a zinc finger protein, wherein the AAV vector nucleic acid is a plasmid, which is subsequently packaged into AAV virus particles (e.g. pg 1280, col. 1), as such is routinely practiced in the art.
Woo et al is considered relevant prior art for having taught the use of rAAV9 expression vectors encoding the artisan’s gene of interest to transduce motor neurons in vitro (e.g. pg 6, col. 1, “we also transduced primary neurons with rAAV9”; pg 13, col. 2, Methods), as well as formulating the rAAV9 viruses in a pharmaceutical composition (e.g. pg 14, col. 1, Methods, stereotaxic injections in mice).
Considering objective evidence present in the application indicating obviousness or nonobviousness.
The focus when making a determination of obviousness should be on what a person of ordinary skill in the pertinent art would have known at the time of the invention, and on what such a person would have reasonably expected to have been able to do in view of that knowledge. This is so regardless of whether the source of that knowledge and ability was documentary prior art, general knowledge in the art, or common sense. M.P.E.P. §2141.
The rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law. In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988); In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992). See also In re Kotzab, 217 F.3d 1365, 1370, 55 USPQ2d 1313, 1317 (Fed. Cir. 2000) (setting forth test for implicit teachings); In re Eli Lilly & Co., 902 F.2d 943, 14 USPQ2d 1741 (Fed. Cir. 1990) (discussion of reliance on legal precedent); In re Nilssen, 851 F.2d 1401, 1403, 7 USPQ2d 1500, 1502 (Fed. Cir. 1988) (references do not have to explicitly suggest combining teachings); and Ex parte Levengood, 28 USPQ2d 1300 (Bd. Pat. App. & Inter. 1993) (reliance on logic and sound scientific reasoning). See MPEP §2144.
Prior to the effective filing date of the instantly claimed invention, it would have been obvious to one of ordinary skill in the art to substitute a first vector, e.g. plasmid, with a second vector, e.g. AAV9 vector, encoding a zinc finger protein with a reasonable expectation of success because the simple substitution of one known element for another would have yielded predictable results to one of ordinary skill in the art at the time of the invention. M.P.E.P. §2144.07 states "The selection of a known material based on its suitability for its intended use supported a prima facie obviousness determination in Sinclair & Carroll Co. v. Interchemical Corp., 325 U.S. 327, 65 USPQ 297 (1945).” “Reading a list and selecting a known compound to meet known requirements is no more ingenious than selecting the last piece to put in the last opening in a jig-saw puzzle." 325 U.S. at 335, 65 USPQ at 301.).” When substituting equivalents known in the prior art for the same purpose, an express suggestion to substitute one equivalent component or process for another is not necessary to render such substitution obvious. In re Fout, 675 F.2d 297, 213 USPQ 532 (CCPA 1982). M.P.E.P. §2144.06. An artisan would have been motivated to substitute a first vector, e.g. plasmid, with a second vector, e.g. AAV9 vector, encoding a zinc finger protein because those of ordinary skill in the art had long-recognized and successfully reduced to practice the packaging of a plasmid vector, including ZFP expression vectors, into AAV virus particles, the as such is routinely practiced in the art, and whereby AAV9 expression vectors have long-been recognized in the art to successfully transduce primary neurons in vitro, thereby delivering the artisan’s transgene of interest to the neuronal cells (Woo et al).
It is proper to "take account of the inferences and creative steps that a person of ordinary skill in the art would employ." KSR Int'l Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741,82 USPQ2d 1385, 1396 (2007). See also Id. At 1742, 82 USPQ2d 1397 ("A person of ordinary skill is also a person of ordinary creativity, not an automaton.").
It should be noted that the KSR case forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness. See the recent Board decision Ex parte Smith, —USPQ2d—, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396) (available at http: www. uspto.gov/web/offices/dcom/bpai/prec/fd071925 .pdf).
The cited prior art meets the criteria set forth in both Graham and KSR, and the teachings of the cited prior art provide the requisite teachings and motivations with a clear, reasonable expectation of success. Thus, the invention as a whole is prima facie obvious.
Conclusion
10. No claims are allowed.
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KEVIN K. HILL
Examiner
Art Unit 1638
/KEVIN K HILL/Primary Examiner, Art Unit 1638