DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment to the claims, filed July 22, 2026, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Claims 1, 3-8, 10, 12, 13, and 15-21 are pending in the application.
Applicant’s remarks filed July 22, 2026 in response to the non-final rejection filed April 22, 2026 have been fully considered.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Restriction/Election
In response to a requirement for restriction/election mailed August 15, 2024, applicant elected species (A2), the first protein of interest is an immunoglobulin or immunoglobulin-like protein (claim 7), and species (B2), the method according to claim 8, wherein selecting the cell with increased capacity to express the first protein of interest comprises performing targeted engineering by applying gene editing methods to introduce, remove or modify genetic material in the genome of said identified cells expressing the first protein of interest (now-canceled claim 11).
Applicant timely traversed the restriction (election) requirement in the reply filed October 9, 2024 and the requirement was deemed proper and made FINAL in the Office action mailed November 29, 2024.
Claims 6 and 10 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected species, there being no allowable generic or linking claim.
Amended claim 1 recites species that are independent or distinct from the invention originally claimed for the following reasons: as amended, claim 1 recites “wherein the attributes used to select the top candidate cell population are selected from the group consisting of: protein expression, protein aggregation, charge heterogeneity, size heterogeneity, glycosylation site occupancy, glycosylation profile, cell growth characteristics, cell metabolic characteristics, tertiary structure profile, protein self-association tendency, DNA profile, mRNA profile, miRNA profile, proteomic profile and genomic stability.” Throughout prosecution, claim 8 has recited “selecting a cell with increased capacity to express the first protein of interest…”, which corresponds to “protein expression” in the Markush grouping of recited attributes used to select the top candidate cell population in claim 1.
Since applicant has received an action on the merits for the originally presented species “protein expression” in the Markush grouping of recited attributes used to select the top candidate cell population in claim 1, this species has been constructively elected by original presentation for prosecution on the merits. Accordingly, the species of “protein aggregation, charge heterogeneity, size heterogeneity, glycosylation site occupancy, glycosylation profile, cell growth characteristics, cell metabolic characteristics, tertiary structure profile, protein self-association tendency, DNA profile, mRNA profile, miRNA profile, proteomic profile and genomic stability” in the Markush grouping of recited attributes used to select the top candidate cell population in claim 1 are withdrawn from consideration as being directed to non-elected species. See 37 CFR 1.142(b) and MPEP § 821.03.
To preserve a right to petition, the reply to this action must distinctly and specifically point out supposed errors in the restriction requirement. Otherwise, the election shall be treated as a final election without traverse. Traversal must be timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are subsequently added, applicant must indicate which of the subsequently added claims are readable upon the elected invention.
Should applicant traverse on the ground that the species are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the species to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the species unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 of the other species.
Claims 1, 3-5, 7, 8, 12, 13, and 15-21 are being examined on the merits.
Claim Objections
The objection to claim 1 is withdrawn in view of applicant’s amendments to replace “I.”, “II.”, “III.”, “IV.”, and “V.” with “I)”, “II)”, “III)”, “IV)”, and “V)”, respectively, to recite “after repeating steps I-II n times” in step IV) of claim 1, and to recite “the cell of step (IV)” in step V) of claim 1.
Claim 1 is objected to in the recitation of “wherein the expression load is gradually increased” and in the interest of improving form, it is suggested that the noted phrase be amended to recite (with markings to show changes made) “wherein the expression load of the first protein of interest is gradually increased.”
Claim 13 is objected to in the recitation of “The method of claim 1…step c) comprises…” As shown in the amendment filed March 6, 2026, step c) of claim 1 corresponds to step IV) of instant claim 1 and in order to update claim 13 to correspond to instant claim 1, the recitation of “step c)” should be amended to recite “step IV).”
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1, 3-5, 7, 12, 13, and 15-17 under 35 U.S.C. 112(b) is withdrawn in view of applicant’s amendment to claim 1 to recite “using the top candidate cell population from step (II)(b) for isolating clones in step (I)” and to recite attributes for selecting the top candidate cell population.
Claims 1, 3-5, 7, 8, 12, 13, and 15-21 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.
This rejection is necessitated by applicant’s amendment to claim 1 and addition of claims 20 and 21.
