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
Applicant amended claims 4-12, 14, 16-20 (2/7/2022). No new matter was added. Thus, claims 1-21 are under examination.
Priority
Claims 1-21 claim a priority date of 8/8/2019, the filing date of U.S. Provisional No. 62/884, 536.
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.
The Information Disclosure Statements from 5/10/2022, 9/2/2022, 3/9/2023, 8/14/2023, 9/25/2023, 11/20/2023, 5/13/2024, 7/19/2024, 9/20/2024 (2), 12/9/2024, 2/26/2025, 5/8/2025 (4) are considered.
Specification
The disclosure is objected to because of the following informalities (see MPEP § 608.01):
The use of the term “Clontech” (p.20) is a trade name or mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 1, 13, 15, and 20 are objected to because of the following informality:
Claim 1 at line 4: “nt” should be spelled out in entirety the first time used, followed by the acronym placed in parentheses.
Claim 13 is objected to because of the following informality:
Claim 13 at line 2: “ATAC-seq” should be spelled out in entirety the first time used, followed by the acronym placed in parentheses.
Claim 15 is objected to because of the following informality:
Claim 15 at line 2: “ChIP-seq” should be spelled out in entirety the first time used, followed by the acronym placed in parentheses.
Claim 20 is objected to because of the following informality:
Claim 20 at lines 2-5: the listing of cell types contains overlap in specific listings (i.e., liver cell and hepatocyte). List should be clarified for further specificity.
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 10-11 and 17 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 10 is rejected. Claim 10 recites “at least about” in line 2 (3 times) and is indefinite. The term “about” creates uncertainty when combined with “at least.” Specifically, it is unclear what numerical range is encompassed by “at least about 2, 3, or 4.” The imprecise boundaries make it impossible to determine the exact scope of the claimed invention.
Claim 11 is rejected. Claim 11 recites “at least about” in line 2 (3 times) and is indefinite. The term “about” creates uncertainty when combined with “at least.” Specifically, it is unclear what numerical range is encompassed by “at least about 2, 3, or 4.” The imprecise boundaries make it impossible to determine the exact scope of the claimed invention.
Claim 17 is rejected. Claim 17 recites “a different sequence tag corresponding to a different promoter sequence” and is indefinite. Specifically, this limitation fails to specify what makes the sequence tag and promoter sequence “different.” Different from what? Different in what way? The instant claim provides no objective criteria for determining what constitutes a “different” sequence tag or promoter sequence.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-20 are rejected under 35 U.S.C. 102 (a)(1) and 102 (a)(2) as being anticipated by Bauer et al. (WO 2016/182893 A1; published 11/17/2016).
Regarding claim 1, Bauer teaches a method of utilizing Cas9-based knockout screens in identifying essential genes and genes involved in drug resistance in various cell lines (Paragraph 10, lines 1-4). Further, Bauer teaches that expression of a gene of interest may be altered by said targeting by at least one guide RNA within the plurality of CRISPR-Cas system guide RNAs and that at least one continuous genomic region may comprise up to the entire genome including a functional element of the genome (i.e., within a coding gene, intronic region, promoter, or enhancer) (Paragraph 16, lines 1-5). Bauer also teaches that the DNA region may comprise an epigenetic insulator and may comprise two or more continuous genomic regions that physically interact or have separate signatures (i.e., histone acetylation, histone methylation, histone ubiquitination, histone phosphorylation, DNA methylation, or a lack thereof) (Paragraph 17, lines 5-10). Specifically, Bauer teaches that functional regions of the previously described DNA regions may comprise over 50 nucleotides (Paragraph 107, lines 1-5).
Additionally, Bauer teaches that targeting may comprise introducing into each cell in the population of cells a vector system of one or more vectors comprising an engineered, non-naturally occurring CRISPR-Cas system (Paragraph 20, lines 1-2). Further, Bauer teaches that specific sites are targeted through monitoring interaction strength with specified promoters via paired-end tag sequencing (Figure 41, Paragraph 72, lines 1-3), occurring via transduction with vectors (i.e., Cas9, sgRNAs) (Figures 8A-B; Paragraph 39, lines 1-3). Bauer further teaches the comparison of ranked enhancers or promoters via transcription levels through monitoring specifically signal intensity of H3K27ac (trait associated haplotypes) following normalization to GAPDH (control) (Figures 1A-1E; Paragraph 32, lines 1-5).
Regarding claim 2, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes screening methods for identifying functional elements in the non-coding genome, more particularly using libraries via targeting Cas9 or other vectors to intergenic regions surrounding single genes and generating a library which flanks 100kb upstream and downstream of target gene with sgRNAs or polynucleotides (Paragraph 96, lines 1-5).
Regarding claim 3, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes strategies to knock-in via homology-directed repair the fluorescent protein for further analyses (Figures 26A-26K; Paragraph 57, lines 1-10).
