DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Claims 1-16 are under examination (8/22/2023).
Priority
Claims 1-16 receive the priority date of 2/23/2021, the filing date of Application No. GB2102557.2.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Information Disclosure Statements from 8/22/2023 and 12/22/2023 are considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”.
Required response - Applicant must provide:
A "Sequence Listing" part of the disclosure; together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide:
A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and
A statement according to item 2) a) or b) above.
Claim Objections
Claim 14 is objected to because of the following informalities:
Claim 14 at line 2: “identify a gene” should be replaced with “identifying a gene.”
Claim 15 is objected to because of the following informalities:
Claim 15 at line 2: “identify a gene” should be replaced with “identifying a gene.”
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-16 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 is rejected. Claim 1 recites the limitation "the cell genome” at step (b) at line 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 1 is further rejected. Claim 1 recites the limitation "the exposed modified cell population” at step (d) at line 1. There is insufficient antecedent basis for this limitation in the claim.
Claims 1-15 are included in this rejection due to their dependency on claim 1.
Claim 16 is rejected. Claim 16 is indefinite under 35 USC 112 (b) because the metes and bounds of the claimed invention cannot be determined with reasonable certainty. Specifically, the phrase “as described herein with reference to the accompanying drawings” attempts to define the claimed method by reference to unspecified portions of the specification and drawings rather than reciting the method steps in the claim itself. Therefore, it is unclear what limitations are actually required by instant claim 16.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1-16 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (US PGPub US 2016/0272965 Al; published 9/22/2016) and Rad et al. (“PiggyBac Transposon Mutagenesis: A Tool for Cancer Gene Discovery in Mice”, Science, published 2010).
Regarding claim 1, Zhang teaches a present invention that generally relates to libraries, compositions, methods, applications, kits and screens used in functional genomics that focus on gene function in a cell and that may use vector systems and other aspects related to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas systems and components thereof (Abstract). Further, Zhang teaches that the formed CRISPR-Cas9 system can give rise to mutations, e.g., breaks, or nicks, deletions, insertions, or substitutions and as members of the library may target different positions within the DNA of the cells, a library of cells, with potentially multiple genotypes arises and such mutations may give rise to a desired phenotypes and thus, the library or libraries of cells are screened for selection of the desired phenotype and as to plants, CRISPR-Cas9 allows for targeted mutagenesis, e.g., CRISPR-Cas9 can be a mutagenic agent, plants expressing a desired phenotype from the mutation, e.g., reduced susceptibility
or resistance to a pathogen or plant disease, are therefore better identified because the CRISPR-Cas9 system (Paragraph 242, lines 10-20). Further, Zhang teaches that simplicity of programming the CRISPR-associated nuclease Cas9 to modify specific genomic loci suggests a new way to interrogate gene function on the genome wide scale, where Applicants showed that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting
18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells, where first, Applicants used the GeCKO library to identify genes essential for cell viability in cancer and pluripotent stem cells (Paragraph 319, lines 1-10). Zhang also teaches that in order to test the efficacy of GeCKO for positive selection, Applicants sought to identify gene knockouts that result in resistance to the BRAF protein kinase inhibitor vemurafenib (PLX) in melanoma (FIG. 27 A) where exposure to PLX resulted in growth arrest of transduced A375 cells, which harbor the V600E gain-of-function BRAF mutation (FIG. 27B), therefore enabling the enrichment of a small group of cells that had been rendered drug-resistant by Cas9:sgRNA-mediated modification (Paragraph 326, lines 1-10).
Zhang specifically teaches that identification of gene candidates: Before any
experiment, it is important to determine the distribution of sgRNAs before any selection pressure has been applied where this baseline sgRNA distribution will be used to infer either depletion
or enrichment of specific sgRNA species and for both positive and negative selection screens, hits are identified by comparing the distribution of sgRNAs after selection with the
baseline sgRNA distribution (Paragraph 333, lines 1-10). Zhang teaches that candidate genes are identified by searching for sgRNAs whose frequency has either significantly reduced or increased after selection for negative and positive screens respectively, where using multiple sgRNAs to target the same gene, and transduction replicates are the main experimental features
that enable discrimination between true and false positive hits (Paragraph 334, lines 1-10).
Regarding claim 2, Zhang teaches that the previously described method includes, in preferred embodiments, the cell is a eukaryotic cell where the eukaryotic cell may be a plant or animal cell; for example, algae or microalgae; vertebrate, preferably mammalian, including murine, ungulate, primate, human; insect (Paragraph 52, lines 30-35).