Claims 1 (claims 3-5, 7, 8, 12, 13, and 15-21 dependent therefrom), 20, and 21 are indefinite in the recitation of “gradually increased.” The term “gradually” is a term of degree and the examiner has reviewed the specification and can find no examples or teachings that can be used for ascertaining the increased expression load that is considered to be encompassed by “gradually increased.” Moreover, there is nothing in the specification or prior art of record to indicate that one of skill in the art could have ascertained the scope of the recited degree. Applicant’s attention is directed to MPEP 2173.05(b).I regarding terms of degree.
Claim 20 recites the limitation “the promoter strength.” There is insufficient antecedent basis for this limitation in the claim.
Claim 21 is confusing in the recitation of “the expression load is gradually increased by using different 5’ and 3’ mRNA untranslated regions.” It is entirely unclear from the claims and specification as to how applicant intends for different 5’ and 3’ mRNA untranslated regions to be used to gradually increase expression load. It is also unclear as to whether or not the recited limitation is intended to limit a recited nucleic acid to a mRNA. In the interest of advancing prosecution, it is suggested that applicant clarify the intended meaning of the phrase “the expression load is gradually increased by using different 5’ and 3’ mRNA untranslated regions.”
Claim Rejections - 35 USC § 112(a)
Claims 20 and 21 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 at the time the application was filed, had possession of the claimed invention.
This rejection is necessitated by applicant’s amendment to add claims 20 and 21.
MPEP § 2163.II.A.3.(b) states, “when filing an amendment an applicant should show support in the original disclosure for new or amended claims”. See also MPEP 714.02. MPEP § 2163.II.A.3.(b) further states, “[i]f the originally filed disclosure does not provide support for each claim limitation, or if an element which applicant describes as essential or critical is not claimed, a new or amended claim must be rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112, para. 1, as lacking adequate written description”. According to MPEP § 2163.I.B, “While there is no in haec verba requirement, newly added claim limitations must be supported in the specification through express, implicit, or inherent disclosure” and “The fundamental factual inquiry is whether the specification conveys with reasonable clarity to those skilled in the art that, as of the filing date sought, applicant was in possession of the invention as now claimed. See, e.g., Vas-Cath, Inc., 935 F.2d at 1563-64, 19 USPQ2d at 1117.”
New claim 20 recites “The method of claim 1, wherein the expression load is gradually increased by increasing the promoter strength” and claim 21 recites “The method of claim 1, wherein the expression load is gradually increased by using different 5’ and 3’ mRNA untranslated regions.” According to applicant’s instant remarks, the limitations of claims 20 and 21 “are supported by at least Figure 2 and paragraph [0081]” (instant remarks at p. 7, middle), however, the specification does not have a paragraph [0081] and Figure 2 fails to provide descriptive support for the limitations “wherein the expression load is gradually increased by increasing the promoter strength” and “wherein the expression load is gradually increased by using different 5’ and 3’ mRNA untranslated regions.” Applicant is invited to show support for the limitations at issue.
Claim Rejections - 35 USC § 103
Claims 1, 3-5, 7, 8, 12, 13, and 15-21 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (Biotechnol. Prog. September 2015, 11 pages; cited on the IDS filed on September 14, 2024; hereafter “Zhang”) and Bahr et al. (WO 2014/205192 A2; cited on the IDS filed on September 14, 2024; hereafter “Bahr”).
This rejection has been modified from its previous version in order to address applicant’s instant amendment to the claims.
As amended, the claims are drawn to (in relevant part) a method to obtain a cell suitable for expressing a protein interest comprising the following steps:
I) isolating clones from a culture of recombinant cells or cell populations or descendants thereof,
II) performing targeted engineering by applying gene editing methods comprising:
a) integrating a nucleic acid molecule encoding a single copy of a first protein of interest into a pre-defined site in the genome of a recipient cell; and
b) identifying cells expressing the first protein of interest;
III) repeating steps I-II n times by using the top candidate cell population from step (II)(b) for isolating clones in step (I),
wherein n is two or more
wherein the expression load is gradually increased during each subsequent iteration, and
wherein the attribute used to select the top candidate cell population is protein expression,
IV) after repeating steps I-II n times, creating a cell bank for cell line development by:
excising the nucleic acid molecule encoding the first protein of interest from the genome of the identified cells and simultaneously introducing one or several functional sequence elements Q enabling targeted introduction of a nucleic acid molecule encoding a single copy of a second protein of interest into said pre-defined site in the genome,
wherein the genome of the recipient cell does not comprise the one or several sequence elements Q prior to excision of the nucleic acid molecule encoding the first protein of interest, and
V) integrating the nucleic acid molecule encoding the second protein of interest into the pre-defined site in the genome of the cell of step (IV).
