Examiner of Record
The Examiner of record has changed.
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 .
Election/Restrictions
Applicant’s election of:
Group I, claim 4, drawn to a method for stable integration, wherein the at least one exogenous sequence encodes a protein
Species a): NCBI Reference Sequence NW_003613934.1, and
Species b): zinc finger nuclease (ZFN),
in the reply filed on Aug 26, 2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claim 5 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to non-elected Group, there being no allowable generic or linking claim between the restrictable groups. Election was made without traverse in the reply filed on Aug 26, 2025.
Claims 1 – 4 and 6 - 20 are being examined on the merits as claims 1 - 3, and 6-20 were indicated as being generic or linking claims between the restrictable groups.
Priority
This application is filed under 35 U.S.C. 371 as a national stage of international application PCT/US2020/028991, filed on April 20, 2020, which claims domestic priority under 35 U.S.C. 119(e) to U.S. provisional application no. 62/835,810, filed on April 18, 2019.
Specification
Abstract
Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, such as instant, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps. Extensive mechanical and design details of an apparatus should not be included in the abstract.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text, in accordance with 37 CFR 1.72(b). See MPEP § 608.01(b).
In addition, Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
In the instant case, the abstract simply states: Methods for integrating exogenous sequences into specific genomic loci by targeted integration, wherein the integration is stable and the exogenous sequence can function predictably and reliably" which reads like a title without any narrative or summary of the invention claimed . A new abstract is required.
Trade Name or a Mark
The use of the term NCBI, and names of various fluorescent dyes such as in para [0029], which are trade names or marks 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 Rejections - 35 USC § 101
Claims 1, 9, and 13 are rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101).
Claim 1 recites, A method for stable integration of at least one exogenous sequence into genomic DNA of a cell...
Claim 8 recites, The method of claim 1, wherein the at least one exogenous sequence comprises at least one recognition sequence for a polynucleotide modification enzyme.
And
Claim 9 recites, The method of claim 8, wherein the at least one recognition sequence comprises a nucleic acid sequence that does not exist endogenously in the genome of the mammalian cell.
Claim 13 recites, A method for preparing a cell comprising an exogenous sequence integrated into genomic DNA, the method comprising: a) introducing into the cell…
The specification does not provide a limiting definition of a cell, and does not expressly exclude cells within a human organism. In fact, in [0075] it states: Suitable cells include mammalian cells or mammalian cell lines. Non-limiting examples of suitable mammalian cells include Chinese hamster ovary (CHO) cells… human lung cells…etc.,. Thus, the term “cell” in above claims could reasonably be interpreted as encompassing cells within a human organism, which is non-statutory subject matter.
This rejection may be overcome by amending above claims to recite “an isolated cell” or “non-human cell”.
Claim Rejections - 35 USC § 112(b)
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.
Claims 1-4 and 6-20 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1 (claims 2-4 and 6-12, dependent therefrom) and 13 (claims 14-20 dependent therefrom) are indefinite in the recitation of “homolog thereof” because the specification does not provide any definition for the term homolog. The art indicates that a homolog must have some sequence identity to a related species. However, as per MeSH, neither the degree of relatedness is specified nor how to determine such relatedness is specified (See MeSH data, 1 page. Retrieved from the United States NCBI webpage on the internet < https://www.ncbi.nlm.nih.gov/mesh/?term=%22sequence+Homolog%22%5BMeSH+Terms%5D> [retrieved on 24 Jan 2026]). One of ordinary skill in the art would not know what entails a homolog of a particular (large) Ref Seq to be reasonably apprised of the scope of the invention. The applicant may consider an amendment to incorporate the nucleotide sequences of “homologs” of NW_003613934.1 into the sequence listing and identify the sequence in claims 1 and 13 by a corresponding sequence identifier rather than the recitation of “homolog thereof”.
Claim 9 recites the limitation "the mammalian cell". There is insufficient antecedent basis for this limitation in the claims. Claim 9 depends from claim 8, which depends from claim 1. Claim 1 recites “a cell”. It is suggested that the applicant clarify “a cell” in claim 1 such as amending “a cell” in claim 1 to recite “an (isolated) mammalian cell”.
