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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 February 17, 2026 has been entered.
Detailed Action
This action is in response to the papers filed February 17, 2026.
Amendments
Applicant's response and amendments, filed February 17, 2026, to the prior Office Action is acknowledged. Applicant has cancelled Claims 2, 5-6, 15, and 18-19, amended Claims 1, 4, 7-11, 14, 16-17, and 20, withdrawn Claims 9 and 13, and added new claims, Claim 21-23.
Claims 1, 3-4, 7-14, 16-17, and 20-23 are pending.
Election/Restrictions
Applicant has elected the following species, wherein:
i) alternative adaptor protein that binds to the sgRNA aptamer is MS2 as recited in Claim 7; and
ii) alternative transcriptional protein fused to the adaptor protein and/or Cas9 enzyme is VP64, as recited in Claims 8 and 12.
Election of Applicant’s invention(s) was made with traverse.
Response to Arguments
Applicant argues that there is no serious burden to search and examine all species.
Applicant’s argument(s) has been fully considered, but is not persuasive. MPEP §803 states that "If the search and examination of all the claims in an application can be made without serious burden, the examiner must examine them on the merits, even though they include claims to independent or distinct inventions."
As discussed in the prior Office Action, there is a search and/or examination burden for the patentably distinct species as set forth above because at least the following reason(s) apply:
A search for modifications a JP34-binding aptamer would not be co-extensive with a search for a TWI8-binding aptamer. Further, a reference rendering a VP64 fusion as anticipated or obvious over the prior art would not necessarily also render a SID4X fusion as anticipated or obvious over the prior art. Because these inventions are distinct for reasons given above, and because a search of one does not necessarily overlap with that of another, it would be unduly burdensome for the examiner to search and examine all the subject matter being sought in the presently pending claims and thus, restriction for examination purposes as indicated is proper.
It is noted that should Applicant traverse the species election requirement, that Applicant was invited to submit evidence or identify such evidence now of record showing the species to be obvious variants or clearly admit on the record that this is the case. Applicant has not done so.
The requirement is still deemed proper and is therefore made FINAL.
Claims 1, 3-4, 7-14, 16-17, and 20-23 are pending.
Claims 9 and 13 are pending but withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
Claims 1, 3-4, 7-8, 10-12, 14, 16-17, and 20-23 are under consideration.
Priority
This application is a continuation of application 15/620,391 filed on June 12, 2017, now abandoned, which is a continuation-in-part of application PCT/US2015/065393 filed on December 11, 2015.
Applicant’s claim for the benefit of a prior-filed application provisional applications:
62/237,496 filed on October 5, 2015;
62/180,681 filed on June 17, 2015;
62/096,324 filed on December 23, 2014; and
62/091,462 filed on December 12, 2014 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 February 19, 2026 that has been considered.
The information disclosure statement filed February 19, 2026 fails to comply with the provisions of 37 CFR 1.97, 1.98 and MPEP § 609 because 37 CFR 1.98(b) requires that each item of information in an IDS be identified properly. Each publication must be identified by publisher, author (if any), title, relevant pages of the publication, and date and place of publication. The date of publication supplied must include at least the month and year of publication, except that the year of publication (without the month) will be accepted if the applicant points out in the information disclosure statement that the year of publication is sufficiently earlier than the effective U.S. filing date and any foreign priority date so that the particular month of publication is not in issue.
See also MPEP 707.05(e) for electronic documents, including, but not limited to:
(D) reference to the unique Digital Object Identifier (DOI) number, or other unique identification number, if known.
NPL citations have been lined through for being defective of one or more requirements.
The signed and initialed PTO Forms 1449 are mailed with this action.
Claim Objections
1. The prior objection to Claims 1 and 20 is withdrawn in light of Applicant’s amendment to the claims canceling the word “interests”.
Double Patenting
2. Claim 20 is objected to under 37 CFR 1.75 as being a substantial duplicate of Claim 1. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Both claims result in the same result, transcriptional suppression of a target gene of interest in a eukaryotic cell.
Both claims require the presence and expression of a Cas9 enzyme having DNA cleavage activity.
Both claims require the use of a sgRNA comprising a guide sequence consisting of 11-15 contiguous nucleotides 100% complementary to a target DNA sequence, thereby directing the Cas9 enzyme to the complex with the target DNA.
3. Claim 21 is objected to under 37 CFR 1.75 as being a substantial duplicate of Claim 4. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Both claims result in the same result, transcriptional modulation (upregulation or downregulation) of a target gene of interest in a eukaryotic cell.
Both claims require the presence and expression of a Cas9 enzyme having DNA cleavage activity.
Both claims require the use of a sgRNA comprising a guide sequence consisting of 11-15 contiguous nucleotides 100% complementary to a target DNA sequence, thereby directing the Cas9 enzyme to the complex with the target DNA.
Both claims require the use of a sgRNA comprising at least the tetraloop and/or loop2 modified to comprise an aptamer that binds to an adaptor protein fused to a transcriptional activator or repressor domain.
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(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
4. Claim 16 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 4 is directed to methods for transcriptional modulation (upregulation or downregulation) of a target gene locus of interest.
Claim 16 recites wherein the target DNA sequence is a gene coding sequence.
Claim 16 is not considered to further limit the independent Claim 4 because it is axiomatic that the target DNA sequence of the gRNA in Claim 4 is “a gene coding sequence”.
The specification fails to disclose a definition (syn. closed language) of a “gene coding sequence”, and those of ordinary skill in the art have long-recognized that a ‘gene coding sequence’ inherently comprises, per natural law of cell biology and genetics, nucleotide sequences that are 5’ upstream to the expressed RNA molecule (syn. gene), be it a non-protein coding RNA or protein-coding RNA, as well as sequences that are 3’ downstream to the expressed RNA molecule (syn. gene).
The claims fail to recite, and the specification fails to disclose, a gRNA target DNA sequence that targets a target gene locus of interest (Claim 4), yet does not target a gene coding sequence (Claim 16).
Thus, while Claim 16 is worded differently, it fails to further limit the target DNA sequence of the gRNA of the independent claim.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
The Examiner suggests amending the claim to recite ‘wherein the target DNA sequence is a protein-coding sequence’, for example.
5. Claims 1, 3-4, 7-8, 10-12, 14, 16-17, and 20-23 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1 and 20 are directed to methods for transcriptional suppression of a target gene locus of interest in a eukaryotic cell, comprising the step(s) of introducing into the eukaryotic cell an engineered CRISPR-Cas9 system,
wherein the engineered CRISPR-Cas9 system comprises:
(a) a Cas9 enzyme having DNA cleavage activity; and
(b) a single guide polynucleotide comprising a guide sequence consisting of 11-15
contiguous nucleotides that are 100% complementary to a target DNA sequence at the target gene locus of interest,
wherein the single guide polynucleotide forms a CRISPR complex with the Cas9 enzyme and directs sequence-specific binding of the CRISPR complex to the target DNA sequence.
Claims 4 and 21 are directed to methods for transcriptional modulation (upregulation or downregulation) of a target gene locus of interest in a eukaryotic cell, comprising the step(s) of introducing into the eukaryotic cell an engineered CRISPR-Cas9 system,
wherein the engineered CRISPR-Cas9 system comprises:
(a) a Cas9 enzyme having DNA cleavage activity; and
(b) a single guide polynucleotide comprising a guide sequence consisting of 11-15
contiguous nucleotides that are 100% complementary to a target DNA sequence at the target gene locus of interest,
wherein the gRNA comprises an aptamer that binds to an adaptor protein fused to at least one transcriptional activator domain or transcriptional repressor domain,
wherein the single guide polynucleotide forms a CRISPR complex with the Cas9 enzyme and directs sequence-specific binding of the CRISPR complex to the target DNA sequence.
Claim 3 recites wherein the guide sequence consists of 13-15 nucleotides that are complementary to a target DNA.
Claim 7 recites a genus of adaptor proteins, including elected species MS2.
Claims 22-23 recite a subgenus of adaptor proteins, including elected species MS2.
Claim 8 recites a genus of transcriptional activator domains, including elected species VP64.
Claim 12 recites a genus of transcriptional activator domains, including elected species VP64.
Claim 11 recites wherein the Cas9 is fused to a generic transcriptional activator or repressor.
Claim 16 recites wherein the target DNA sequence is a gene coding sequence.
The Examiner incorporates herein the above 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, rejection.
Claim 17 recites wherein the target DNA sequence is a promoter, enhancer, or silencer sequence.
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 Examiner provides below an illustration of a target gene locus of interest in a eukaryotic cell.
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Lopes et al (Gene Size Matters: An Analysis of Gene Length in the Human Genome, Frontiers in Genetics (12): e559998; doi.org/10.3389/fgene.2021.559998; February 10, 2021) is considered relevant art for having taught that the length of human genes may range from about 30,355-119,000 nucleotides in length (Table 1).
Bai et al (Bioinformatics Analysis of MSH1 Genes of Green Plants: Multiple Parallel Length Expansions, Intron Gains and Losses, Partial Gene Duplications, and Alternative Splicing, Int. J. Mol. Sci. 24(17): e13620; doi:10.3390/ijms241713620; September 2023) is considered relevant art for having taught that the length of plant genes may range from about 3250-805,900 nucleotides in length (Abstract; pg 3, para 2, “gene length….over 50kb, …even over 500kb” (syn. 500,000 nucleotides)).
The claims encompass an enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of structurally undisclosed target DNA sequences (“?”, shown below) essentially anywhere in a genomic locus of interest in a eukaryotic cell, whereby said genomic locus may be as large as 50kb, 500kb, or 806kb.
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The art does not teach, and the specification fails to disclose, the ability of a CRISPR/Cas9 system comprising the enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of structurally undisclosed target DNA sequences essentially anywhere in a target gene being as large as 50kb, 500kb, or 806kb so as to necessarily and predictably suppress transcription of said target gene locus via the CRISPR/Cas9 system, in and of itself, including in the absence of transcriptional repressor domain (Claims 1 and 20), nor
so as to necessarily and predictably modulate (syn. increase or decrease) transcription of a target gene locus via the CRISPR/Cas9 system comprising the use of an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest (Claims 4 and 21).