Regarding the claim 1 limitation “A method to obtain a cell suitable for expressing a protein of interest,” Zhang relates to recombinase-mediated cassette exchange for monoclonal antibody expression in the commercially relevant CHOK1SV cell line (p. 1, title) and generally discloses a method for constructing a site-specific integration (SSI) system for monoclonal antibody expression in a CHOK1SV cell line (p. 1, Abstract).
Regarding steps I), II), and III) of claim 1 and claims 8 and 17-19, Zhang teaches selecting the industrially relevant CHOK1SV cell line for site-specific integration (p. 2, column 2, top) and teaches a vector encoding a single copy of monoclonal antibody cB72.3 flanked by wild-type FRT (F) and mutant FRT (F5) recombination sequences (Figure 1A; p. 4, column 2, middle). Zhang teaches Phase I of the method, which is integrating the vector encoding a single copy of monoclonal antibody cB72.3 into a “hot spot” within the genome of CHOK1SV cells suitable for expression of a gene of interest (p. 4, column 2) and screening cell pools for production of the monoclonal antibody cB72.3 at 3 weeks post-transfection and following evaluation, the top 6 best-performing clones based on antibody production and growth characteristics were selected (paragraph bridging pp. 4-5). Given a broadest reasonable interpretation, the recitation of “wherein the attributes used to select the top candidate cell population are selected from the group consisting of: protein expression…” in claim 1 is interpreted as meaning selection based on one or more of the recited attributes selection based on antibody production and growth characteristics according to Zhang is considered to be encompassed by selection based on the recited attributes in claim 1.
Zhang does not teach “hot spot” as a pre-defined site in the CHOK1SV genome (as recited in step II) a) of claim 1).
However, Bahr teaches a “hot spot” can be a known, chosen genomic locus for recombinant gene expression (paragraph [0064]). Bahr describes a “hot spot” as sites that are recognized as regions in the genome that are known to be transcriptionally active and resistant to gene silencing mechanisms to allow for stable gene expression (paragraph [0064]). Bahr teaches various genomic loci in CHO cells suitable for integrating an exogenous nucleic acid (paragraph [0064] and Table 2) and teaches methods for integrating an exogenous nucleic acid into the genome including the loci of Table 2 (e.g., paragraphs [0079] and [0080]).
In view of the combined teachings of Zhang and Bahr, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Zhang to integrate the vector encoding a single copy of monoclonal antibody cB72.3 into a known, chosen genomic locus, e.g., a locus taught by Bahr. One would have been motivated to and would have expected success to integrate the vector encoding a single copy of monoclonal antibody cB72.3 into a known, chosen genomic locus because Zhang taught integrating the vector into a “hot spot” of a CHOK1SV cell and Bahr taught a “hot spot” can be a known, chosen genomic locus for recombinant gene expression and teaches various genomic loci in CHO cells for integrating an exogenous nucleic acid.
Zhang also does not teach repeating steps I-II n times by using the top candidate cell population from step (II)(b) as the recombinant cell in step I, wherein n is two or more (as recited in step III of claim 1) and wherein n is three or more (as recited in claim 17), and wherein the expression load is gradually increased during each subsequent iteration.
However, Bahr teaches an exogenous nucleic acid sequence containing recognition sequences for at least one polynucleotide modification enzyme may be integrated into three, four, five, six, seven, eight, nine, or ten or more genomic locations, noting that multiple copies of the same exogenous nucleic acid sequence may be inserted (paragraph [0065]) and teaches sequentially repeating integration steps with additional exogenous nucleic acid sequences in order to integrate additional exogenous nucleic acid sequences at a different genomic locus (paragraph [0076]). Bahr teaches increased protein expression may be observed in cells transformed with multiple copies of a payload sequence comprising an expression construct (paragraph [0016]).