Claim 13 is indefinite in the recitation of “b) maintaining the cell under conditions such that…” because it is unclear as to the meaning of the term “conditions”. In [0072], the specification discloses, “In general, the cell is maintained under conditions appropriate for cell growth and/or maintenance.”. However, this does not indicate, that the conditions so stated are conditions such that the exogenous sequence is integrated into the target site of the genomic sequence. In fact, the term “conditions” is a term of degree and the examiner has reviewed the specification and can find no examples or teachings that can be used for clearly ascertaining the variance intended by the recited term of degree. Moreover, there is nothing in the specification or prior art of record to indicate that one of ordinary skill in the art could have ascertained the scope of the recited degree. See MPEP 2173.05(b).I.
Claim 15 is indefinite in the recitation of “by sequences having substantial sequence identity to sequences flanking the target site in the genomic sequence” because it is unclear as to the meaning of the phrase “substantial sequence identity”. The term "substantial" is not defined by the claim, the specification does not provide a clear definition for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. In fact, the term “substantial” is a term of degree and the examiner has reviewed the specification and can find no examples or teachings that can be used for clearly ascertaining the variance intended by the recited term of degree. Moreover, there is nothing in the specification or prior art of record to indicate that one of ordinary skill in the art could have ascertained the scope of the recited degree. See MPEP 2173.05(b).I.
Claim Rejections - 35 USC § 112(a)
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.
Improper Incorporation by Reference
Claim 1 is rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, as based on a disclosure which is not enabling. The disclosure does not enable one of ordinary skill in the art to practice the invention without the sequences of the GenBank accession numbers recited, which are critical or essential to the practice of the invention but not included in the claim(s). See In re Mayhew, 527 F.2d 1229, 188 USPQ 356 (CCPA 1976).
In the instant case, the particular Ref Seq is large; without any indication of a locus or loci, one would not know where stable integration should occur.
Thus the incorporation by reference of essential material (i.e., the sequences of the GenBank accession numbers) by reference to an electronic database is an improper incorporation by reference.
Written Description
Claims 1-4 and 6-20 are rejected under 35 U.S.C. 112(a) 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.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
MPEP § 2163 further states that “[s]atisfactory disclosure of a ‘representative number’ depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions 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…Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.’ Such correlations may be established ‘by the inventor as described in the specification,’ or they may be ‘known in the art at the time of the filing date.’"
The factors considered in the Written Description requirement are (1) level of skill and knowledge in the art, (2) partial structure, (3) physical and/or chemical properties, (4) functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the (5) method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient." MPEP § 2163.
Claims 1-4 and 6-20 are drawn to (in relevant part) a method for stable integration of at least one exogenous sequence into genomic DNA of a cell, the method comprises integrating the at least one exogenous sequence into a site within a genomic sequence, wherein the site within the genomic sequence is NCBI Reference Sequence NW003613934.1, or homolog thereof.
Claims 1-4 and 6-20 are drawn to (in relevant part) a method for preparing a cell comprising an exogenous sequence integrated into genomic DNA, the method comprising:
a) introducing into the cell (i) a targeting endonuclease or nucleic acid encoding a targeting endonuclease, which is targeted to a target site within a genomic sequence, wherein the target site is NCBI Reference Sequence NW_003613934.1, or homolog thereof and (ii) a donor polynucleotide comprising the exogenous sequence; and
b) maintaining the cell under conditions such that the exogenous sequence is integrated into the target site of the genomic sequence.
Scope of the Invention
Given a broadest reasonable interpretation, the recited “homolog thereof” is interpreted as being unlimited with respect to nucleotide sequence. Consequently, the site of genomic integration within the cell is unlimited. Further, see above, the 112b rejection of this limitation.