Regarding claims 4-5, Bauer teaches a method of prior library design with specified sgRNAs cloned into lentiviral vectors following synthesized onto an array prior to the transduction of BRAF mutant and control cells that are again sequenced via deep-sequencing readout for further identification for early time point comparisons (Figures 30A-30D; Paragraph 61, lines 1-20).
Regarding claims 6-7, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes a DNA region that may comprise an epigenetic insulator and may comprise two or more continuous or similar genomic regions that physically interact or have completely separate signatures (i.e., histone acetylation, histone methylation, histone ubiquitination, histone phosphorylation, DNA methylation, or a lack thereof) (Paragraph 17, lines 5-10). Specifically, Bauer teaches that functional regions of the previously described DNA regions may comprise over 50 nucleotides (Paragraph 107, lines 1-5).
Regarding claims 8-9, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes methods that allow for the identification of targets in the 5’ and 3’ region of a gene which may affect a phenotypic change only under particular circumstances or only for particular cells or tissues in an organism (Paragraph 79, lines 1-10).
Regarding claim 10, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes methods that specifically target a multitude of sequences or DNA fragments within the continuous genomic region of interest via introducing into each cell of a population of cells a vector system of one or more vectors comprising an engineered, non-naturally occurring CRISPR-Cas system comprising: at least one Cas protein, and one or more guide RNAs of the guide RNA library where the Cas protein and the one or more guide RNAs may be on the same or on different vectors of the system and are integrated into each cell, whereby each guide sequence targets a sequence within the continuous genomic region in each cell in the population of cells (Paragraph 89, lines 1-10).
Regarding claim 11, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes regulatory sequences and are intended to include promoters, enhancers and other expression control elements (i.e., polyadenylation signals) (Paragraph 119, lines 1-5). For example, Bauer teaches that these promoters include such genes (HbSC, HbS/P+, HbS/PO) that cause a reduction in the amount of hemoglobin produced as compared to a normal or standard condition (Paragraph 134, lines 1-15).
Regarding claims 12-15, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes the identification of targets in the 5’ and 3’ region of a gene which may affect a phenotypic change only under particular circumstances or only for particular cells or tissues in an organism where the genomic region of interest comprises a transcription factor binding site, a region of DNase I hypersensitivity, a transcription enhancer or repressor element, including the genomic region of interest comprises an epigenetic signature for a particular disease or disorder (Paragraph 79, lines 5-10). Further Bauer teaches that additionally or alternatively the genomic region of interest may comprise an epigenetic insulator where the guide RNA library is directed to a genomic region which comprises two or more continuous genomic regions or cell types (Paragraph 79, lines 10-15).
Bauer further teaches that to calculate the fold enrichment of the sgRNAs in proximity to other molecular hallmarks for hypersensitivity (DNAse-seq, ATAC-seq, conservation), the average sgRNA enrichment of sgRNAs near the peaks of these molecular hallmarks were examined (Paragraph 323, lines 1-5).
Bauer also teaches that further hallmarks for comparison between cell types using the previously described method are induced via enhancer sequences that bind transcription factors and chromatin regulators and are correlated with specific chromatin features including reduced DNA methylation, characteristic histone modifications, heightened chromatin accessibility, long-range promoter interactions, and bidirectional transcription. Recent chromatin mapping has demonstrated the abundance of distal regulatory elements bearing an enhancer chromatin signature (Paragraph 232, lines 1-10). Bauer teaches that specifically histone modifications in human H3K27ac can be monitored via ChIP-seq (Paragraph 252, lines 1-2).
Regarding claim 16, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes the comparison of ranked enhancers or promoters via transcription levels through monitoring specifically signal intensity of H3K27ac (trait associated haplotypes) following normalization to GAPDH (control) (Figures 1A-1E; Paragraph 32, lines 1-5). Specifically, Bauer teaches that quantitative sequencing or qPCR can be used to assess the specified gene expression described previously (Figures 14A-14D; Paragraph 45, lines 1-5).
Regarding claim 17, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes a “3C”design template that utilizes a target sequence or ‘bait’ (i.e., a restriction fragment of choice that encompasses a selected gene) ligated to many different nucleotide sequences of interest or sequence tags (representing this gene's genomic environment) where the template is cleaved by another, secondary or different, restriction enzyme and subsequently re-ligated to form small DNA circles and advantageously, the one or more nucleotide sequences of interest that are ligated to the target nucleotide sequence are amplified using at least two oligonucleotide primers or promoters, wherein at least one primer or promoter hybridizes to the target sequence to flank the nucleotide of interest labeled and optionally hybridized to an array, typically against a control sample containing genomic DNA digested with the same combination of restriction enzymes (Paragraph 102, lines 1-30). Bauer teaches that this previously described method can be used to search the complete genome for interacting DNA elements (Paragraph 102, lines 25-30).