In view of the combined teachings of Zhang and Bahr, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Zhang by sequentially repeating integration of a vector encoding a single copy of monoclonal antibody cB72.3 with selected best-performing clones in order to integrate the vector into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations. Given Bahr’s teaching that increased protein expression may be observed in cells transformed with multiple copies of a payload sequence comprising an expression construct, one of ordinary skill in the art would have expected that integrating the vector encoding a single copy of monoclonal antibody cB72.3 into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations, would increase protein expression of the monoclonal antibody cB72.3. Although the combination of Zhang and Bahr do not teach or suggest the protein expression is “gradually increased” as recited in step III) of claim 1, given the indefiniteness of the term “gradually” as described above, and in the interest of advancing prosecution, modifying Zhang by sequentially repeating integration of a vector encoding a single copy of monoclonal antibody cB72.3 with selected best-performing clones in order to integrate the vector into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations, is considered to be encompassed by “expression load is gradually increased during each subsequent iteration” as recited in step III) of claim 1.
Regarding step IV of claim 1, Zhang teaches Phase II of the method, which is excision of the nucleic acid encoding the mAb cB72.3 by integrating a the null targeting vector to replace the mAb cB72.3 in the same “hot spot” to create a “landing pad,” thus generating a SSI cell (p. 1, abstract; Figure 1B, step (2); p. 6, column 2, bottom). The null targeting vector comprises at least one sequence element that was not present on the genome prior to integrating the null targeting vector, e.g., TK and PAC selection markers.
Regarding step V of claim 1, Zhang teaches Phase III of the method, which is integrating a vector encoding a single copy of Myo mAb, into the F and F5 recombination sites of the landing pad (Figure 1B, step (3); p. 8, columns 1-2).
Regarding claims 3-5, Zhang teaches recombinant production of Pfizer’s Myo mAb in Phase III (p. 2, column 2, bottom; p.3, Figure 1; p. 8, columns 1-2). Claim 3 does not structurally and/or functionally limit the recited recombinant protein and given a broadest reasonable interpretation, Myo mAb is considered to be “an active pharmacological ingredient.” Also, Bahr teaches the recombinant protein can be a recombinant protein that is useful in a biotherapeutic application; the recombinant protein can be a recombinant protein that is useful in a diagnostic application; and the recombinant protein can be a recombinant protein that is useful in industrial applications (paragraph [0097]).
Regarding claim 7, Zhang teaches the vector of Phase I encodes mAb cB72.3 (Figure 1; p. 4, column 2, middle).
Regarding claim 12, Zhang teaches the vector of Phase II comprises positive and negative selection markers TK and PAC (paragraph bridging pp. 5-6).
Regarding claim 13, Phase II of Zhang’s method creates a landing pad by recombinase-mediated cassette exchange (p. 1, abstract; Figure 1B, step (2); p. 6, column 2, bottom). Zhang does not teach or suggest creating a landing pad by forming a double strand break with a specific gene editing DNA nuclease at sequence z being unique or rare in the genome.
Bahr teaches a targeting endonuclease may be used for targeted integration of the landing pad (paragraph [0072]). More specifically, Bahr teaches introducing into a cell a targeting endonuclease, introducing into the cell at least one donor polynucleotide comprising an exogenous nucleic acid comprising at least one recognition sequence for a polynucleotide modification enzyme (i.e., landing pad), which is flanked by sequences with substantial sequence identity with either side of the genomic locus, and maintaining the cell under conditions that the targeting endonuclease introduces a double-stranded break at the targeted genomic locus and the double-stranded break is repaired by a homology-directed process such that the exogenous nucleic acid is integrated into the targeted site within or proximal to the genomic locus (paragraph [0072]). Bahr teaches the targeting endonuclease may be a “rare-cutter” endonuclease whose recognition sequence occurs rarely or only one in a genome (paragraph [0024]).