Disclosure of a Complete or Partial structure
The specification discloses a single working example of randomly integrating the at least one exogenous sequence into a site within a genomic sequence, wherein the site within the genomic sequence is NCBI Reference Sequence NW003613934.1, or homolog thereof –between nucleotides 1,090,000 - 1,127,000 of the sequence of NW_003613934.1, called D145. The specification also discloses two other CHO genomic insertion sites similarly determined as above (Table 1). Other than the genomic locations of a CHO cell disclosed in Table 1 of the specification, the specification fails to disclose or provide guidance regarding homologs thereof. While the specification indicates that random integration occurred in a particular locus of the recited Accession number, Fig. 6 indicates that a decrease in expression of the exogenous gene is seen in late stage cultures when inserted into site MP 58. Thus, the specification fails to disclose or provide guidance regarding insertion(s) into homologs thereof.
In instant case, other than integrating at least one exogenous sequence into the genome of a Chinese Hamster Ovary (CHO) cell, wherein the at least one exogenous sequence is integrated into the genome of the CHO cell at a nucleotide insertion site between nucleotides 859,501 and 1,053,101 of the sequence of NW_003613934.1, there are no other disclosed species genomic integration sites within NW_003613934.1 or a homolog thereof as encompassed by the claims. The genus of recited cells and genomic integration sites within NW_003613934.1 or a homolog thereof are considered to encompass widely variant species and the single disclosed representative species fails to reflect the substantial variation among the members of the genus. In view of the substantial variation among the members of the genus of cells and genomic integration sites within NW_003613934.1 or a homolog thereof, the high level of unpredictability in the art, and the disclosure of only a single species among a widely variant genus, one of skill in the art would not accept the disclosed representative species as being representative of homologs thereof as encompassed by the claims. As such, the specification, fails to satisfy the written description requirement of 35 U.S.C. 112(a).
Conclusion of Written Description:
In summary, the claims embrace targeted, enzymatic integration of an exogenous gene (of any nucleotide sequence) into any loci in any cell, exemplified by random insertion of an exogenous gene in to a CHO cell line. The specification as filed provides no guidance that would allow one of skill in the art to predict which nucleic acid sequences, inserted in to any locus within homologs of the recited Accession number, will support expression of the exogenous gene, and do so with stability, predictability, and reproducibility. The disclosure of one loci within each of the three recited accession numbers and their homologs that support random integration does not provide any guidance towards the practically infinite number of loci embraced by the claims such that insertion with stability, predictability, and reproducibility of exogenous gene expression can be achieved. The disclosure of only three species does not convey to one of skill that Applicant was in possession of the breadth of the genus that is claimed.
Examiner Suggestion: Amend the claims to delete the phrase “or homolog thereof” in claims 1 and 13.
Scope of Enablement
The following rejection is limited to the elected species: NW_003613934.1.
Claims 1-4 and 6-20 are rejected under 35 U.S.C. 112(a) because the specification, while being enabling for a method of integrating at least one exogenous sequence into the genome of a Chinese hamster ovary (CHO) cell in vitro, wherein the at least one exogenous sequence is integrated into the genome of the CHO cell at nucleotides 1,090,000 - 1,127,000 of the sequence of NW_003613934.1, called D145, does not reasonably provide enablement for all methods as encompassed by the claims, particularly with respect to the scope of cells and genomic integration sites. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
“The test of enablement is not whether any experimentation is necessary, but whether, if experimentation is necessary, it is undue.” In re Angstadt, 537 F.2d 498, 504, 190 USPQ 214, 219 (CCPA 1976). Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)) as follows: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. See MPEP § 2164.01(a). The Factors considered to be most relevant to the instant rejection are addressed in detail below.
The nature of the invention: According to the specification “[t]he key to successful site-specific targeted integration of transgenes relies a suitable genomic location (i.e., a "safe harbor") to target for integration”. This location must be amenable to transgene or exogenous sequence insertion, allow for predictable and stable expression of the transgene, and must not interfere with cellular growth and function…viable sites in many cells used for therapeutic protein production have not been identified. Thus, there is a need to identify and verify suitable genomic locations in Chinese hamster ovary (CHO) and other cells for the successful integration of therapeutic protein cassettes or other exogenous sequences” (paragraph [0004]).