Huimin et al (Analysis of Intron Sequence Features Associated with Transcriptional Regulation in Human Genes, PLoS One 7(10): e46784; doi.org/10.1371/journal.pone.0046784, 2012) is considered relevant prior art for having taught that the length of eukaryotic introns may range from about 5,850-36,450 nucleotides (Table 1) and that intron lengths as large as 10,000 nucleotides are known (e.g. pg 3, col. 1).
Schoenfelder et al (Long-range enhancer–promoter contacts in gene expression control, Nature Reviews Genetics 20: 437-455, May 13, 2019) is considered relevant art for having taught that enhancer elements affecting the transcription of a gene may exist as many as 600,000 nucleotides (syn. 600kb), 850kb, or even 900kb (pg 440, col. 1), away from the promoter of a given gene (illustrated below),
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whereby the enhancer element may even within an entirely different gene (e.g. Figure 2a; ZRS element in Lmbr1 gene, about 850kb away from and acting on Shh gene, shown below), whereby the enhancer does not appear to act through a canonical enhancer-promoter contact (e.g. pg 439, col. 2).
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However, instant claims fail to recite, and the specification fails to disclose, the enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of structurally undisclosed target DNA sequences (“?”, shown below) essentially anywhere in a genomic locus of interest being as large as 50kb, 500kb, or 806kb in a eukaryotic cell,
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so as to necessarily and predictably suppress transcription of a target gene locus via the CRISPR/Cas9 system, in and of itself, including in the absence of transcriptional repressor domain (Claims 1 and 20), nor
so as to necessarily and predictably modulate (syn. increase or decrease) transcription of a target gene locus via the CRISPR/Cas9 system comprising the use of an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest (Claims 4 and 21).
Those of ordinary skill in the art would immediately recognize that the aptamer nucleic acid sequence of SEQ ID NO:85 that binds MS2 does not adequately represent, let alone adequately describe, the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, because both the genus of aptamer nucleic acid sequences and the genus of “adaptor proteins” are each recited at a high level of generality and composed of enormously vast genus of different nucleic acid and amino acid structures, respectively.
Instant claims fail to recite, and the specification fails to disclose, the enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of structurally undisclosed target DNA sequences in:
i) the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence, whereby said genes may be as large as 30kb, 50kb, 119kb, 500kb, or 800kb nucleotides in length;
ii) whereby said genes may comprise a multitude of structurally different exon coding sequences within the body of the gene of interest, whereby the gRNA may target any of said exons, including 3’ terminal exons;
iii) whereby said genes may comprise a multitude of structurally different, and functionally undisclosed nucleotide sequences within introns ranging from about 5,850-36,450 nucleotides, to as large as 10,000 nucleotides, whereby the gRNA may target any of said introns; and/or
iv) whereby said genes may comprise a multitude of structurally different, and functionally undisclosed nucleotide sequences that are to have the functional property of being an enhancer, promoter, or silencer sequence (e.g. Claim 17), said enhancer and/or silencer existing as many as 600,000 nucleotides (syn. 600kb), 850kb, or even 900kb (pg 440, col. 1), away from the promoter of a given gene, including within the nucleotide sequence of an entirely different gene,
so as to necessarily and predictably suppress transcription of a target gene locus via the CRISPR/Cas9 system, in and of itself, including in the absence of transcriptional repressor domain (Claims 1 and 20), nor
so as to necessarily and predictably modulate (syn. increase or decrease) transcription of a target gene locus via the CRISPR/Cas9 system comprising the use of an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest (Claims 4 and 21).
Church et al (U.S. 2014/0356956; of record) is considered relevant prior art for having taught a CRISPR/Cas9-transcriptional activator system does not increase transcription of a synthetic promoter-reporter expression cassette when the gRNA targets a sequence that is greater than 1kb away from the transcription start site (e.g. Figure 6A).
Rather, at best, Applicant’s specification discloses a CRISPR/Cas9 system comprising the use of a single specific aptamer sequence (e.g. [00697], SEQ ID NO:85) that has the functional property of binding to an MS2 adaptor protein, wherein the truncated gRNA is targeted to a DNA sequence within 200 nucleotides of the transcriptional start site of the target gene (e.g. [00681], “within 200 nucleotides of the transcriptional start site”).
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The breadth of the claims reasonably encompasses an enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of structurally undisclosed target DNA sequences of a genomic locus of interest in a eukaryotic cell.
The specification fails to disclose a structure/function nexus between the length of the dead guide sequence, its corresponding amount of complementarity to its corresponding target sequence to which it is to hybridize, and the corresponding resulting amount of indel activity, e.g. less than 20%, less than 15%, less than 10%, less than 8%, less than 5%, less than 3%, less than 0.2% indel activity, less than 0.1% indel activity, and/or 0% indel activity.
Figure 6C evidences that:
(a) a Cas9 enzyme having DNA cleavage activity; and
(b) a single guide polynucleotide comprising a guide sequence consisting of 11-15 nucleotides,
wherein said guide sequence is 100% complementary to a target DNA sequence at the genomic locus of interest, and
wherein the single guide polynucleotide forms a CRISPR complex with the Cas9 enzyme and directs sequence-specific binding of the CRISPR complex to the target DNA sequence,
produces a double-stranded break at the genomic locus of interest, e.g. 3% or less indel frequencies, depending upon the nucleotide sequence of the guide sequence consisting of 11-15 nucleotides.
Qi et al (Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression, Cell 152: 1173-1183, February 28, 2013; of record in IDS and cited in prior Office Actions) is considered relevant prior art for having taught that a guide sequence of 12 nucleotides is minimally sufficient to allow a guide polynucleotide complexed with Cas9 to hybridize to a target sequence (pg 1177, col. 1, “[T]he minimal length of the base-pairing region need…was 12bp, with further truncation leading to complete loss of function”).
Zhang et al (U.S. Patent 10,494,621; of record) is considered relevant prior art for having disclosed that while truncated guide sequences may reduce off-target activity at some reference target site(s), they increased off-target activity at other target sites (Example 14, col. 464, lines 52-54).
Xie et al (RNA-Guided Genome Editing in Plants Using a CRISPR–Cas System, Molecular Plant 6(6): 1975-1983, 2013; available online August 17, 2013; of record in IDS) is considered relevant prior art for having taught that guide sequences of 22 nucleotides in length comprising one or more nucleotide mismatches relative to a first target site (PS3), wherein said guide sequence is now capable of hybridizing to said first target site and to a second, different target site (“off-target”), even though at least 10 nucleotides of the guide sequence seed region remain unchanged (Figure 4).
Cho et al (Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases, Genome Research 24: 132-141, 2013; available online November 19, 2013; of record in IDS and parent application 15/620,391) is considered relevant prior art for having taught guide sequences of 20 nucleotides in length comprising one or more nucleotide mismatches relative to a first target site (“on”), wherein said guide sequence is no longer capable of hybridizing to said first target site but instead to a second, different off-target site (“Off4”, “Off5”), even though at least 10 nucleotides of the guide sequence seed region remain unchanged (Figure 1B).
Thus, while the single guide polynucleotide comprising a guide sequence of 10 to 16 nucleotides in length appears to have lost the recited functional property relative to a first, arbitrary “target sequence”, it has gained the recited functional property relative to a second, arbitrary “target sequence”.
Joung et al (U.S. 2014/0295557; of record) is considered relevant prior art for having disclosed truncated guide RNAs that, when bound with enzymatically Cas9 enzymes have essentially no detectable % indel activity (Figures 2H (15nt guide sequence); 3A (16 nt guide sequence).
Similarly, Church et al (U.S. 2014/0356956; of record) is considered relevant prior art for having disclosed truncated guide RNAs that are 11 or 15 nucleotides in length (Figure 16D-2), for which no indel activity is detectable.
The claims fail to recite, and the specification fails to disclose, the structure/function nexus between the Cas9 enzyme directed to the genomic locus of interest via the single guide polynucleotide comprising a guide sequence consisting of 11-15 contiguous nucleotides that are 100% complementary to a target DNA sequence at the genomic locus of interest that is able to produce a double-stranded break at the genomic locus of interest, as opposed to the Cas9 enzyme directed to the genomic locus of interest via the single guide polynucleotide comprising a guide sequence consisting of 11-15 contiguous nucleotides that are 100% complementary to a target DNA sequence at the genomic locus of interest that is not able to produce a double-stranded break at the genomic locus of interest.
The claims fail to recite, and the specification fails to disclose, how to transform or otherwise modify a first single guide polynucleotide of the enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences comprising a guide sequence consisting of 11-15 contiguous nucleotides that are complementary to a target DNA sequence at the genomic locus of interest that when complexed with a Cas9 enzyme having DNA cleavage activity and directs said Cas9 to the target DNA produces a double-stranded break at the genomic locus of interest into a second single guide polynucleotide of the enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences comprising a guide sequence consisting of 11-15 contiguous nucleotides that are complementary to a target DNA sequence at the genomic locus of interest that when complexed with a Cas9 enzyme having DNA cleavage activity and directs said Cas9 to the target DNA now necessarily and predictably do not produce a double-stranded break at the genomic locus of interest for example.
The claims fail to recite, and the specification fails to disclose, the common core structure of the enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that when complexed with a Cas9 enzyme having DNA cleavage activity and directs said Cas9 to the target DNA necessarily and predictably have the functional property of not producing a double-stranded break at the genomic locus of interest.
Without a correlation between structure and function, the claim does little more than define the claimed invention by function. That is not sufficient to satisfy the written description requirement. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406 (“definition by function … does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is”).
The claims are broad for reciting the eukaryotic cell at a high level of generality, encompassing all extant eukaryotic lifeforms.
Sweetlove (Nature News doi:10.1038/news.2011.498, August, 2011; waynesword.palomar.edu/trfeb98.htm, last visited April 8, 2021) is considered relevant prior art for having taught that there is an estimated 8.7 million species of eukaryotic organisms, including about 250,000 species of eukaryotic protists, about 100,000 species of fungi, about 250,000 species of plants, and about 1,000,000 species of animals
BBC News (https://www.bbc.com/news/science-environment-14616161; August 23, 2011) is considered relevant prior art for having taught that there is an estimated 8.7 million different species on the planet, comprising about 7.77 million animal species, about 610,000 fungal species, about 300,000 plant species, and about 40,000 protozoan species.