In view of the combined teachings of Zhang and Bahr, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Phase II of Zhang’s method by creating a landing pad according to the noted teachings of Bahr. One would have been motivated to and would have had a reasonable expectation of success to do this because Zhang teaches creating a landing pad by recombinase-mediated cassette exchange, while Bahr acknowledges the alternative of creating a landing pad by targeting endonuclease cassette exchange.
Regarding claim 15, Zhang teaches the vector of Phase I encodes mAb cB72.3 (Figure 1; p. 4, column 2, middle) and teaches the vector of Phase III encodes Myo mAb (p. 2, column 2, bottom; p. 3, Figure 1; p. 8, columns 1-2), i.e., the vectors of Phase I and Phase III each encode monoclonal antibodies.
Regarding claim 16, Zhang teaches integrating a single copy of the nucleic acid encoding the Myo mAb in Phase III (p. 8, column 2, bottom to p. 9, columns 1-2).
Regarding claim 20, as stated above, claim 20 lacks antecedent basis in the recitation of “the promoter strength” and in the interest of compact prosecution, claim 20 has been included in the rejection. In the interest of advancing prosecution, claim 20 is interpreted as encompassing the combined method of Zhang and Bahr (i.e., the method of Zhang modified by sequentially repeating integration of a vector encoding a single copy of monoclonal antibody cB72.3 with selected best-performing clones in order to integrate the vector into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations). The vector encoding a single copy of monoclonal antibody cB72.3 comprises a promoter (see Figure 1A of Zhang) and integrating the vector into different genomic loci according to the combined method of Zhang and Bahr would cumulatively increase the number of promoters integrated along with the vector, thereby increasing the cumulative promoter strength.
Regarding claim 21, as stated above, it is entirely unclear as to applicant’s intended meaning of “wherein the expression load is gradually increased by using different 5’ and 3’ mRNA untranslated regions and in the interest of compact prosecution, claim 21 has been included in the rejection. In the interest of advancing prosecution, claim 21 is interpreted as encompassing the combined method of Zhang and Bahr (i.e., the method of Zhang modified by sequentially repeating integration of a vector encoding a single copy of monoclonal antibody cB72.3 with selected best-performing clones in order to integrate the vector into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations). One of ordinary skill in the art would have recognized that a mRNA transcribed from the integrated vector encoding a single copy of the monoclonal antibody cB72.3 comprises 5’ and 3’ untranslated regions that are different. For example, one of ordinary skill in the art would have recognized that a mRNA transcript transcribed from an integrated vector encoding a single copy of monoclonal antibody cB72.3 comprises a ribosome binding site, which is a 5’ untranslated region and comprises a translation terminator, which is a 3’ untranslated region. A ribosome binding site and a translation terminator are different 5’ and 3’ mRNA untranslated regions.
Therefore, claims 1, 3-5, 7, 8, 12, 13, and 15-21 would have been obvious to one of ordinary skill in the art before the effective filing date.
RESPONSE TO REMARKS: In summary, applicant argues the combination of Zhang and Bahr fails to teach or suggest “gradually increased” protein expression as required by amended claim 1 and does not teach or suggest the limitations of new claims 20 and 21.
Applicant’s arguments are not found persuasive. It is acknowledged that the combination of Zhang and Bahr does not teach or suggest the protein expression is “gradually increased” as recited in step III) of claim 1. However, given the indefiniteness of the term “gradually” as described above, and in the interest of advancing prosecution, modifying Zhang by sequentially repeating integration of a vector encoding a single copy of monoclonal antibody cB72.3 with selected best-performing clones in order to integrate the vector into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations, is considered to be encompassed by “expression load is gradually increased during each subsequent iteration” as recited in step III) of claim 1.
Regarding applicant’s argument addressing instant claim 20, as stated above, claim 20 lacks antecedent basis in the recitation of “the promoter strength” and for reasons described above, claim 20 is interpreted as encompassing the combined method of Zhang and Bahr (i.e., the method of Zhang modified by sequentially repeating integration of a vector encoding a single copy of monoclonal antibody cB72.3 with selected best-performing clones in order to integrate the vector into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations).
