DETAILED CORRESPONDENCE
Status of the Application
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 August 26, 2025 has been entered.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1, 3-6, 8-13, 16-23, and 25-29 are pending in the application.
The text of those sections of Title 35 U.S. Code not included in the instant action can be found in a prior Office action.
Restriction/Election
In response to a requirement for restriction/election mailed on November 8, 2023, the applicant elected:
species A2), SEQ ID NO: 12, NCBI Reference Sequence NW_006880577.1,
species B1), exogenous sequence encodes a protein including a therapeutic protein, a recombinant protein, and an industrial protein,
species C10), targeting endonuclease which is zinc finger nuclease (ZFN), and
species D1), the exogenous sequence in the donor polynucleotide is flanked by sequences having substantial sequence identity to sequences flanking the target site in the genomic sequence, and wherein the exogenous sequence is integrated into the genome by a homology-directed process.
Election was made without traverse in the reply filed on February 8, 2024.
Claims 5, 11, 17, 18, 22, and 28 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to non-elected species, there being no allowable generic or linking claim.
Claims 1, 3, 4, 6, 8-10, 12, 13, 16, 19-21, 23, 25-27, and 29 are being examined on the merits with claims 3, 10, 12, 19, 20, 27, and 29 being examined only to the extent the claims read on the elected subject matter.
Claim Objections
The objections to claims 13 and 16 for minor informalities are withdrawn in view of the instant amendment to the claims.
Claim Rejections - 35 USC § 112(b)
Claims 1, 3, 4, 6, 8-10, and 12 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.
Claim 1 (claims 3, 4, 6, 8-10, and 12 dependent therefrom) is indefinite in the recitation of “…the genomic DNA comprises SEQ ID NO: 12 or homolog thereof…integrating the at least one exogenous sequence into the genomic DNA at a target site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12.” The method requires integration of the at least one exogenous sequence into the genomic DNA at a target site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12, however, in view of the recitation of “the genomic DNA comprises SEQ ID NO: 12 or homolog thereof,” it is unclear as to whether or not the genomic DNA comprises SEQ ID NO: 12. In the interest of advancing prosecution, it is suggested that the phrase “or homolog thereof” be deleted from claim 1.
Claim Rejections - 35 USC § 112(a)
Claims 1, 3, 4, 6, 8-10, 12, 13, 16, 19-21, 23, 25-27, and 29 are rejected under 35 U.S.C. 112(a) because the specification, while being enabling for a method for 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 nucleotide 83,801 of SEQ ID NO: 11, nucleotide 1,248,580 of SEQ ID NO: 14, nucleotide 191,785 of SEQ ID NO: 15, nucleotide 284,534 of SEQ ID NO: 16, nucleotide 5,522 of SEQ ID NO: 17, nucleotide 1,661,086 of SEQ ID NO: 18, nucleotide 1,707,191 of SEQ ID NO: 19, or nucleotide 3,678,411 of SEQ ID NO: 20, does not reasonably provide enablement for stable genomic integration at any site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12. 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 [0005]).
The breadth of the claims: As amended, claims 1, 3, 4, 6, 8-10, and 12 are drawn to a method for stable integration of at least one exogenous sequence into genomic DNA of a Chinese hamster ovary (CHO) cell, wherein the genomic DNA comprises SEQ ID NO: 12 or homolog thereof, the method comprising integrating the at least one exogenous sequence into the genomic DNA at a target site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12.
As amended, claims 13, 16, 19-21, 23, 25-27, and 29 are drawn to a method for preparing a CHO cell comprising an exogenous sequence integrated into genomic DNA, wherein the genomic DNA comprises SEQ ID NO: 12, the method comprising:
a) introducing into the cell (i) a targeting endonuclease or nucleic acid encoding a targeting endonuclease, which cleaves at a target site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 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.
The amount of direction provided by the inventor and The existence of working examples: The specification at p. 26, Table 1 discloses stable integration sites in the genome of CHO cells at nucleotide 83,801 of SEQ ID NO: 11, nucleotide 1,248,580 of SEQ ID NO: 14, nucleotide 191,785 of SEQ ID NO: 15, nucleotide 284,534 of SEQ ID NO: 16, nucleotide 5,522 of SEQ ID NO: 17, nucleotide 1,661,086 of SEQ ID NO: 18, nucleotide 1,707,191 of SEQ ID NO: 19, and nucleotide 3,678,411 of SEQ ID NO: 20. Other than these specific nucleotide insertion sites, the specification also discloses a nucleotide insertion site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12, however, the specification fails to identify the specific nucleotide insertion site(s) between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 that is/are safe harbor(s) for stable integration of an exogenous nucleic acid.
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, 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 the IDS filed on April 21, 2023). However, as noted above, the claims encompass a broad scope of genomic integration sites at any nucleotide between nucleotides 859,901 and 1,053,101 of SEQ ID NO: 12.
According to the reference of Pilorough et al. (PLoS ONE 4:e8432, December 2009, 11 pages; cited on the IDS filed on April 21, 2023), isolating recombinant mammalian cell lines for large-scale production remains costly and time-consuming, due to substantial variation and unpredictable stability of expression amongst transfected cells, requiring extensive clone screening to identify suitable high producers (p. 1, Abstract), noting that even among clones, expression can be surprisingly heterogeneous (p. 1, Abstract), and that efforts to define the molecular determinants of stability have so far achieved only limited success and stability is still routinely assessed by directly monitoring each clone over several months of growth (paragraph bridging pp. 1-2).