The breadth of the claims: Claims 1-4 and 6-20 are drawn to (in relevant part) a method for stable integration of at least one exogenous sequence into genomic DNA of a cell, the method comprises integrating the at least one exogenous sequence into a site within a genomic sequence, wherein the site within the genomic sequence is NCBI Reference Sequence NW003613934.1, or homolog thereof.
Claims 1-4 and 6-20 are drawn to (in relevant part) a method for preparing a cell comprising an exogenous sequence integrated into genomic DNA, the method comprising:
a) introducing into the cell (i) a targeting endonuclease or nucleic acid encoding a targeting endonuclease, which is targeted to a target site within a genomic sequence, wherein the target site is NCBI Reference Sequence NW_003613934.1, or homolog thereof and (ii) a donor polynucleotide comprising the exogenous sequence; and
b) maintaining the cell under conditions such that the exogenous sequence is integrated into the target site of the genomic sequence.
In the independent claims, the recited “cell” is unlimited and encompasses any cell type.
Also, given a broadest reasonable interpretation, the recited “homolog thereof” is interpreted as being unlimited with respect to nucleotide sequence. Consequently, the site of genomic integration within the cell is unlimited.
The state of the prior art; The level of one of ordinary skill; and The level of predictability in the art:
According to MPEP 2164.03, “…what is known in the art provides evidence as to the question of predictability” and “[I]f one skilled in the art cannot readily anticipate the effect of a change within the subject matter to which that claimed invention pertains, then there is lack of predictability in the art.”
Before the effective filing date of the claimed invention, the prior art of record discloses genomic loci in CHO cells suitable for integrating an exogenous nucleic acid sequence and a method for integrating an exogenous nucleic acid sequence into the genome of a CHO cell (see, e.g., Bahr et al., WO 2014/205192 A2, particularly pp. 25-27 and claim 11; cited on IDS of 2/28/2023). However, as noted above, the claims encompass a broad scope of cells and genomic integration sites.
According to the reference of Lai et al., (Poster at ESACT Meeting 2015 in Barcelona, No.P-1.29, p.119, Barcelona, Spain, May 31- June 3, 2015, 1 page; cited on Form PTO-892),
“Chromosomal instability is one of the key characteristics observed in Chinese Hamster Ovary (CHO) cells, which often occurs as a random event in an uncontrollable manner. This occasionally complicates the process of establishing stable and high-producing CHO cell lines.”, (lines 1-3, Abstract). Lai et al., also observe that substantial variation and unpredictable stability of expression exists amongst transfected CHO cells, requiring extensive clone screening to identify suitable high producers noting that even among clones, expression can be surprisingly heterogeneous (all treated clones did not exhibit a consistent chromosomal number; Instead, a wide range of aneuploidy was observed within each clone., middle of right column; clonal variability in antibody production, bottom two graphs).
Even after the effective filing date, Hertel et al. (Front. Bioengineer. Biotechnol. 10:1010719, 2022, 12 pages; cited on the attached Form PTO-892) disclose “[i]nstability within recombinant CHO cells can occur at any or all of the genome, transcriptome, or proteome level” (p. 2, column 1, bottom) and that even the characteristics of “safe harbors” are “poorly understood and differ substantially between the relatively few known regions…To date, the ongoing efforts to identify additional safe harbor regions in the CHO genome has mostly been conducted via empirical methods” (p. 2, column 2, bottom)
Dahodwala et al. (Curr. Opin. Biotechnol. 60:128-137, 2019; cited on the attached Form PTO-892) disclose “[v]arious mechanisms have been identified as causes of the observed instability, such as gene loss, gene silencing, and increased susceptibility to cellular stresses. Production instability has also been known to arise from distal factors such as increasing apoptosis and global gene changes as well as whole genome/epigenome changes. Unintended and unpredictable gene changes also come with a risk of changing the expression of cellular genes associated with glycosylation, protein folding, proteases and molecular chaperones” (paragraph bridging pp. 129-130).