Regarding applicant’s argument addressing instant claim 21, as stated above, it is entirely unclear as to applicant’s intended meaning of “wherein the expression load is gradually increased by using different 5’ and 3’ mRNA untranslated regions and for reasons described above, claim 21 is interpreted as encompassing the combined method of Zhang and Bahr (i.e., the method of Zhang modified by sequentially repeating integration of a vector encoding a single copy of monoclonal antibody cB72.3 with selected best-performing clones in order to integrate the vector into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations).
Claim Rejections – Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 1, 3-5, 7, 8, 12, 13, and 15-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, 9, and 11 of U.S. Patent No. 11,136,598 B2 (cited on the IDS filed on September 14, 2023; hereafter “patent”) in view of Zhang and Bahr. Although the claims at issue are not identical, they are not patentably distinct from each other.
This rejection has been modified from its previous version in order to address applicant’s instant amendment to the claims.
Regarding instant claim 1, claim 1 of the patent is drawn to a method for creating a mammalian cell bank for cell line development comprising the following steps:
a) providing a recombinant mammalian cell comprising (i) a genomic region that is transcriptionally active during suspension culture of said recombinant cell in a serum free culture medium, and (ii) a recombinant template DNA construct integrated at said genomic region, said recombinant template DNA construct having a region containing elements needed for expression of a template protein of interest and one or several sequence elements enabling the introduction of a donor DNA construct into said template DNA construct;
b) generating one or several candidate cells or cell populations descended from the recombinant mammalian cell;
c) measuring production traits of said generated candidate cells or cell populations and selecting a top candidate cell or cell population having improved characteristics for production of said template protein of interest when compared with production of the template protein of interest by the recombinant mammalian cell;
d) creating a cell bank for cell line development from said top candidate cell or cell population; and
e) identifying in the cell bank increases in template protein of interest expression compared to the recombinant mammalian cell following introduction of a modified template DNA construct having been modified to provide increased expression for said template protein of interest by using promoters with increasing strength and/or by using different combinations of translation enhancement elements in the 5'-UTR of genes coding for said template protein of interest;
claim 8 of the patent recites the method according to claim 1, further comprising exchanging expression of the template protein of interest for expression of the desired protein of interest by using an expression vector to introduce said donor DNA construct into said genomic region of a cell or cell population obtained from said cell bank;
claim 9 of the patent recites the method according to claim 8, wherein the exchange of template DNA construct to said modified template DNA constructs is achieved in the following way:
(a) each template DNA construct is designed to have conserved sequence stretches in their 5′- and 3′-ends that are homologous to said genomic region;
(b) each template DNA construct is designed to have a gene editing nuclease target sequence where the sequence differs between generation z and z+1;
(c) template DNA constructs of generation z and z+1 contain different selection marker(s);
(d) a template DNA construct of generation z+1 is introduced together with a gene editing expression vector construct into a cell or cell population containing a DNA construct of generation z and wherein the gene editing expression vector codes for a gene editing nuclease with specificity for said target sequence of the template DNA construct of generation z;
(e) cells having undergone the correct exchange via double strand break catalyzed cellular repair mechanisms are enriched by using the difference in selection markers between DNA constructs of generation z and z+1; and
(f) DNA analysis methods are applied to ensure the correct exchange for the cells; and
claim 11 of the patent is drawn to the method of according to claim 1, wherein the donor DNA construct comprises a region encoding a desired protein of interest belonging to the same class as the template protein of interest and the desired protein of interest and template protein of interest are selected from: i) a protein encoded by two or more genes of interest selected from monoclonal antibodies based on naturally occurring scaffolds, bi-specific antibodies based on naturally occurring scaffolds, Fabs, and virus like particles, and ii) a protein encoded by a single gene of interest, selected from growth factors, blood clotting factors, cytokines, hormones, erythropoietins, albumins, virus proteins, virus protein mimics, bacterial proteins, bacterial protein mimics, domain antibodies, ScFvs, Affibodies, DARPINs, multimerization domains, IgG Fc domains, albumin binding domains, and Fc receptor binding domains and fusion proteins based on combinations of the single gene of interest.
The claims of the patent do not recite limitations corresponding to a single copy integration (as recited in step (II)(b) of claim 1 and claim 16; repeating steps I-II n times wherein n is two or more and expression load is gradually increased during each subsequent iteration (as recited in step III of claim 1); and the limitations of claims 17-21.