Regarding claim 18, Bauer teaches that the previously described identification method for promoter or enhancer sequences includes the comparison of ranked enhancers or promoters via transcription levels through monitoring specifically signal intensity of specified sequences of interest or tagged sequences involving H3K27ac (trait associated haplotypes) following normalization to GAPDH (control) (Figures 1A-1E; Paragraph 32, lines 1-5). Specifically, Bauer teaches that quantitative sequencing or qPCR can be used to assess the specified gene expression described previously (Figures 14A-14D; Paragraph 45, lines 1-5). For example, Bauer teaches that the previously described methods of monitoring transcription levels can be used for motif analysis to evaluate the human and mouse enhancer regions across different cell types for potential binding sites for known transcription factors (Paragraph 258, lines 1-3).
Regarding claim 19, Bauer teaches a method of prior library design with specified sgRNAs cloned into lentiviral vectors following synthesized onto an array prior to the transduction of BRAF mutant and control cells that are again sequenced via deep-sequencing readout for further identification for early time point comparisons (Figures 30A-30D; Paragraph 61, lines 1-20).
Regarding claim 20, Bauer teaches that the previously described method of library design for promoters or enhancers can be applied to analyze multiple populations of eukaryotic cells including embryonic stem (ES) cells, neuronal cells, epithelial cells, immune cells, endocrine cells, muscle cells, erythrocytes, lymphocytes, plant cells, or yeast cells (Paragraph 90, lines 1-5).
Bauer teaches each and every limitation of claims 1-20, and therefore Bauer anticipates claims 1-20.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 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.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Bauer et al. (WO 2016/182893 A1; published 11/17/2016), as applied to claims 1-20 above, in view of Ahfeldt et al. (WO 2018/129486 A2; published 7/12/2018).
As previously discussed, teaches a method of utilizing Cas9-based knockout screens in identifying essential genes and genes involved in drug resistance in various cell lines (Paragraph 10, lines 1-4). Further, Bauer teaches that expression of a gene of interest may be altered by said targeting by at least one guide RNA within the plurality of CRISPR-Cas system guide RNAs and that at least one continuous genomic region may comprise up to the entire genome including a functional element of the genome (i.e., within a coding gene, intronic region, promoter, or enhancer) (Paragraph 16, lines 1-5). Bauer also teaches that the DNA region may comprise an epigenetic insulator and may comprise two or more continuous genomic regions that physically interact or have separate signatures (i.e., histone acetylation, histone methylation, histone ubiquitination, histone phosphorylation, DNA methylation, or a lack thereof) (Paragraph 17, lines 5-10). Specifically, Bauer teaches that functional regions of the previously described DNA regions may comprise over 50 nucleotides (Paragraph 107, lines 1-5).
Regarding claim 21, Bauer teaches that the previously described method of library design for promoters or enhancers can be applied to analyze multiple populations of eukaryotic cells including embryonic stem (ES) cells, neuronal cells, epithelial cells, immune cells, endocrine cells, muscle cells, erythrocytes, lymphocytes, plant cells, or yeast cells (Paragraph 90, lines 1-5).
Bauer does not teach or suggest that the specific neuronal cell sub-type includes dopaminergic, gabaergic or glutamatergic neurons.
Ahfeldt teaches techniques for enhanced expression of the reporter gene when a gene of interest is important for continued biomedical research (Paragraph 2, lines 1-5) via the detection of co-expression of reporter genes (i.e., dopaminergic neurons) to study Parkinson’s Disease (Paragraph 2, lines 1-5). Further, Ahfeldt teaches that differentiation of the embryonic stem cells into dopaminergic neurons can then be tracked or differentiated cells can be isolated using the properties of the reporter (i.e., fluorescence) (Figure 5E; Paragraph 27, lines 1-10) via CRISPR mediated knock-out mutagenesis to create specified lines from a WT donor line (Figures 4B and 9 A-D; Paragraph 129, lines 1-5).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine Bauer’s promoter identification method with Ahfeldt’s specific neuronal subtypes because both references are directed towards the same field of identifying and utilizing cell-specific gene expression systems. Moreso, Ahfeldt specifically teaches the importance of dopaminergic neurons for biomedical research, and one of ordinary skill in the art would recognize that Bauer’s general method for identifying tissue-specific promoters would be directly applicable to the specific neuronal subtypes taught by Ahfeldt. Further, a person of ordinary skill in the art would have a reasonable expectation of success in combining these reference because Ahfeldt demonstrates that dopaminergic neurons can be successfully differentiated and tracked using reporter systems, confirming these cells are amenable to the expression vector approaches taught by Bauer and therefore it would have been obvious to apply Bauer’s promoter identification methodology to the well-characterized neuronal subtypes specifically disclosed by Ahfeldt.
Conclusions
No claim is allowed.
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/ELIZABETH ROSE LAFAVE/Examiner, Art Unit 1684
/NANCY J LEITH/Primary Examiner, Art Unit 1636