Finlay (Global dispersal of free-living microbial eukaryote species, Science 296: 1061-1063, 2002) is considered relevant prior art for having taught that there is an estimated 20,000 different single-celled eukaryotic (protozoan) species, and as many as 5,000,000 different insect species (pg 1061, col. 2).
Mongabay (How many plant species are there in the world? Scientists now have an answer, https://news.mongabay.com/2016/05/many-plants-world-scientists-may-now-answer/; May 12, 2016) is considered relevant prior art for having taught that there is an estimated 391,000 different vascular plant species currently known to science, according to a report by the Royal Botanic Gardens, Kew, in the United Kingdom.
Mammalian subject reasonably encompasses some 6,400 species (including Humans), distributed in about 1,200 genera, 152 families and up to 46 orders (en.wikipedia.org/wiki/Mammal, last visited August 31, 2022).
The claims are broad for reciting the genomic locus of interest at a high level of generality.
Medline Plus (What is a gene?; medlineplus.gov/genetics/understanding/basics/gene; last visited March 4, 2024) teach that the number of genes in the human genome is between 20,000 and 25,000 genes.
Wikipedia (Non-coding RNA; en.wikipedia.org/wiki/Non-coding_RNA; last visited March 4, 2024) teach that the number of non-coding RNAs within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest that there are thousands of non-coding RNA transcripts.
Hjelman (Genome size and chromosome number are critical metrics for accurate genome assembly assessment in Eukaryota, Genetics 227(4): iyae099 (15 pages), doi:10.1093/genetics/iyae099, available online August 7, 2024) is considered relevant post-filing art for having taught that only 2,300 eukaryotic species have had their genomes sequenced.
Thus, the claims reasonably encompass the remainder of the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence.
The claims are broad for reciting the guide sequence at a high level of generality.
[0096] discloses “truncated guides” whose guide sequence consists of (e.g. Figure 6B) only 11-15 nucleotides.
4^11 = 4194304 possible sequence variants,
4^12 = 16777216 possible sequence variants,
4^13 = 67108864 possible sequence variants,
4^14 = 268435456 possible sequence variants, and
4^15 = 1073741824 possible sequence variants.
which yields more than 5.7x10^9 structurally undisclosed guide RNA target sequences.
(www.calculator.net/exponent-calculator; last visited May 30, 2025)
Thus, the breadth of the claims reasonably encompasses an enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of structurally undisclosed target DNA sequences of a genomic locus of interest in a eukaryotic cell,
whereby said sgRNA, when complexed with a Cas9 having DNA cleavage activity, may or may not result in the production of a double-stranded break at the genomic locus of interest,
thereby modulating transcription of the genomic locus of interest.
However, the specification fails to disclose working examples whereby an sgRNA comprising a truncated guide sequence consisting of 11-15 contiguous nucleotides complementary to a target sequence necessarily and predictably, when complexed with only a Cas9 having DNA cleavage activity, e.g. wildtype Cas9:
results in the production of a double-stranded break at the genomic locus of interest, thereby modulating transcription of the genomic locus of interest, e.g. activate transcription; nor
does not result in the production of a double-stranded break at the genomic locus of interest, thereby modulating transcription of the genomic locus of interest, e.g. suppress transcription.
The claims fail to recite, and the specification fails to disclose, an sgRNA comprising a truncated guide sequence consisting of 11-15 contiguous nucleotides complementary to a target sequence within the body of the artisan’s gene of interest, e.g. internal exon and/or internal intron, necessarily and predictably, when complexed with only a Cas9 having DNA cleavage activity, e.g. wildtype Cas9:
results in the production of a double-stranded break at the genomic locus of interest, thereby modulating transcription of the genomic locus of interest, e.g. activate transcription; nor
does not result in the production of a double-stranded break at the genomic locus of interest, thereby modulating transcription of the genomic locus of interest, e.g. suppress transcription.
Rather, the working examples are directed to sgRNAs directed to a promoter upstream of the HBG1 gene (e.g. [0097], “the promoter regions of…HBG1”), said sgRNAs comprising an aptamer that binds MS2, thereby bringing in a MS2-p65-HIF1 transcriptional activation complex (Figure 6C, [0097]).
Those of ordinary skill in the art immediately recognize Claim 1 being far broader in scope than Applicant’s examples. The breadth of Claim 1 encompasses embodiments including the absence of recruiting an endogenous or heterologous transcriptional activation and/or repression complex, support for which is simply not found in the instant application, specifically, let alone for the enormously vast breadth of the instant claims.
Claims 4-5 are broad for reciting the aptamer sequence at a high level of generality, wherein said aptamers are to have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides.
Without a correlation between structure and function, the claim does little more than define the claimed invention by function. That is not sufficient to satisfy the written description requirement. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406 (“definition by function … does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is”).
Rich et al (U.S. 2017/0165376) is considered relevant art for having disclosed aptamers being 200, 100, 50, 40, or 35 nucleotides in length (e.g. [0030]).
Doyle et al (U.S. Patent 8,105,982) is considered relevant prior art for having disclosed aptamers being 20-50 nucleotides in length (e.g. col. 4, lines 13-14), whereby the aptamers may have an enormous range of binding affinities to its corresponding target molecule, ranging from as low as 10^-4 M, 10^-5 M, 10^-6M, 10^-8M, or 10^-9M (col. 12, lines 5-7; col 14, lines 1-2), a range of at least 5 orders of magnitude.
4^200 = about 2x10^120 structurally undisclosed aptamers.
4^150 = about 2x10^90 structurally undisclosed aptamers.
4^100 = about 1x10^60 structurally undisclosed aptamers.
4^75 = about 1x10^45 structurally undisclosed aptamers.
4^50 = about 1x10^30 structurally undisclosed aptamers.
4^30 = about 1x10^18 structurally undisclosed aptamers.
Cho et al (Quantitative selection and parallel characterization of aptamers, PNAS 110(46): 18460-18465, 2013; of record in IDS) is considered relevant prior art for having taught that, while aptamers with high affinity and specificity have been previously reported for a wide range of molecular targets, including proteins, and that recent advances in selection and sequencing techniques have greatly increased the efficiency of aptamer discovery, despite these advances, the generation of high-quality aptamers remains a time-consuming and low-throughput process (pg 18460, Introduction). Screening a library of 10^14 molecules (pg 18464, col. 1, Methods) yielded only about 235 initial candidate aptamers, of which only 8 possessed sufficient high affinity to their target (e.g. Figure 3).
Thus, it is considered undue experimentation to synthesize and screen the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides.
Claims 6-7 are broad for reciting the aptamer sequence at a high level of generality, wherein said aptamers are to have the functional property of binding an adaptor protein, also recited at a high level of generality, that is to be fused to a transcriptional activator domain or a transcriptional repressor domain, also recited at a high level of generality.
The claims encompass the resulting functional properties of producing a double-stranded cleavage of the DNA target sequence in addition to modulating transcription of the target locus via the transcriptional activator or repressor domain fused to the adaptor protein.
The specification fails to disclose a sgRNA that, when complexed with a Cas9 protein having DNA cleavage activity, necessarily and predictably achieves the functional properties of both:
producing a double-stranded cleavage of the DNA target sequence; and
modulating transcription of the target locus via the transcriptional activator or repressor domain fused to the adaptor protein.
While Claim 7 recites a genus of about 29 adaptor proteins, Claims 4-6, being broader in scope, reasonably encompasses a far greater genus of structurally and functionally undisclosed proteins, identified solely using functional language “adaptor”.
Without a correlation between structure and function, the claim does little more than define the claimed invention by function. That is not sufficient to satisfy the written description requirement. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406 (“definition by function … does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is”).
Tiessen et al (Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes, BMC Research Notes 5(85): 23 pages, doi:10.1186/1756-0500-5-85, 2012) is considered relevant prior art for having taught that the average eukaryotic protein is about 472 amino acids in length (Abstract).
20^470 = an infinite genus of structurally undisclosed amino acid sequences.
20^425 = an infinite genus of structurally undisclosed amino acid sequences.
20^375 = an infinite genus of structurally undisclosed amino acid sequences.
20^325 = an infinite genus of structurally undisclosed amino acid sequences.
20^275 = an infinite genus of structurally undisclosed amino acid sequences.
20^225 = about 5x10^292 structurally undisclosed amino acid sequences.
20^175 = about 5x10^227 structurally undisclosed amino acid sequences.
20^125 = about 4x10^162 structurally undisclosed amino acid sequences.
20^75 = about 4x10^97 structurally undisclosed amino acid sequences.
20^25 = about 3x10^32 structurally undisclosed amino acid sequences.
Thus, the breadth of the claims reasonably encompasses an infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”.
The claims fail to recite, and the specification fails to disclose, a first aptamer of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that necessarily and predictably has the functional property of binding to a first “adaptor protein” of the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, as opposed to a second aptamer of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that necessarily and predictably has the functional property of binding to a second “adaptor protein” of the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, for example.
The claims fail to recite, and the specification fails to disclose, how to transform or otherwise modify a first aptamer of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that does not have the functional property of binding to a MS2 “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, into a second aptamer of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that now necessarily and predictably has the functional property of binding to a MS2 “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, for example.
The claims fail to recite, and the specification fails to disclose, the common core structure of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to a MS2 “adaptor protein”.
The claims fail to recite, and the specification fails to disclose, what nucleotides of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences must remain present in order to necessarily and predictably have the functional property of binding to a MS2 “adaptor protein”, as opposed to what nucleotides of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences may be absent, yet still necessarily and predictably have the functional property of binding to a MS2 “adaptor protein”, for example.
While Claim 8 recites a genus of about 6 transcription factor proteins comprising a transcriptional activation domain, Claims 4-6, being broader in scope, reasonably encompasses a far greater genus of structurally and functionally undisclosed transcription factor proteins comprising a transcriptional activation domain, identified solely using functional language “comprising a transcriptional activation domain”.