Zhang teaches integrating a single copy of a construct encoding a monoclonal antibody into a “hot spot” within the genome of CHOK1SV cells (p. 4, column 2) and screening cell pools for production of the monoclonal antibody cB72.3 at 3 weeks post-transfection and following evaluation, the top 6 best-performing clones based on antibody production and growth characteristics were selected (paragraph bridging pp. 4-5).
Bahr teaches an exogenous nucleic acid sequence containing recognition sequences for at least one polynucleotide modification enzyme may be integrated into three, four, five, six, seven, eight, nine, or ten or more genomic locations, noting that multiple copies of the same exogenous nucleic acid sequence may be inserted (paragraph [0065]) and teaches sequentially repeating integration steps with additional exogenous nucleic acid sequences in order to integrate additional exogenous nucleic acid sequences at a different genomic locus (paragraph [0076]). Bahr teaches increased protein expression may be observed in cells transformed with multiple copies of a payload sequence comprising an expression construct (paragraph [0016]).
In view of the teachings of Zhang and Bahr, it would have been obvious to one of ordinary skill in the art to modify the method of the claims of the patent by sequentially repeating steps a) to c) of claim 1 with the selected top candidate cell population based on the attributes of protein expression and growth characteristics in order to integrate a single copy of the recombinant template DNA construct into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations. Given Bahr’s teaching that increased protein expression may be observed in cells transformed with multiple copies of a payload sequence comprising an expression construct, one of ordinary skill in the art would have expected that integrating a single copy of the recombinant template DNA construct into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations, would increase protein expression of the recombinant template DNA construct. Although the combination of Zhang and Bahr do not teach or suggest the protein expression is “gradually increased” as recited in step III) of claim 1, given the indefiniteness of the term “gradually” as described above, and in the interest of advancing prosecution, modifying the method of the claims of the patent by sequentially repeating steps a) to c) of claim 1 with the selected top candidate cell population based on the attributes of protein expression and growth characteristics in order to integrate a single copy of the recombinant template DNA construct into different genomic loci is considered to be encompassed by “expression load is gradually increased during each subsequent iteration” as recited in step III) of claim 1.
Regarding instant claims 3, 7, and 15, claim 11 of the patent recites the method of according to claim 1, wherein the donor DNA construct comprises a region encoding a desired protein of interest belonging to the same class as the template protein of interest and the desired protein of interest and template protein of interest are selected from: i) a protein encoded by two or more genes of interest selected from monoclonal antibodies based on naturally occurring scaffolds, bi-specific antibodies based on naturally occurring scaffolds, Fabs, and virus like particles, and ii) a protein encoded by a single gene of interest, selected from growth factors, blood clotting factors, cytokines, hormones, erythropoietins, albumins, virus proteins, virus protein mimics, bacterial proteins, bacterial protein mimics, domain antibodies, ScFvs, Affibodies, DARPINs, multimerization domains, IgG Fc domains, albumin binding domains, and Fc receptor binding domains and fusion proteins based on combinations of the single gene of interest.
Regarding instant claims 4 and 5, Bahr teaches the recombinant protein can be a recombinant protein that is useful in a biotherapeutic application; the recombinant protein can be a recombinant protein that is useful in a diagnostic application; and the recombinant protein can be a recombinant protein that is useful in industrial applications (paragraph [0097]).
Regarding instant claims 8 and 17, claim 7 of the patent recites the method according to claim 1, wherein steps (a) to (e) of claim 1 are iterated in the following way:
(i) in a next iteration the top candidate cell population from previous step (e) is used as said recombinant mammalian cell in step (a) after having exchanged said template DNA construct for a modified template DNA construct having been modified to provide increased expression for said template protein of interest compared to template DNA constructs in earlier iterations; and
(ii) repeating (a) to (e) until the top candidate cell or cell population has desired properties, based on the accumulation of one or multiple targeted changes.