Based on the evidence of record, one of skill in the art would recognize a high level of unpredictability in making the full scope of claimed methods, particularly with respect to the scope of cells and genomic integration sites.
The amount of direction provided by the inventor and The existence of working examples: The specification discloses a single working example of randomly integrating the at least one exogenous sequence into a site within a genomic sequence, wherein the site within the genomic sequence is NCBI Reference Sequence NW003613934.1, or homolog thereof –between nucleotides 1,090,000 - 1,127,000 of the sequence of NW_003613934.1, called D145. The specification also discloses two other CHO genomic insertion sites similarly determined as above for the unelected Ref Seqs (Table 1). Other than the genomic locations of a CHO cell disclosed in Table 1 of the specification, the specification fails to disclose or provide guidance regarding other cells and genomic integration sites. While the specification indicates that random integration occurred in a particular locus of the recited Accession number, Fig. 6 indicates that a decrease in expression of the exogenous gene is seen in late stage cultures when inserted into site MP 58. Thus, the specification fails to disclose or provide guidance regarding the stability, predictability, and reproducibility of such insertion(s).
The quantity of experimentation needed to make or use the invention based on the content of the disclosure: While methods of genomic integration were known before the effective filing date, it was not routine in the art to make all cells with all genomic integrations of an exogenous nucleic acid as broadly encompassed by the claims.
The principles that govern which nucleic acid sequences can be integrated, and into which loci, and which cannot, are not disclosed in the specification or explicitly in the prior art and art, and one of skill is left to determine, on a case-by-case basis which sequences and loci will work within the invention, or is left to determine the principles themselves. Each newly discovered integration loci would be structurally distinct from those disclosed in the specification in a manner that is entirely unpredictable. Such extensive experimentation, and/or the determination of principles that would allow one to predict how the invention would work represent undue experimentation.
In view of the overly broad scope of the claims, the lack of guidance and working examples provided in the specification, and the high degree of unpredictability as evidenced by the prior art, undue experimentation would be necessary for a skilled artisan to make and use the entire scope of the claimed invention. Applicants have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims.
The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
Conclusion of Scope of Enablement:
The specification taught that random integration of one exogenous gene (lox-flanked mAb gene) into CHO cells, results in random integration into three different loci identified by three different Accession numbers. High mAb expressing single copy clones were identified and characterized. Thus, it appears as if, not all ensuing clones resulted in integration of the one exogenous gene tested, or at least did not result in sufficiently high expression of the exogenous gene. In view of the unpredictability disclosed by the specification and the art, targeted insertion of exogenous gene (of any nucleotide sequence) into any cell type, is unpredictable. The specification as filed provides no guidance that would allow one of skill in the art to predict which nucleic acid sequences, inserted in to any locus within the recited Accession number, will support expression of the exogenous gene, and do so with stability, predictability, and reproducibility. In view of the breadth of the claims, the nature of the invention, the unpredictability of art, and the level of guidance in the specification, one of skill in the art would have to perform undue experimentation in order to practice the invention commensurate in scope with the claims.
Examiner Suggestion: Amend the claims to recite the loci for integration and provide a declaration that such integration is stable, predictable, and reproducible; and delete the phrase “or homolog thereof” in claims 1 and 13.
Claim Rejections - 35 USC § 102
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 1-4 and 6-20 are rejected under 35 U.S.C. 102(a)(1) or 35 U.S.C. 102(a)(2) as being anticipated by Bahr et al. (WO 2014/205192 A2; cited on IDS of 02/28/2023; hereafter “Bahr”).
Claims 1-4 and 6-20 are drawn to (in relevant part) a method for stable integration of at least one exogenous sequence into genomic DNA of a cell, the method comprises integrating the at least one exogenous sequence into a site within a genomic sequence, wherein the site within the genomic sequence is NCBI Reference Sequence NW003613934.1, or homolog thereof.