The art recognizes that the human genome encodes about 2800 proteins containing a DNA-binding domain, with about 2000 being described as transcription factors (e.g. Transcription factor, Wikipedia, en.wikipedia.org/wiki/Transcription_factor; last visited May 30, 2025).
Thus, the breadth of the claims reasonably encompasses an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to have the functional property of:
binding to an infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”,
wherein said enormously vast genus of “adaptor” proteins are to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors.
Claim 16 is broad for reciting at a high level of generality that the genomic locus of interest is a gene coding sequence.
As discussed above, the claims reasonably encompass the remainder of the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence.
Claim 17 is broad for reciting at a high level of generality that the genomic locus of interest is a promoter, enhancer, or silencer sequence.
Blanco et al (Transcription Factor Map Alignment of Promoter Regions, PLoS Computational Biology 2(5): e49, 14 pages, DOI: 10.1371/journal.pcbi.0020049, May, 2006) is considered relevant prior art for having taught that while sequence comparisons and alignments are among the most powerful tools in research in biology, such has limitations because often similar functions are encoded by higher order elements which do not hold a univocal relationship to the underlying primary sequence. In consequence, similar functions are frequently encoded by diverse sequences. Promoter regions, which are functionally defined genetic elements, are a case in point. Often, promoter sequences of genes with similar expression patterns do not show conservation. This is because, even though their expression may be regulated by a similar arrangement of transcription factors, the binding sites for these factors may exhibit great sequence variability (e.g. pg 2, col. 1).
Heinz et al (The selection and function of cell type-specific enhancers, Nat Rev Mol Cell Biol 16, 144–154, doi.org/10.1038/nrm3949, available online February 4, 2015) is considered relevant post-filing art for having taught that enhancers, which are functionally defined genetic elements, may be located at distances ranging from hundreds to millions of nucleotides away from a given target gene (pg 144, col. 1). Beyond the simple annotation of regulatory regions in the genome, it is important to understand how cells select the full complement of enhancers that are required for maintaining their identities and functions. Defining functional enhancer–promoter interactions remains an important goal. Despite being informative, chromatin connectivity maps do not directly relate chromatin interactions to the regulation of gene expres-sion. Definitive evidence that a specific enhancer-like region exerts a transcriptional regulatory function requires the study of mutational effects on that region (e.g. pg 152, col. 2).
Pang et al (Systematic identification of silencers in human cells, Nature Genetics 52: 254-263, doi.org/10.1038/s41588-020-0578-5, available online February 24, 2020) is considered relevant post-filing art for having taught that regions the repress gene expression—silencers—have not been systematically studied. Silencers, which are functionally defined genetic elements, can act on multiple genes, at the level of chromosomal domains, and via long-range interactions (Abstract). Although silencers are an important class of regulatory elements, to date most studies have been performed on identification and characterization of individual silencer regions. and high-throughput methods have not been described to systematically identify genomic silencers. As such, we do not know how many silencers exist, how they operate at the level of chromosomal domains or whether they exhibit ubiquitous or cell-type-specific activity (e.g. pg 254, col. 1, Introduction). In one study, only about 2% of the silencers identified in a first cell type were shared with the silencers identified in a second cell type (e.g. pg 256, col. 2). Future genome-wide analysis of silencers is required to provide a clearer picture of all possible silencing signatures (e.g. pg 261, col. 1).
Maston et al (Transcriptional Regulatory Elements in the Human Genome, Ann. Rev. Genomics Hum. Genet. 7: 29-59, 2006) is considered relevant prior art for having taught that one of the main emerging challenges for genomics research is to identify all functional elements in the genome, including those that regulate gene expression (pg 30, col. 1). The structure of human gene promoters can be quite complex, typically consisting of multiple transcriptional regulatory elements. The presence of multiple regulatory elements within promoters confers combinatorial control of regulation, which exponentially increases the potential number of unique expression patterns. Such transcriptional regulatory elements include locus control regions (LCRs), insulators, silencers, enhancer, the core promoter, and proximal promoter elements (Figure 1), whereby the distal elements such as LCRs, insulators, silencers, and enhancers may well be over 1 megabase (1 million nucleotides in length) away from the promoter. These regulatory elements can be widely dispersed from the corresponding target gene each regulates (pg 42, col. 2). Identifying the promoter of a specific target gene can be a challenge because the core promoter is often distantly located from the first coding exon (pg 45, col. 1). In addition, because promoters can contain any one of a number of combinations of core promoter elements [and, conversely, many promoters have only one or no such elements (68)], simply searching for the co-occurrence of known core promoter motifs has had only limited success (pg 45, col. 2). Although much improved over earlier prediction programs, these methods still have limited sensitivity and specificity when applied to genome-scale sequence data (pg 45, col. 2). While a number of bioinformatics approaches attempt to list potential transcription factor binding sites based on a statistical match between a region in the sequence and a site matrix. This analysis is often hampered by the prediction of a large number of sites, a significant fraction of which are likely false positives. In addition to the false-positive problem, the completeness of these databases is also an issue; it is likely that not all DNA-binding transcription factors have been identified, and even for some known factors, their binding specificity has not yet been fully characterized. (pg 46, col. 2). Transcription factor binding sites are small and degenerate, are often located distantly from the promoter upon which they act, and are not always conserved through evolution. These properties make regulatory elements difficult to identify through computational means alone (pg 48, col. 2).
Similarly, Thakurta (Computational identification of transcriptional regulatory elements in DNA sequence, Nucleic Acids Res. 34(12): 3585-3598, 2006) is considered relevant prior art for having taught that identification and annotation of all the functional elements in the genome, including genes and the regulatory sequences, is a fundamental challenge in genomics and computational biology. Since regulatory elements are frequently short and variable, their identification and discovery using computational algorithms is difficult (Abstract). However, our knowledge of the transcriptional regulatory elements in the genome and their contribution to gene expression in different spatial and temporal contexts is still limited. Given the complex pattern of regulatory interactions, the challenges involved in the complete elucidation of these elements in the genome are substantial (pg 3593, Conclusion).
However, neither the prior art nor the instant specification disclose the structural identity of the enormous genus of regulatory elements including silencers, enhancers, and promoters, of the enormous genus of (target) genes within all recognized eukaryotic life forms.
The specification fails to make up for the deficiencies of the global scientific community.
Thus, the breadth of the claims reasonably encompasses an enormously vast genus of structurally undisclosed and yet-to-be identified genetic elements that are to have the functional property of being a promoter, enhancer, or silencer, whereby those of ordinary skill in the art have long-recognized that the identification of such elements is predicated on a functional analysis, as similar functions are frequently encoded by diverse sequences, and the binding sites for these factors may exhibit great sequence variability.
The claims fail to recite, and the specification fails to disclose, the structure/function nexus of a structurally undisclosed and yet-to-be identified genetic element having the functional property of being a enhancer and its corresponding gene of interest in the genomes of the enormously vast genus of about 8.7 million eukaryotic species whose genomes simply have not been sequenced, and thus are technically unknown, when the art recognizes that enhancers may be located hundreds to thousands to millions of nucleotides away from a given gene of interest and the binding sites for these transcription factors may exhibit great sequence variability.
The claims fail to recite, and the specification fails to disclose, the structure/function nexus of a structurally undisclosed and yet-to-be identified genetic element having the functional property of being a promoter and its corresponding gene of interest in the genomes of the enormously vast genus of about 8.7 million eukaryotic species whose genomes simply have not been sequenced, and thus are technically unknown, when the art recognizes that the binding sites for these transcription factors may exhibit great sequence variability.
The claims fail to recite, and the specification fails to disclose, the structure/function nexus of a structurally undisclosed and yet-to-be identified genetic element having the functional property of being a silencer and its corresponding gene of interest in the genomes of the enormously vast genus of about 8.7 million eukaryotic species whose genomes simply have not been sequenced, and thus are technically unknown, when the art recognizes that enhancers may be located hundreds to thousands to millions of nucleotides away from a given gene of interest and the binding sites for these transcription factors may exhibit great sequence variability.
The claims fail to recite, and the specification fails to disclose, the nucleotide sequence of a first guide sequence of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that is to have the functional property of being complementary to an enormously vast genus of structurally undisclosed and yet-to-be identified genetic elements having the functional property of being a promoter, as opposed to
the nucleotide sequence of a first guide sequence of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that is to have the functional property of being complementary to an enormously vast genus of structurally undisclosed and yet-to-be identified genetic elements having the functional property of being an enhancer, as opposed to
the nucleotide sequence of a first guide sequence of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that is to have the functional property of being complementary to an enormously vast genus of structurally undisclosed and yet-to-be identified genetic elements having the functional property of being a silencer, for example.
The claims fail to recite, and the specification fails to disclose, how to transform or otherwise modify a first nucleotide sequence of a first guide sequence of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that does not have the functional property of being complementary to a genetic element having the functional property of being a silencer, into a second nucleotide sequence of a first guide sequence that now necessarily and predictably has the functional property of being complementary to a genetic element having the functional property of being a silencer, for example.
The claims fail to recite, and the specification fails to disclose, how to transform or otherwise modify a first nucleotide sequence of a first guide sequence of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that does not have the functional property of being complementary to a genetic element having the functional property of being an enhancer, into a second nucleotide sequence of a first guide sequence that now necessarily and predictably has the functional property of being complementary to a genetic element having the functional property of being an enhancer, for example.
As discussed above, the claims reasonably encompass the remainder of the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a genetic element having the functional property of being a promoter, an enhancer, and/or a silencer sequence.
Thus, it is considered undue experimentation to design and screen the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences in the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a genetic element having the functional property of being a promoter, an enhancer, and/or a silencer sequence so as to functionally identify which genetic elements are enhancers, silencers, and/or promoters.
"The claimed invention as a whole may not be adequately described if the claims require an essential or critical element which is not adequately described in the specification and which is not conventional in the art", "when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus", "in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus''. MPEP §2163
An applicant shows possession of the claimed invention by describing the claimed invention with all of its limitations using such descriptive means as words, structures, figures, diagrams, and formulas that fully set forth the claimed invention. Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997).