Regarding instant claims 12 and 13, claim 9 of the patent recites the method according to claim 8, wherein the exchange of template DNA construct to said modified template DNA constructs is achieved in the following way:
(a) each template DNA construct is designed to have conserved sequence stretches in their 5′- and 3′-ends that are homologous to said genomic region;
(b) each template DNA construct is designed to have a gene editing nuclease target sequence where the sequence differs between generation z and z+1;
(c) template DNA constructs of generation z and z+1 contain different selection marker(s);
(d) a template DNA construct of generation z+1 is introduced together with a gene editing expression vector construct into a cell or cell population containing a DNA construct of generation z and wherein the gene editing expression vector codes for a gene editing nuclease with specificity for said target sequence of the template DNA construct of generation z;
(e) cells having undergone the correct exchange via double strand break catalyzed cellular repair mechanisms are enriched by using the difference in selection markers between DNA constructs of generation z and z+1; and
(f) DNA analysis methods are applied to ensure the correct exchange for the cells.
Regarding instant claim 16, Zhang teaches integrating a single copy of a nucleic acid encoding a monoclonal antibody (p. 8, column 2, bottom to p. 9, columns 1-2).
Regarding instant claims 18-20, step e) of claim 1 of the patent recites identifying in the cell bank increases in template protein of interest expression compared to the recombinant mammalian cell following introduction of a modified template DNA construct having been modified to provide increased expression for said template protein of interest by using promoters with increasing strength and/or by using different combinations of translation enhancement elements in the 5'-UTR of genes coding for said template protein of interest.
Regarding instant claim 21, as stated above, it is entirely unclear as to applicant’s intended meaning of “wherein the expression load is gradually increased by using different 5’ and 3’ mRNA untranslated regions and in the interest of compact prosecution, claim 21 has been included in the rejection. In the interest of advancing prosecution, it is noted that one of ordinary skill in the art would have recognized that a mRNA transcribed from the recombinant template DNA construct comprises different 5’ and 3’ untranslated regions. For example, a ribosome binding site as an example of a mRNA 5’ untranslated region and a translation terminator as an example of a mRNA 3’ untranslated region are different 5’ and 3’ mRNA untranslated regions.
Therefore, claims 1, 3-5, 7, 8, 12, 13, and 15-21 of this application are unpatentable over claims 1, 8, 9, and 11 of the patent in view of Zhang and Bahr.
RESPONSE TO REMARKS: In summary, applicant argues claim 1 as amended requires that the expression load is “gradually increased,” and claims 20 and 21 require specific methods of gradually increasing the expression load; and applicant contends that claims 1, 8, 9 and 11 of the patent do not teach or suggest a “gradually increased” expression load, and certainly do not teach or suggest any specific method of doing so.
Applicant’s arguments are not found persuasive. It is acknowledged that the claims of the patent do not recite protein expression is “gradually increased” as recited in step III) of claim 1. However, given the indefiniteness of the term “gradually” as described above, and in the interest of advancing prosecution, modifying the method of the claims of the patent by sequentially repeating steps a) to c) of claim 1 with the selected top candidate cell population based on the attributes of protein expression and growth characteristics in order to integrate a single copy of the recombinant template DNA construct into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations, is considered to be encompassed by “expression load is gradually increased during each subsequent iteration” as recited in step III) of claim 1.
Regarding applicant’s argument addressing instant claim 20, step e) of claim 1 of the patent recites increased expression for said template protein of interest by using promoters with increasing strength.
Regarding applicant’s argument addressing instant claim 21, as stated above, it is entirely unclear as to applicant’s intended meaning of “wherein the expression load is gradually increased by using different 5’ and 3’ mRNA untranslated regions and for reasons described above, claim 21 is interpreted as encompassing the method of the claims of the patent modified by sequentially repeating steps a) to c) of claim 1 with the selected top candidate cell population based on the attributes of protein expression and growth characteristics in order to integrate a single copy of the recombinant template DNA construct into different genomic loci, e.g., three, four, five, six, seven, eight, nine, or ten or more genomic locations.
For these reasons, the claims of this application are unpatentable over claims 1, 8, 9, and 11 of the patent.
Conclusion
Status of the claims:
Claims 1, 3-8, 10, 12, 13, and 15-21 are pending.
Claims 6 and 10 are withdrawn from further consideration.
Claims 1, 3-5, 7, 8, 12, 13, and 15-21 are rejected.
No claim is in condition for allowance.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/David Steadman/Primary Examiner, Art Unit 1656
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