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 the claimed invention, particularly with respect to stable genomic integration of an exogenous polynucleotide at any site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 in the absence of a teaching or guidance regarding the specific nucleotide insertion site(s) between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 for stable integration of an exogenous nucleic acid.
The quantity of experimentation needed to make or use the invention based on the content of the disclosure: Methods of genomic integration were known before the effective filing date. However, as acknowledged by Hertel et al. (supra), identification of safe harbor regions in the CHO genome has mostly been conducted via empirical methods (p. 2, column 2, bottom) and in view of the evidence of record, it was not routine in the art to empirically determine all safe harbor sites between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 for stable integration of an exogenous nucleic acid.
In view of the overly broad scope of the claims, particularly the genomic integration site(s) at any nucleotide between nucleotides 859,901 and 1,053,101 of SEQ ID NO: 12 for stable integration of an exogenous nucleic acid, the lack of guidance and working examples provided in the specification, and the high degree of unpredictability as evidenced by the cited 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).
Claims 1, 3, 4, 6, 8-10, 12, 13, 16, 19-21, 23, 25-27, and 29 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.2.(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.
As amended, claims 1, 3, 4, 6, 8-10, and 12 are drawn to a method for stable integration of at least one exogenous sequence into genomic DNA of a Chinese hamster ovary (CHO) cell, wherein the genomic DNA comprises SEQ ID NO: 12 or homolog thereof, the method comprising integrating the at least one exogenous sequence into the genomic DNA at a target site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12.
As amended, claims 13, 16, 19-21, 23, 25-27, and 29 are drawn to a method for preparing a CHO cell comprising an exogenous sequence integrated into genomic DNA, wherein the genomic DNA comprises SEQ ID NO: 12, the method comprising:
a) introducing into the cell (i) a targeting endonuclease or nucleic acid encoding a targeting endonuclease, which cleaves at a target site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 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.
The specification discloses the reduction to practice of stable integration sites in the genome of CHO cells at nucleotide 83,801 of SEQ ID NO: 11, nucleotide 1,248,580 of SEQ ID NO: 14, nucleotide 191,785 of SEQ ID NO: 15, nucleotide 284,534 of SEQ ID NO: 16, nucleotide 5,522 of SEQ ID NO: 17, nucleotide 1,661,086 of SEQ ID NO: 18, nucleotide 1,707,191 of SEQ ID NO: 19, and nucleotide 3,678,411 of SEQ ID NO: 20. Other than these specific nucleotide insertion sites, the specification also discloses a nucleotide insertion site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12, however, fails to identify the specific nucleotide insertion site(s) between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 for stable integration of an exogenous nucleic acid.
According to the reference of Pilorough et al. (PLoS ONE 4:e8432, December 2009, 11 pages; cited on the IDS filed on April 21, 2023), isolating recombinant mammalian cell lines for large-scale production remains costly and time-consuming, due to substantial variation and unpredictable stability of expression amongst transfected cells, requiring extensive clone screening to identify suitable high producers (p. 1, Abstract), noting that even among clones, expression can be surprisingly heterogeneous (p. 1, Abstract), and that efforts to define the molecular determinants of stability have so far achieved only limited success and stability is still routinely assessed by directly monitoring each clone over several months of growth (paragraph bridging pp. 1-2).
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 such as random lentiviral integrations” (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).
Given the high level of unpredictability in the art of stably integrating an exogenous polynucleotide into the genome of a CHO cell and the general requirement for empirically determining a “safe harbor” site, and because the specification fails to identify the specific nucleotide insertion site(s) between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 for stable integration of an exogenous nucleic acid, one of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus, and thus, that applicant was not in possession of the claimed genus of polypeptides. In this case, the specification appears to provide no more than a research plan for identifying “safe harbor” sites between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12 for stable integration. Therefore, the claimed subject matter is not supported by an adequate written description because a representative number of species has not been described.
RESPONSE TO REMARKS: Applicant argues the rejections under 35 U.S.C. 112(a) are obviated in view of the amendment to delete the phrase “or homolog thereof” in claims 1 and 13.
Applicant’s argument is not found persuasive. For the reasons set forth above, the specification in combination with state of the art fail to adequately describe and enable the full scope of the claimed invention.
Claim Rejections - 35 USC § 102
The rejection of claims 1, 3, 4, 6, 8-10, 12, 13, 16, 19-21, 23, 25-27, and 29 under 35 U.S.C. 102(a)(1) as being anticipated by Bahr et al. (WO 2014/205192 A2; cited on the IDS filed on April 21, 2023; hereafter “Bahr”) is withdrawn in view of the instant amendments to claims 1 and 13 to limit integration of the at least one exogenous sequence into the genomic DNA at a target site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12. Bahr does not teach or suggest integration of an exogenous sequence into genomic DNA at a target site between nucleotides 859,501 and 1,053,101 of SEQ ID NO: 12.
Conclusion
Status of the claims:
Claims 1, 3-6, 8-13, 16-23, and 25-29 are pending.
Claims 5, 11, 17, 18, 22, and 28 are withdrawn from consideration.
Claims 1, 3, 4, 6, 8-10, 12, 13, 16, 19-21, 23, 25-27, and 29 are rejected.
No claim is in condition for allowance.
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/David Steadman/Primary Examiner, Art Unit 1656