Possession may also be shown in a variety of ways including description of an actual reduction to practice, or by showing that the invention was ''ready for patenting'' such as by the disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention. See, e.g., Pfaff v. Wells Elecs., Inc., 525 U.S. 55, 68, 1 19 S.Ct. 304, 312, 48 USPQ2d 1641, 1647 (1998), Regents of the University of California v. Eli Lilly, 119 F.3d 1559, 1568, 43 USPQ2d 1398, 1406 (Fed. Cir. 1997)*, Amgen, Inc. v. Chugai Pharmaceutical, 927 F.2d 1200, 1206, 18 USPQ2d 1016, 1021 (Fed. Cir. 1991) (one must define a compound by ''whatever characteristics sufficiently distinguish it'').
Therefore, conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. See Fiers v. Revel, 25 USPQ2d 1602 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481, 1483. In Fiddes, claims directed to mammalian FGF's were found to be unpatentable due to lack of written description for that broad class. The specification provided only the bovine sequence.
Without a correlation between structure and function, the claim does little more than define the claimed invention by function. That is not sufficient to satisfy the written description requirement. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406 (“definition by function … does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is”).
In Amgen, Inc., v. Sanofi (872 F.3d 1367 (2017)
At 1375, [T]he use of post-priority-date evidence to show that a patent does not disclose a representative number of species of a claimed genus is proper.
At 1377, [W]e questioned the propriety of the "newly characterized antigen" test and concluded that instead of "analogizing the antibody-antigen relationship to a `key in a lock,'" it was more apt to analogize it to a lock and "a ring with a million keys on it." Id. at 1352.
An adequate written description must contain enough information about the actual makeup of the claimed products — "a precise definition, such as by structure, formula, chemical name, physical properties, or other properties, of species falling within the genus sufficient to distinguish the genus from other materials," which may be present in "functional" terminology "when the art has established a correlation between structure and function." Ariad, 598 F.3d at 1350. But both in this case and in our previous cases, it has been, at the least, hotly disputed that knowledge of the chemical structure of an antigen gives the required kind of structure-identifying information about the corresponding antibodies. See, e.g., J.A. 1241 (549:5-
16) (Appellants' expert Dr. Eck testifying that knowing "that an antibody binds to a particular amino acid on PCSK9 ... does not tell you anything at all about the structure of the antibody"); J.A. 1314 (836:9-11) (Appellees' expert Dr. Petsko being informed of Dr. Eck's testimony and responding that "[m]y opinion is that [he's] right"); Centocor, 636 F.3d at 1352 (analogizing the antibody-antigen relationship as searching for a key "on a ring with a million keys on it") (internal citations and quotation marks omitted).
In the instant case, knowing that the sgRNA is to comprise a guide sequence consisting of 11-15 contiguous nucleotides that are complementary to a target DNA sequence at a genomic locus of interest does not tell you anything at all about:
the nucleotide sequence [structure] of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest.
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 method encompasses an entire universe of structurally and functionally undisclosed sgRNA nucleic acids.
“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.
Accordingly, this limited information is not deemed sufficient to reasonably convey to one skilled in the art that the applicant is in possession of the broadly claimed method using the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences consisting of 11-15 contiguous nucleotides that are complementary to a target DNA sequence that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest, at the time the application was filed.
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. Applicant is reminded that 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 claim(s).
Response to Arguments
Applicant argues that the sgRNAs are expressly designed to bind within -1000 to +1 nucleic acids upstream of the transcription start site (e.g. [0077]).
Applicant’s argument(s) has been fully considered, but is not persuasive.
As a first matter, 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). Instant independent claims fail to recite this limitation.
As a second matter, [0077] discloses “The sgRNA may be designed…”. Thus, the breadth of the claimed sgRNAs are not, in fact, expressly designed to bind within -1000 to +1 nucleic acids upstream of the transcription start site.
Applicant argues that Examples 1-8 disclose truncated/dead guides in CRISPR/Cas9 systems.
Applicant’s argument(s) has been fully considered, but is not persuasive. Those ordinary skill in the art would immediately recognize that the instant claims are vastly broader in scope than the working examples of truncated/dead guides directed to target sequences within 200 nucleotides upstream of the gene’s transcription target sequence.
Applicant argues that the skilled artisan knew how to design CRISPR-Cas9 gRNAs against any given gene in a eukaryotic cell, e.g., by scanning the genome for candidate targets adjacent to a protospacer motif (PAM) and identifying unique target sequences among the candidate targets.
Applicant’s argument(s) has been fully considered, but is not persuasive. Instant claims fail to recite, and the specification fails to disclose, the enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of structurally undisclosed target DNA sequences in:
i) the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence, whereby said genes may be as large as 30kb, 50kb, 119kb, 500kb, or 800kb nucleotides in length;
ii) whereby said genes may comprise a multitude of structurally different exon coding sequences within the body of the gene of interest, including 3’ terminal exons;
iii) whereby said genes may comprise a multitude of structurally different, and functionally undisclosed nucleotide sequences within introns ranging from about 5,850-36,450 nucleotides, to as large as 10,000 nucleotides; and/or
iv) whereby said genes may comprise a multitude of structurally different, and functionally undisclosed nucleotide sequences that are to have the functional property of being an enhancer, promoter, or silencer sequence (e.g. Claim 17), said enhancer and/or silencer existing as many as 600,000 nucleotides (syn. 600kb), 850kb, or even 900kb (pg 440, col. 1), away from the promoter of a given gene, including within the nucleotide sequence of an entirely different gene,
so as to necessarily and predictably suppress transcription of a target gene locus via the CRISPR/Cas9 system, in and of itself, including in the absence of transcriptional repressor domain (Claims 1 and 20), nor
so as to necessarily and predictably modulate (syn. increase or decrease) transcription of a target gene locus via the CRISPR/Cas9 system comprising the use of an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest (Claims 4 and 21).
Rather, at best, Applicant’s specification discloses a CRISPR/Cas9 system comprising the use of a single specific aptamer sequence (e.g. [00697], SEQ ID NO:85) that has the functional property of binding to an MS2 adaptor protein, wherein the truncated gRNA is targeted to a DNA sequence within 200 nucleotides of the transcriptional start site of the target gene (e.g. [00681], “within 200 nucleotides of the transcriptional start site”).
Applicant is essentially requiring the ordinary artisans to discover for themselves that which Applicant fails to disclose.
“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”.
Applicant argues that [0023, 73, and 81] disclose aptamers that bind adaptor proteins.
Applicant’s argument(s) has been fully considered, but is not persuasive.
[0024] is generic for the bacteriophage coat proteins, including, but not limited to, MS2, and is silent to the nucleotide sequence(s) of said aptamers that are to have the required functional properties.
[0072] discloses a genus of adaptor proteins, and is silent to the nucleotide sequence(s) of said aptamers that are to have the required functional properties.
[0082] discloses the generic concept of aptamers (high level of generality) binding to adaptor proteins (high level of generality).
None of these paragraphs provide adequate written description for the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein” encompassed by the independent claims.
Those of ordinary skill in the art would immediately recognize that the single aptamer nucleic acid sequence of SEQ ID NO:85 that binds MS2 does not adequately represent, let alone adequately describe, the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, because both the genus of aptamer nucleic acid sequences and the genus of “adaptor proteins” are each recited at a high level of generality and composed of enormously vast genus of different nucleic acid and amino acid structures, respectively.
Applicant argues that the bacteriophage coat proteins MS2, PP7, Qbeta, R17, fr, BZ13, GA, PRR1, MX1, NL95, JP501, and KU1 have been shown to bind cognate RNA hairpin structures (e.g. Rolfsson et al (2010; Exhibit A); Lim et al (2001; Exhibit B), and that the other listed phage coat proteins are also characterized to bind specific RNA hairpins (Rolfsson et al (2016; Exhibit C).
Applicant’s argument(s) has been fully considered, but is not persuasive.
Instant independent claims encompass an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein” encompassed by the independent claims.
As it pertains to the bacteriophage coat proteins, instant independent claims encompass an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to said genus of bacteriophage coat proteins.
Rolfsson et al (2010; Exhibit A) teaches that MS2 is well-characterized for its sequence-specific interaction with a specific RNA stem-loop (e.g. pg 2). Rolfsson et al (2010; Exhibit A) does not adequately describe the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to claimed genus of bacteriophage coat proteins, concordantly and respectively.
Lim et al (2001; Exhibit B) teach the PP7 operator (syn. aptamer) sequence differs significantly from those of other RNA phages (e.g. pg 22512, col. 1), including variations in the length of the stem, the size of the loop, and the position and importance of the bulge, which, for many, is essential (e.g. pg 22513, col. 2). Lim et al teach three specific aptamer sequences (Figure 1; MS2 aptamer, Qbeta aptamer, PP7 aptamer), which does not adequately describe the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to claimed genus of bacteriophage coat proteins, concordantly and respectively.
Rolfsson et al (2016; Exhibit C) teaches a genus of nucleic sequence(s) comprising a MS2 CP-binding motif (e.g. Table 1), for which there is no clear common core nucleotide sequence shared amongst all the sequences that identify them as necessarily and predictably being a MS2-binding aptamer. Rolfsson et al (Table 1) does not adequately describe the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to the claimed genus of bacteriophage coat proteins, concordantly and respectively.
Applicant is essentially requiring the ordinary artisans to discover for themselves that which Applicant fails to disclose.
“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 independent claims are enormously broad for encompassing:
the nucleotide sequence [structure] of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest.
The specification discloses variants of a single gRNA whose guide sequence is, respectively, directed to IL1B, LPAR5, ITGA9, EGFR, MED12, CUL3, TADA2B, EMX1, VEGFA, DNMT, TPCN2, NRG2, CACNA2D4, ADAMTSL1. However, said gRNA(s) is/are directed to the promoter region of the respective target genes (e.g. [0098]). Independent Claim 1 is vastly broader in scope that Applicant’s working examples because the claim encompasses gRNAs directed to any location within a target gene locus, e.g. 5’ region upstream of promoter and/or transcription start site, intron, exon, 3’ untranslated region, etc…, for which the specification fails to disclose that such gRNAs directed to these disparate structural and functional locations will necessarily and predictably achieve increased and/or decreased transcription of a genomic locus.