Regarding claim 3, Zhang teaches that in other aspects, the invention encompasses methods of identifying the genetic basis of one or more medical symptoms exhibited by a subject, the method comprising obtaining a biological sample from the subject and isolating a
population of cells having a first phenotype from the biological sample; contacting the cells having the first phenotype with a composition comprising a vector system comprising one or more packaged vectors comprising a) a first regulatory element operably linked to a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide sequence that targets a DNA molecule encoding a gene product, wherein the polynucleotide sequence comprises (a) a guide sequence capable of hybridizing to a target sequence, (b) a tracr mate sequence, and ( c) a tracr sequence, and b) a second regulatory element wherein components (a) and (b) are located on same or different vectors of the system, wherein each cell is transfected with a single packaged vector,
selecting for successfully transfected cells, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in the genomic loci of the DNA molecule encoding
the gene product, wherein the CRISPR complex comprises a CRISPR enzyme complexed with (1) the guide sequence that is hybridizable to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the guide sequence is selected from the library of the invention, wherein the guide RNAs target the genomic loci of the DNA molecule encoding the gene product and the CRIS PR enzyme cleaves the genomic loci of the DNA molecule encoding the gene product, whereby each cell in the population of cells has a unique gene knocked out in parallel, applying the selective pressure, selecting the cells that survive under the selective pressure, determining the genomic loci of the DNA molecule that interacts with the first phenotype and identifying the genetic basis of the one or more medical symptoms exhibited by the subject (Paragraphs 39-43).
Regarding claims 4-6, Zhang teaches that in preferred embodiments, the targeting is of about 100 or more sequences, about 1000 or more sequences or about 20,000 or more sequences or the entire genome and in other embodiments a panel of target sequences is focused on a relevant or desirable pathway, such as an immune pathway or cell division (Paragraph 45, lines 10-20), including those linked to pain/taste (Table C) and/or calcium signaling (Table F).
Regarding claims 7-8, Zhang teaches that there are two ways to package Cas9 coding nucleic acid molecules, e.g., DNA, into viral vectors to mediate genome modification
in vivo are preferred: To achieve NHEJ-mediated gene knockout: Single Virus Vector:
Vector containing two or more expression cassettes: Promoter-Cas9 coding nucleic acid molecule-terminator; Promoter-gRNAl-terminator; Promoter-gRNA2-terminator; Promoter-gRNA(N)-terminator (up to size limit of vector); Double Virus Vector: Vector 1 containing one expression cassette for driving the expression of Cas9; Promoter-Cas9 coding nucleic acid molecule-terminator; Vector 2 containing one more expression cassettes for driving the expression of one or more guide RNAs; Promoter-gRNAl-terminator; Promoter-gRNA(N)-terminator (up to size limit of vector) (Paragraphs 175-187).
Regarding claims 9-11, Zhang teaches that aspects of the invention also encompass a two vector, genome-wide KO system, and details are as follows: 1) Applicants utilize A375 (BRAF V600E mutation-containing) cells having Cas9 alone integrated into the genome and this may be done with lentivirus but may also be done with other methods of integration (integrase, recombinase, transposes, etc.), where typically the integration cassette will include Cas9 and
a selectable marker to make sure that only cells with Cas9 active are kept. For e.g., the vector is EF1a-Cas9-2A-Blasticidin (Paragraph 370, lines 1-10).
Regarding claim 12, Zhang teaches that in preferred embodiments, the targeting is of about 100 or more sequences, about 1000 or more sequences or about 20,000 or more sequences or the entire genome and in other embodiments a panel of target sequences is focused on a relevant or desirable pathway, such as an immune pathway or cell division (Paragraph 45, lines 10-20), including those linked to pain/taste (Table C) and/or calcium signaling (Table F).
Regarding claims 13-15, Zhang teaches that the formed CRISPR-Cas9 system can give rise to mutations, e.g., breaks, or nicks, deletions, insertions, or substitutions and as members of the library may target different positions within the DNA of the cells, a library of cells, with potentially multiple genotypes arises and such mutations may give rise to a desired phenotypes and thus, the library or libraries of cells are screened for selection of the desired phenotype. As to plants, CRISPR-Cas9 allows for targeted mutagenesis, e.g., CRISPR-Cas9 can be a mutagenic agent, plants expressing a desired phenotype from the mutation, e.g., reduced susceptibility
or resistance to a pathogen or plant disease, are therefore better identified because the CRISPR-Cas9 system (Paragraph 242, lines 10-20). Further, Zhang teaches that simplicity of programming the CRISPR-associated nuclease Cas9 to modify specific genomic loci suggests a new way to interrogate gene function on the genome wide scale, where Applicants showed that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting
18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells, where first, Applicants used the GeCKO library to identify genes essential for cell viability in cancer and pluripotent stem cells (Paragraph 319, lines 1-10). Zhang also teaches that in order to test the efficacy of GeCKO for positive selection, Applicants sought to identify gene knockouts that result in resistance to the BRAF protein kinase inhibitor vemurafenib (PLX) in melanoma (FIG. 27 A) where exposure to PLX resulted in growth arrest of transduced A375 cells, which harbor the V600E gain-of-function BRAF mutation (FIG. 27B), therefore enabling the enrichment of a small group of cells that had been rendered drug-resistant by Cas9:sgRNA-mediated modification (Paragraph 326, lines 1-10).