Claims 13-20 are drawn to (in relevant part) a method for preparing a cell comprising an exogenous sequence integrated into genomic DNA, the method comprising:
a) introducing into the cell (i) a targeting endonuclease or nucleic acid encoding a targeting endonuclease, which is targeted to a target site within a genomic sequence, wherein the target site is NCBI Reference Sequence NW_003613934.1, or homolog thereof and (ii) a donor polynucleotide comprising the exogenous sequence; and
b) maintaining the cell under conditions such that the exogenous sequence is integrated into the target site of the genomic sequence.
Regarding claims 1, 8, 13, 15, and 17, claim 11 of the reference of Bahr discloses a method for preparing a cell comprising at least one exogenous nucleic acid sequence comprising at least one recognition sequence for a polynucleotide modification enzyme, the method comprising
a) introducing into a cell at least one targeting endonuclease that is targeted to a sequence within or proximal to a genomic locus listed in Table 2,
b) introducing into the cell at least one donor polynucleotide comprising the exogenous nucleic acid that is flanked by (i) sequences having substantial sequence identity to the targeted genomic locus or (ii) the recognition sequence of the targeting endonuclease; and
c) maintaining the cell under conditions such that the exogenous nucleic acid is integrated into genome of the cell.
According to Bahr, this process generates a “landing pad” in the genome of the cell (paragraphs [0012] and [0014]).
The recitation of “homolog thereof” in claims 1 and 13 is interpreted as being unlimited with respect to nucleotide sequence and encompassing any one of the genomic loci listed in Table 2 of Bahr.
Also, Clone #89 Site 1 (NW_003617688.1), Clone #89 Site 2 (NW_003615226.1), and AP3D1 (NW 003613904.1) of Bahr’s Table 2 are considered to be sites within NW_003613934.1.
Regarding claims 2 and 14, claim 12 of Bahr recites wherein the cell is a CHO cell.
Regarding claims 3, 4, and 20, Bahr discloses the exogenous nucleic acid includes a sequence encoding a fluorescence protein, which is considered to be a “recombinant protein”. Alternatively, Bahr discloses a recombinant protein expression cassette, referred to as a “payload”, can be integrated into the “landing pad” of the cell’s genome (paragraph [0016]).
Regarding claim 6, Bahr discloses the landing pad includes a promoter (paragraph [0018]) and the payload includes a promoter (paragraph [0010]).
Regarding claim 7, in view of the indefiniteness of the phrase “wherein expression of the exogenous sequence is stable, predictable and reproducible”, claim 7 is included in the instant rejection.
Regarding claim 9, claim 3 of Bahr recites wherein the at least one recognition sequence comprises a nucleic acid sequence that does not exist endogenously in the genome of the cell.
Regarding claims 10 and 11, claim 4 of Bahr recites wherein the polynucleotide modification enzyme is selected from the group consisting of a targeting endonuclease, a site-specific recombinase, and combinations thereof; and Bahr paragraph [0010] discloses: the polynucleotide modification enzyme is a targeting endonuclease (e.g., zinc finger nuclease (ZFN), ….), a site-specific recombinase (e.g., lambda integrase, Cre recombinase, FLP recombinase, gamma-delta resolvase, …), or combinations thereof.
Regarding claims 12 and 19, claim 5 of Bahr recites wherein the targeting endonuclease is a zinc finger nuclease (ZFN).
Regarding claim 16, claim 13 of Bahr recites wherein the exogenous nucleic acid is integrated into the genome by a homology-directed process.
Regarding claim 18, claim 14 of Bahr recites wherein the exogenous nucleic acid is integrated into the genome by a direct ligation process.
Therefore, Bahr anticipates claims 1-4 and 6-20 as written.
Conclusion
No claim is in condition for allowance.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHABANA MEYERING, Ph.D. whose telephone number is (703)756-4603. The examiner can normally be reached M - F: 9am to 5pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram Shukla can be reached at (571) 272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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SHABANA S. MEYERING, Ph.D.
Examiner
Art Unit 1635
/SHABANA S MEYERING/ Examiner, Art Unit 1635
/RAM R SHUKLA/ Supervisory Patent Examiner, Art Unit 1635