Applicant’s amendment to Claims 1 and 20 does nothing to address the lack of adequate written description for the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci because the claimed genus is highly variant.
Those of ordinary skill in the art would immediately recognize that said single gRNA target sequence species directed to the promoter region of the respective target genes is/are not representative of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci because the claimed genus is highly variant.
Applicant’s amendment to Claims 1 and 20 does nothing to address the lack of adequate written description for the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence.
Those of ordinary skill in the art would immediately recognize that Applicant’s use of human host cells in vitro (e.g. [00100, 666]) to assay the few gRNA species is/are not representative of the enormously vast genus of about 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence, whereby the method encompasses both in vitro and in vivo contexts, because the claimed genus is highly variant.
Applicant’s amendment to Claims 1 and 20 does nothing to address the lack of adequate written description for the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides (Claims 4-6), let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”.
Those of ordinary skill in the art would immediately recognize that the specification’s disclosure of an aptamer that binds MS2 (e.g. [00697], SEQ ID NO:85) is not representative of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides encompassed by the independent claims because the claimed genus is highly variant.
Applicant’s amendment to Claims 1 and 20 does nothing to address the lack of adequate written description for the enormous genus of about 2000 (at least within the human genome) structurally and functionally different transcription factors (Claims 6-8 and 12), thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest.
Those of ordinary skill in the art would immediately recognize that the specification’s disclosure of MS2 and/or p65 (e.g. Figure 6A) is not representative of the enormous genus of about 2000 (at least within the human genome) structurally and functionally different transcription factors (Claims 6-8 and 12), thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest because the genus is highly variant.
Applicant argues that the skilled artisan can scan the genome for candidate target PAM motifs and identify unique target sequences among the candidate targets.
Applicant’s argument(s) has been fully considered, but is not persuasive.
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 broadly claimed method encompasses using the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences consisting of 11-15 contiguous nucleotides that are complementary to a target DNA sequence that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest.
Applicant is essentially requiring the ordinary artisans to discover for themselves that which Applicant fails to disclose.
“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.
6. Claims 1, 3-8, 10-12, 14, 16-17, and 20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while enabling for:
A) a method for transcriptional suppression of a target gene locus of interest in a eukaryotic cell, the method comprising the step of introducing into the eukaryotic cell an engineered CRISPR/Cas9 system, wherein the CRISPR/Cas9 system comprises:
i) a Cas9 enzyme having DNA cleavage activity; and
ii) a single guide polynucleotide comprising a guide sequence consisting of 11-15 contiguous nucleotides that are 100% complementary to a target DNA sequence within 200 nucleotides of the transcriptional start site of the target gene locus of interest (Claims 1 and 20); and
B) a method for transcriptional modulation of a target gene locus of interest in a eukaryotic cell, the method comprising the step of introducing into the eukaryotic cell an engineered CRISPR/Cas9 system, wherein the CRISPR/Cas9 system comprises:
i) a Cas9 enzyme having DNA cleavage activity; and
ii) a single guide polynucleotide comprising:
a) a guide sequence consisting of 11-15 contiguous nucleotides that are 100% complementary to a target DNA sequence within 200 nucleotides of the transcriptional start site of the target gene locus of interest; and
b) at least one of the tetraloop and loop2 is modified by insertion of an aptamer comprising SEQ ID NO:85 that binds to bacteriophage coat protein MS2,
wherein the MS2 is fused to at least one transcriptional activator domain or transcriptional repressor domain (Claims 4 and 21),
does not reasonably provide enablement for:
the enormously vast genus of about 6x10^9, 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being 100% complementary to an enormous genus of structurally undisclosed target DNA sequences in:
i) the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence, which are only functionally-defined elements, whereby said genes may be as large as 30kb, 50kb, 119kb, 500kb, or 800kb nucleotides in length;
ii) whereby said genes may comprise a multitude of structurally different exon coding sequences within the body of the gene of interest, whereby the gRNA may target any of said exons, including 3’ terminal exons;
iii) whereby said genes may comprise a multitude of structurally different, and functionally undisclosed nucleotide sequences within introns ranging from about 5,850-36,450 nucleotides, to as large as 10,000 nucleotides, whereby the gRNA may target any of said introns; and/or
iv) whereby said genes may comprise a multitude of structurally different, and functionally undisclosed nucleotide sequences that are to have the functional property of being an enhancer, promoter, or silencer sequence (e.g. Claim 17), said enhancer and/or silencer existing as many as 600,000 nucleotides (syn. 600kb), 850kb, or even 900kb (pg 440, col. 1), 5’ and/or 3’ away from the promoter of a given gene, including within the nucleotide sequence of an entirely different gene,
so as to necessarily and predictably suppress transcription of a target gene locus via the CRISPR/Cas9 system, in and of itself, including in the absence of transcriptional repressor domain (Claims 1 and 20), nor
so as to necessarily and predictably modulate (syn. increase or decrease) transcription of a target gene locus via the CRISPR/Cas9 system comprising the use of an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest (Claims 4 and 21).
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.
Applicant is essentially requiring the ordinary artisans to discover for themselves that which Applicant fails to disclose.
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.
The instant portion of the invention, as claimed, falls under the "germ of an idea" concept defined by the CAFC. The court has stated that "patent protection is granted in return for an enabling disclosure, not for vague intimations of general ideas that may or may not be workable". The court continues to say that "tossing out the mere germ of an idea does not constitute an enabling disclosure" and that "the specification, not knowledge in the art, that must supply the novel aspects of an invention in order to constitute adequate enablement". (See Genentech Inc v. Novo Nordisk A/S 42 USPQ2d 1001, at 1005).
The claimed methods of using the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a genetic element having the functional property of being a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest, constitutes such a "germ of an idea".
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.
Applicant is essentially requiring the ordinary artisans to discover for themselves that which Applicant fails to disclose.
In Amgen, Inc., v. Sanofi (872 F.3d 1367 (2017)
At 1375, [T]he use of post-priority-date evidence to show that a patent does not disclose a representative number of species of a claimed genus is proper.
At 1377, [W]e questioned the propriety of the "newly characterized antigen" test and concluded that instead of "analogizing the antibody-antigen relationship to a `key in a lock,'" it was more apt to analogize it to a lock and "a ring with a million keys on it." Id. at 1352.
An adequate written description must contain enough information about the actual makeup of the claimed products — "a precise definition, such as by structure, formula, chemical name, physical properties, or other properties, of species falling within the genus sufficient to distinguish the genus from other materials," which may be present in "functional" terminology "when the art has established a correlation between structure and function." Ariad, 598 F.3d at 1350. But both in this case and in our previous cases, it has been, at the least, hotly disputed that knowledge of the chemical structure of an antigen gives the required kind of structure-identifying information about the corresponding antibodies. See, e.g., J.A. 1241 (549:5-
16) (Appellants' expert Dr. Eck testifying that knowing "that an antibody binds to a particular amino acid on PCSK9 ... does not tell you anything at all about the structure of the antibody"); J.A. 1314 (836:9-11) (Appellees' expert Dr. Petsko being informed of Dr. Eck's testimony and responding that "[m]y opinion is that [he's] right"); Centocor, 636 F.3d at 1352 (analogizing the antibody-antigen relationship as searching for a key "on a ring with a million keys on it") (internal citations and quotation marks omitted).
In the instant case, knowing that the sgRNA is to comprise a guide sequence consisting of 11-15 contiguous nucleotides that are complementary to a target DNA sequence at a genomic locus of interest does not tell you anything at all about:
the nucleotide sequence [structure] of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a genetic element having the functional property of being a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest.
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 method encompasses an entire universe of structurally and functionally undisclosed sgRNA nucleic acids.
“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.
Accordingly, this limited information is not deemed sufficient to reasonably convey to one skilled in the art that the applicant is in possession of, nor enabling for, the broadly claimed method using the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences consisting of 11-15 contiguous nucleotides that are complementary to a target DNA sequence that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a genetic element having the functional property of being a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest, at the time the application was filed.
The specification fails to make up for the deficiencies of the global scientific community.
Applicant is essentially requiring the ordinary artisans to discover for themselves that which Applicant fails to disclose.
Therefore, limiting Claims 1 and 20 to a method for transcriptional suppression of a target gene locus of interest in a eukaryotic cell, the method comprising the step of introducing into the eukaryotic cell an engineered CRISPR/Cas9 system, wherein the CRISPR/Cas9 system comprises:
i) a Cas9 enzyme having DNA cleavage activity; and
ii) a single guide polynucleotide comprising a guide sequence consisting of 11-15 contiguous nucleotides that are 100% complementary to a target DNA sequence within 200 nucleotides of the transcriptional start site of the target gene locus of interest, is proper.
Limiting Claims 4 and 21 to a method for transcriptional modulation of a target gene locus of interest in a eukaryotic cell, the method comprising the step of introducing into the eukaryotic cell an engineered CRISPR/Cas9 system, wherein the CRISPR/Cas9 system comprises:
i) a Cas9 enzyme having DNA cleavage activity; and
ii) a single guide polynucleotide comprising:
a) a guide sequence consisting of 11-15 contiguous nucleotides that are 100% complementary to a target DNA sequence within 200 nucleotides of the transcriptional start site of the target gene locus of interest; and
b) at least one of the tetraloop and loop2 is modified by insertion of an aptamer comprising SEQ ID NO:85 that binds to bacteriophage coat protein MS2,
wherein the MS2 is fused to at least one transcriptional activator domain or transcriptional repressor domain, is proper.
Thus, for the reasons outlined above, it is concluded that the claims do not meet the requirements for enablement under 35 U.S.C. 112, first paragraph. Applicant is reminded that 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 claim(s).
Response to Arguments
Applicant argues that the skilled artisan can scan the genome for candidate target PAM motifs and identify unique target sequences among the candidate targets.
Applicant’s argument(s) has been fully considered, but is not persuasive.