Further, Zhang teaches that in preferred embodiments of the invention, the method further comprises extracting DNA and determining the depletion or enrichment of the guide sequences by deep sequencing (Paragraph 57, lines 45-50).
Specifically, Zhang teaches that as mentioned previously, a critical aspect of the
invention is gene knock-out and not knock-down (which can be done with genome-wide siRNA or shRNA libraries), where applicants have provided the first demonstration of genome-wide
knockouts that are barcoded and can be easily readout with next generation sequencing and every single gene (or a subset of desired genes, for example, those relating to a particular
enzymatic pathway or the like (e.g., including but not limited to pathways involved in signaling, metabolism, gene regulation, immune response, disease resistance, drug response and/or resistance, etc.) may be knocked OUT in parallel and this allows quantification of how well each gene KO confers a survival advantage (Paragraph 72, lines 1-10).
Regarding claim 16, Zhang teaches a present invention that generally relates to libraries, compositions, methods, applications, kits and screens used in functional genomics that focus on gene function in a cell and that may use vector systems and other aspects related to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas systems and components thereof (Abstract). Further, Zhang teaches that the formed CRISPR-Cas9 system can give rise to mutations, e.g., breaks, or nicks, deletions, insertions, or substitutions and as members of the library may target different positions within the DNA of the cells, a library of cells, with potentially multiple genotypes arises and such mutations may give rise to a desired phenotypes and thus, the library or libraries of cells are screened for selection of the desired phenotype and as to plants, CRISPR-Cas9 allows for targeted mutagenesis, e.g., CRISPR-Cas9 can be a mutagenic agent, plants expressing a desired phenotype from the mutation, e.g., reduced susceptibility or resistance to a pathogen or plant disease, are therefore better identified because the CRISPR-Cas9 system (Paragraph 242, lines 10-20).
Zhang does not teach or suggest that the specific expression cassette is an activating transposon, including a piggyBac transposon.
Rad teaches that transposons are mobile DNA segments that can disrupt gene function by inserting in or near genes, and here, we show that insertional mutagenesis by the PiggyBac transposon can be used for cancer gene discovery in mice (Abstract). Specifically, Rad teaches that another transposon, PiggyBac (PB) from the cabbage looper moth Trichoplusia ni, was recently engineered to be highly active in mammalian cells and has been shown to have biological properties distinct from those of SB, where PB can move larger DNA fragments (allowing complex transgene designs to be incorporated into the transposon), and it has a weaker tendency for local hopping in vitro (which makes it an attractive candidate for genome-wide mutagenesis) and furthermore, in contrast to SB, PB does not leave undesired footprint mutations after transposition (Introduction: Paragraph 1). Specifically, Rad teaches that promoter and enhancer elements, a splice donor, bidirectional SV40 polyadenylation signals, and two splice acceptors were introduced in between the ITRs to allow gain- or loss-of-function mutations, depending on the transposon orientation and its spatial relation to genes (Introduction: Paragraph 2; Figure 3).
It would have been obvious to a person of ordinary skill in the art at or before the time of the invention to modify Zhang’s phenotypic screening system with the activating piggyBac transposon of Rad because both references are directed to genome-wide functional screening for identification of genes associated with a selected phenotype. Rad teaches that piggyBac transposons containing promoter and enhancer elements can generation gain-of-function mutations through activation of nearby genes and are useful for genome-wide gene discovery in mammalian cells. Therefore, given the well-known use of transposon-mediated insertional mutagenesis and CRISPR-based perturbation libraries as alternative functional genomics tools for gen discovery, a person of ordinary skill in the art would have been motivated to employ Rad’s activating piggyBac transposon as the gain-in-function construct of Zhang to provide an alternative known mutagenesis platform for identifying phenotype-associated genomic targets, with a reasonable expectation of success because both references utilize genetically modified mammalian cell populations, phenotypic selection, and subsequent identification of the causative genetic loci.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIZABETH ROSE LAFAVE whose telephone number is (703)756-4747. The examiner can normally be reached Compressed Bi-Week: M-F 7:30-4:30.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached on 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ELIZABETH ROSE LAFAVE/ Examiner, Art Unit 1684
/HEATHER CALAMITA/ Supervisory Patent Examiner, Art Unit 1684
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