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 broadly claimed method encompasses using the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences consisting of 11-15 contiguous nucleotides that are complementary to a target DNA sequence that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest.
The independent claims are enormously broad for encompassing:
the nucleotide sequence [structure] of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci in
the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence,
whereby said sgRNA comprises further comprises an enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides, let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”, wherein said “adaptor” protein is to be fused to as many as about 2000 (at least within the human genome) structurally and functionally different transcription factors, thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest.
The specification discloses variants of a single gRNA whose guide sequence is, respectively, directed to IL1B, LPAR5, ITGA9, EGFR, MED12, CUL3, TADA2B, EMX1, VEGFA, DNMT, TPCN2, NRG2, CACNA2D4, ADAMTSL1. However, said gRNA(s) is/are directed to the promoter region of the respective target genes (e.g. [0098]). Independent Claim 1 is vastly broader in scope that Applicant’s working examples because the claim encompasses gRNAs directed to any location within a target gene locus, e.g. 5’ region upstream of promoter and/or transcription start site, intron, exon, 3’ untranslated region, etc…, for which the specification fails to disclose that such gRNAs directed to these disparate structural and functional locations will necessarily and predictably achieve increased and/or decreased transcription of a genomic locus.
Applicant’s amendment to Claims 1 and 20 does nothing to address the lack of adequate written description for the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci because the claimed genus is highly variant.
Those of ordinary skill in the art would immediately recognize that said single gRNA target sequence species directed to the promoter region of the respective target genes is/are not representative of the enormously vast genus of about 1x10^9, 2x10^8, 6x10^7, 1x10^7, and/or 4x10^6 structurally undisclosed guide sequences that are to have the functional property of being complementary to an enormous genus of about 26,000 or more structurally undisclosed target DNA sequences of protein-coding and protein-non-coding genomic loci because the claimed genus is highly variant.
Applicant’s amendment to Claims 1 and 20 does nothing to address the lack of adequate written description for the 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence.
Those of ordinary skill in the art would immediately recognize that Applicant’s use of human host cells in vitro (e.g. [00100, 666]) to assay the few gRNA species is/are not representative of the enormously vast genus of about 8.7 million eukaryotic genomes whose genomes have not been sequenced, for which the global scientific community simply does not know the corresponding nucleotide sequences, let alone the corresponding nucleotide sequences of an enormously vast genus of structurally undisclosed “genomic locus of interest”, let alone those that are a gene coding sequence, a promoter, an enhancer, and/or a silencer sequence, whereby the method encompasses both in vitro and in vivo contexts, because the claimed genus is highly variant.
Applicant’s amendment to Claims 1 and 20 does nothing to address the lack of adequate written description for the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides (Claims 4-6), let alone to the infinite and/or an enormously vast genus of about 5x10^292, 5x10^227, 4x10^162, 4x10^97, and/or 3x10^32 structurally and functionally undisclosed amino acid sequences that are to have the functional property of being an “adaptor protein”.
Those of ordinary skill in the art would immediately recognize that the specification’s disclosure of an aptamer that binds MS2 (e.g. [00697], SEQ ID NO:85) is not representative of the enormously vast genus of about 2x10^120, 2x10^90, 1x10^60, 1x10^45, 1x10^30, and/or 1x10^18 structurally undisclosed aptamer sequences that are to necessarily and predictably have the functional property of binding to an essentially infinite genus of structurally undisclosed target small molecules, chemical compounds, fatty acids, carbohydrates, nucleic acids, amino acid peptides and/or polypeptides encompassed by the independent claims because the claimed genus is highly variant.
Applicant’s amendment to Claims 1 and 20 does nothing to address the lack of adequate written description for the enormous genus of about 2000 (at least within the human genome) structurally and functionally different transcription factors (Claims 6-8 and 12), thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest.
Those of ordinary skill in the art would immediately recognize that the specification’s disclosure of MS2 and/or p65 (e.g. Figure 6A) is not representative of the enormous genus of about 2000 (at least within the human genome) structurally and functionally different transcription factors (Claims 6-8 and 12), thereby necessarily and predictably modulating the transcription of said enormously vast genus of structurally undisclosed genomic loci of interest because the genus is highly variant.
Applicant is essentially requiring the ordinary artisans to discover for themselves that which Applicant fails to disclose.
“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.
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.
7. Claims 1, 3, and 20 are rejected under AIA 35 U.S.C. 103 as being unpatentable over Qi et al (Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression, Cell 152: 1173-1183, available February 28, 2013; of record in IDS; hereafter Qi-1) in view of Larson et al (CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols 8(11): 2180-2196, available online October 17, 2013; of record in IDS; co-authors to Qi et al; hereafter Qi-2) in view of May et al (U.S. 2014/0315985; of record), Joung et al (U.S. 2014/0295557; of record), and Church et al (U.S. 2014/0356956; of record).
Determining the scope and contents of the prior art, and Ascertaining the differences between the prior art and the claims at issue.
Qi-1 is considered relevant prior art for having taught a method for transcriptional suppression of a target gene locus of interest in a eukaryotic cell (e.g. Abstract, “mammalian cells”), the method comprising the step of introducing into the eukaryotic cell an engineered CRISPR/Cas9 system, wherein the CRISPR/Cas9 system comprises:
i) a Cas9 enzyme having impaired DNA cleavage activity (e.g. Figure 1; dCas9); and
ii) a single guide polynucleotide comprising a guide sequence that is 100% complementary to a target DNA sequence within 200 nucleotides of the transcriptional start site of the target gene locus of interest (e.g. Figure 2D).
Qi-1 taught that the minimal length of base-pairing region needed for gene silencing was 12 bp (e.g. pg 1177, col. 1).
Qi-1 taught that the CRISPR/Cas9 system binding to the promoter region target DNA sequence sterically blocks RNA polymerase (e.g. pg 1178, col. 1; pg 1180, col. 2), thereby suppressing transcription of the target gene.
Similarly, Qi-2 is considered relevant prior art for having taught a method for transcriptional suppression of a target gene locus of interest in a eukaryotic cell (e.g. Abstract, “human cells”), the method comprising the step of introducing into the eukaryotic cell an engineered CRISPR/Cas9 system, wherein the CRISPR/Cas9 system comprises:
i) a Cas9 enzyme having impaired DNA cleavage activity (e.g. pg 2180, col. 2, dCas9); and
ii) a single guide polynucleotide comprising a guide sequence that is 100% complementary to a target DNA sequence within 200 nucleotides of the transcriptional start site of the target gene locus of interest (e.g. pg 2181, col. 1, “sgRNA targets the promoter region”; Figure 1, as shown below:
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Qi-2 taught that the sgRNA targeting specificity is determined only by a 14-nucleotide long region composed of 12 nucleotides of the guide sequence that are 100% complementary to a target DNA sequence and 2 nucleotides of the PAM motif (e.g. pg 2812, col. 1; Figure 3 legend, “12-nt seed region”).
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).
There is no evidence of criticality or other secondary consideration for the genus of sgRNA guide sequences consisting of 11-15 nucleotides, as opposed to the sgRNA guide sequences consisting of 12 nucleotides taught by Qi-1 and/or Qi-2.
Qi-2 taught that the CRISPR/Cas9 system binding to the promoter region target DNA sequence sterically blocks RNA polymerase (e.g. Abstract, “steric block that halts transcript elongation by RNA polymerase”; pg 2181, col. 1; Figure 1, legend; pg 2183, col. 1), thereby suppressing transcription of the target gene.
Qi-1 and Qi-2 do not teach wherein the Cas9 enzyme has DNA cleavage activity.
As evidenced by Applicant’s Figure 6C, the breadth of the instant claims encompass gRNAs whose guide sequence consists of 15, 14, 13, 12, and/or 11 contiguous nucleotides that are 100% complementary to a target DNA sequence at a genomic locus of interest are still able to yield measurable and/or detectable production of a double-stranded break when complexed with a Cas9 enzyme having DNA cleavage activity, although a reduced levels as compared to guide sequences with 16, 17, 18, 19, 20, 21, or 22 contiguous nucleotides that are 100% complementary to a target DNA sequence.
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However, prior to the effective filing date of the instantly claimed invention, May et al is considered relevant prior art for having disclosed CRISPR/Cas9 systems, wherein:
i) the sgRNA comprises a guide sequence (syn. spacer) consisting of 12-20 nucleotides (e.g. [0084, 298]); and
ii) the Cas9 enzyme has enzymatic activity (e.g. [0170], “can introduce double-stranded breaks”), or may be catalytically inactive (e.g. Example 5, [0886], “will be enzymatically inactive”…or “will be enzymatically active”), being able to bind a target nucleic acid.
Similarly, Joung et al is considered relevant prior art for having disclosed truncated guide RNAs consisting of 15 or 16 nucleotides that, when bound with enzymatically Cas9 enzymes have essentially no detectable % indel activity (Figures 2H (15nt guide sequence); 3A (16 nt guide sequence). Joung et al disclosed the truncated guide RNAs achieve greater specificity, as they are more sensitive to small numbers of sequence mismatches at the gRNA-target DNA interface (e.g. [0059, 61]). Joung et al disclosed the Cas9 enzyme may be catalytically active (e.g. [0086]) or inactive (e.g. [0087]).
Similarly, Church et al is considered relevant prior art for having disclosed truncated guide RNAs that are 11 or 15 nucleotides in length (Figure 16D-2), for which no indel activity is detectable when paired with a Cas9 enzyme having DNA cleavage activity. Church et al disclosed wherein the CRISPR/Cas9 system may comprise a Cas9 enzyme that is catalytically active or inactive (e.g. [0079-80]).
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 CRISPR/Cas9 editing system. 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 substitute a first Cas9 enzyme, e.g. a nuclease-deficient Cas9, as taught by Qi-1 and Qi-2, with a nuclease-active Cas9 enzyme, as disclosed by May et al, Joung et al, and Church et al, in a method of suppressing transcription of a eukaryotic target gene 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 first Cas9 enzyme, e.g. a nuclease-deficient Cas9, with a nuclease-active Cas9 enzyme, in a method of suppressing transcription of a eukaryotic target gene comprising the use of a CRISPR/Cas9 system in which the sgRNA comprises a guide sequence consisting of 11-15 nucleotides that are 100% complementary to a target sequence within 200 nucleotides of the target gene’s transcription start site because:
i) Qi-1 and Qi-2 taught that Qi-1 taught that the CRISPR/catalytically inactive Cas9 system binding to the promoter region target DNA sequence sterically blocks RNA polymerase, thereby suppressing transcription of the target gene;
ii) Qi-1 and Qi-2 taught that the minimal length of base-pairing region needed for gene silencing was a 12 nucleotide guide sequence that is 100% complementary to the target DNA sequence;
iii) Joung et al and Church et al disclosed that a CRISPR/Cas9 system comprising a catalytically active Cas9 enzyme and a sgRNA whose guide sequence consists of 15 or fewer nucleotides did not yield detectable indel activity;
iv) May et al, Joung et al, and Church et al disclosed the CRISPR/Cas9 system may comprise either catalytically active or catalytically inactive Cas9 enzymes, and thus the ordinary artisans previously recognized these two options to be substitutable;
v) those of ordinary skill in the art would have reasonably understood that a CRISPR/Cas9 system comprising a catalytically active Cas9 enzyme and a sgRNA whose guide sequence consists of 15 or fewer nucleotides which yields reduced indel activity, generating DNA breaks at the promoter region target site, would result in the suppression of the transcription of the target gene due to the formation of deletions and insertions, per natural law of cell biology and enzymology of the CRISPR/Cas9 system; and
vi) those of ordinary skill in the art would have reasonably understood that a CRISPR/Cas9 system comprising a catalytically active Cas9 enzyme and a sgRNA whose guide sequence consists of 15 or fewer nucleotides which yields no indel activity would still be able to sterically block RNA polymerase, thereby recapitulating the CRISPR/catalytically inactive Cas9 system of Qi-1 and Qi-2, thereby suppressing transcription of the target gene.
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.
8. Claims 4, 7-8, 10-12, 14, 16-17, and 21-23 are rejected under AIA 35 U.S.C. 103 as being unpatentable over Qi et al (available February 28, 2013; of record in IDS; hereafter Qi-1) in view of Larson et al (available online October 17, 2013; of record in IDS; co-authors to Qi et al; hereafter Qi-2) in view of May et al (U.S. 2014/0315985; of record), Joung et al (U.S. 2014/0295557; of record), and Church et al (U.S. 2014/0356956; of record), as applied to Claims 1, 3, and 20 above.
Determining the scope and contents of the prior art, and Ascertaining the differences between the prior art and the claims at issue.
Neither Qi-1 nor Qi-2 teach wherein the sgRNA comprises an aptamer,
wherein said aptamer binds to an MS2 adaptor protein, and
wherein said MS2 adaptor protein is fused to a transcriptional activator domain or a transcriptional repressor domain.
However, prior to the effective filing date of the instantly claimed invention, Joung et al is considered relevant prior art for having disclosed a CRISPR/Cas9 system in eukaryotic cells (e.g. [0050], “in human cells”), the CRISPR/Cas9 system comprising an enzymatically active Cas9 or an enzymatically inactive Cas9 (e.g. [0010], “Cas9 nuclease or nickase”; [0086-87], “catalytically inactive”) and truncated guide RNAs whose guide sequences consist of 15 or 16 contiguous nucleotides that are 100% complementary to a target DNA sequence (e.g. Figures 2H, 3A; [0030, 31]).
Joung et al disclosed the Cas9 protein may be fused to a transcriptional activator domain, e.g. VP64 or p65, or a MS2 adaptor protein (e.g. [0020, 93-94, 98]).
Joung et al disclosed that the truncated guide sequences are advantageous because they minimize genomic off-target frequencies, thereby optimizing for the artisan’s specific target site choice (e.g. [0054]).
Joung et al do not disclose wherein the sgRNA comprises an aptamer that binds to the adaptor protein.
However, prior to the effective filing date of the instantly claimed invention, Church et al is considered relevant prior art for having disclosed a CRISPR/Cas9 system in eukaryotic cells (e.g. [0007), the CRISPR/Cas9 system comprising an enzymatically active Cas9 or an enzymatically inactive Cas9 (e.g. [0079-81]) and truncated guide RNAs whose guide sequences consist of 15 or 11 contiguous nucleotides that are 100% complementary to a target DNA sequence (e.g. Figure 16D-2). Church et al disclosed wherein the sgRNA further comprises an aptamer that provides a binding site for an adaptor protein, wherein the adaptor protein is MS2 (e.g. Figure 1B, [0098]), wherein the MS2 adaptor protein is fused to a VP64 transcriptional activator domain (e.g. Figure 1B).
Similarly, May et al disclosed wherein the Cas enzyme is able to alter the transcription of the target gene (e.g. [0038]), wherein the sgRNA further comprises a nucleotide sequence, e.g. aptamer (e.g. [0134], “synthetic RNA aptamer”) that provides a binding site for an adaptor protein, wherein the adaptor protein is MS2 (e.g. [0134, 742, 743, 745]), and wherein said MS2 is fused to a transcriptional activator domain (e.g. [0745], eIF4).
May et al disclosed an example of the aptamer introduced at the sgRNA terminus (e.g. Figure 12, element 1220 or 1250; [0668]; Figure 30F), and also disclosed that the tetraloop domain (Figure 1A, element 120) may also comprise an aptamer (e.g. [0338-341], “a protein-interacting hairpin”).
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 a truncated sgRNA of a CRISPR/Cas9 system, as disclosed by May et al, Joung et al, and Church et al, to further comprise an aptamer that binds to the MS2 adaptor protein fused to at least a transcriptional activation domain in a method of modulating the transcription of a target gene of interest with motivation and a reasonable expectation of success because those of ordinary skill in the art previously recognized the scientific and technical concepts that:
i) sgRNAs had been successfully reduced to practice to further comprise an aptamer that binds MS2, said aptamer being placed at the 3’ terminus domain (Church et al; May et al), whereby May et al disclosed that the aptamer may also be placed in, at least, the tetraloop domain; and
ii) MS2 fused to at least a transcriptional activator domain, i.e. VP64, had been successfully reduced to practice and used in a CRISPR/Cas9 system that targets the promoter of the artisan’s target gene of interest, thereby modulating the transcription of said target gene (e.g. Church et al).
It would have been obvious to one of ordinary skill in the art to try modifying the tetraloop domain or loop2 domain of an sgRNA to further comprise an aptamer that binds MS2 with a reasonable expectation of success because “a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipate success, it is likely that product not of innovation but of ordinary skill and common sense.”
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One of ordinary skill in the art previously recognized that there is a finite list of known options where an aptamer may be placed in an sgRNA without interfering with the ability of the sgRNA to bind Cas9 (illustrated above), whereby the number of possible locations from which to choose is neither astronomical nor insurmountable, and given the guidance of May et al disclosing that the tetraloop domain may also be modified to comprise an aptamer, it would be only routine experimentation to determine the ability of such an aptamer placed in the tetraloop and/or loop2 domain(s) to bind the MS2 adaptor protein.
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 14, Qi-1 taught wherein the Cas9 enzyme is from S. pyogenes (e.g. pg 1174, col. 2).
Qi-2 taught wherein the Cas9 enzyme is from S. pyogenes (e.g. Abstract).
Joung et al disclosed wherein the Cas9 enzyme is from S. pyogenes (e.g. [0057]).
Church et al disclosed wherein the Cas9 enzyme is from S. pyogenes (e.g. [0083]).
May et al disclosed wherein the Cas9 enzyme is from S. pyogenes (e.g. [0145]).
With respect to Claim 10, Qi-1 taught wherein the Cas9 enzyme further comprises a nuclear localization signal (NLS; e.g. pg 1178, col. 2).
Qi-2 taught wherein the Cas9 enzyme further comprises a nuclear localization signal (e.g. pg 2193, Critical step, “should be fused with at least two copies of nuclear localization sequences”).
Church et al disclosed wherein the Cas9 enzyme further comprises a nuclear localization signal (e.g. [0144, 148]).
May et al disclosed wherein the Cas9 enzyme further comprises a nuclear localization signal (e.g. [0739-740]).
With respect to Claims 16-17, Qi-1 and Qi-2 taught wherein the sgRNA targets a promoter or enhancer sequence.
Church et al disclosed wherein the sgRNA can target a coding region near the promoter, a promoter or an enhancer (e.g. Figure 6A; [0091], “gRNAs targeting sequences near the promoter, thereby displaying RNA-guided transcriptional activation”).
May et al disclosed wherein the sgRNA can target part or all of a gene, including a promoter or enhancer (e.g. [0776]).
With respect to Claims 7 and 22-23, Joung et al disclosed the Cas9 protein may be fused to a MS2 adaptor protein (e.g. [0020, 93-94, 98]).
Church et al disclosed wherein the adaptor protein is MS2 (e.g. Figure 1B, [0098]).
May et al disclosed wherein the adaptor protein is MS2 (e.g. [0134, 742, 743, 745]).
With respect to Claim 11, Joung et al disclosed the Cas9 protein may be fused to a transcriptional activator domain, e.g. VP64 or p65 (e.g. [0020, 93]).
Church et al disclosed the Cas9 protein may be fused to a transcriptional activator domain, e.g. VP64 (e.g. Figure 1D-1).
May et al disclosed wherein the Cas9 enzyme may be fused to a transcriptional activator or repressor domain (e.g. [0497, 499, 526]).
With respect to Claim 8, Church et al disclosed wherein the MS2 adaptor protein is fused to a VP64 transcriptional activator domain (e.g. Figure 1B).
With respect to Claim 12, Joung et al disclosed the Cas9 protein may be fused to a transcriptional activator domain, e.g. VP64 or p65 (e.g. [0020, 93]).
Church et al disclosed the Cas9 protein may be fused to a transcriptional activator domain, e.g. VP64 (e.g. Figure 1D-1).
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
9. No claims are allowed.
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KEVIN K. HILL
Examiner
Art Unit 1638
/KEVIN K HILL/Primary Examiner, Art Unit 1638