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 .
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 4/23/2026 has been entered.
Withdrawn Rejection
The rejection of claims 1-6, 7-9, 11-15, and 29 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention, is withdrawn. The claims were deemed indefinite for reciting (ii) an allelic ERV devoid wild-type counterpart sequence (i). The amendments remove this recitation.
Claim Objections
Claim 30 is objected to because of the following informalities: Claim 30 is identified as previously presented which is the incorrect status for this claims. Amending the claim status identifier to “Withdrawn” would be remedial. Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 8 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 8 recites, “there are no detectable viral particles comprised in the supernatant of the cell population”. This recitation lack sufficient antecedent basis. Claim 8 dependent upon claim 6 with recites “a cell population” which is recited as only comprising cells. However, claim 8 refers to “the supernatant of the cell population”. This appears to imply that the base cell population also comprises media into which supernatant can be formed. A such, it is not apparent if claim 8 is intended the structural elements of cell in a medium and culture or if this is implicating a function of the cells. As such, the metes and bound of claim 8 are not distinctly and clearly delineated.
Claim Rejections - 35 USC § 112
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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 of carrying out his invention.
Claims 1-6, 8-9, 11-15, and 29 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
When determining if a recited genus has adequate written description for a genus:
(1) the broadest reasonable interpretation of the genus is determined;
(2) the disclosure is examined to determine if the specification has provided a representative number of species to describe the complete structure of the genus;
(3) the disclosure is examined to determine whether a representative number of species have been sufficiently described by other relevant characteristics, specified features and functional attributes that would distinguish different members of the claimed genus; and
(4) the state of the art is examined to the determine if it supports/supplement the genus description in the specification in a manner that would demonstrate the application was in possession of the claimed genus at the time of effectively filing.
Genus: “b) parts of the sequence” in reference to the ERV sequence. This will be referred to as “parts of the ERV sequence” herein.
Breadth of the Genus: The claims recite parts of the ERV sequence. The specification does provide a specific definition for “parts of the sequence”. Thus given its broadest reasonable interpretation, “parts of the sequence” includes any parts of any length in common to the ERV sequence, as little as one nucleotide to an ERV sequence with 100% identity to ERV sequence. The claims further limit the ERV sequence to be “comprising at least nucleotides 29521 to 39747 of SEQ ID NO:1 or a sequence having 95%, 98%, or 99% sequence identity with nucleotides 29521 to 39747 of SEQ ID NO: 1 and/or (ii) nucleotide 29520 to 30520 of SEQ ID NO:2 or a sequence having 95%, 98%, or 99% sequence identity with nucleotide 29520 to 30520 of SEQ ID NO:2”. The ERV sequence is comprising which is open transitional language meaning other sequences can be present in addition to the recited sequences of the claim. The claimed ERV sequence can be as narrow as a species with nucleotides 29520 to 30520 of SEQ ID NO:1 and nucleotide 29520 to 30520 of SEQ ID NO:2; a species with nucleotides 29520 to 30520 of SEQ ID NO:1 or nucleotide 29520 to 30520 of SEQ ID NO:2, for example. However, the ERV sequences also can having as much as a 5% difference from the recited sequences, addition, deletion, substitution in any of the bases, in either or both sequences. As such the ERV sequence has a large but number of species that can be envision by the ordinary artisan. Returning “parts” of the ERV sequence, this recitation broadens the genus of ERV sequence is a ERV sequence is as little as one base and any base within the ERV sequence genus. As such, parts of the ERV sequence has what appears to be an almost infinitely large number of different structural sequences and is vastly broad with heterologous and divergent structural sequences.
Specification Description (citations from the application publication):
[0005] Disclosed is, among others, the stable integration of exogenous nucleic acid sequences, such as transgenes, within or proximal to the insertion sequence of at least part of an endogenous retroviral sequences (ERV) or a LTR-retrotransposon (LTR-RT) of mammalian genome. In certain embodiments this results in high level and/or stable production of transgene expression product(s). This is in certain embodiments accomplished and/or furthered by modulating the DNA repair pathways of the host cell.
[0010] The at least one locus and optionally the corresponding allelic locus into which the transgene is integrated may be an ERV sequence or a LTR-RT sequence insertion locus.
[0011] The at least one locus into which the transgene is integrated may be an allelic wild-type (e.g. ERV-devoid or LTR-RT-devoid) counterpart locus of an ERV sequence insertion locus or a LTR-RT sequence insertion locus (e.g. the ERV-integrated or LTR-RT-integrated genomic sequences). The transgene may also be integrated adjacent to or replace the corresponding ERV sequence or the corresponding LTR-RT sequence at the insertion locus. The transgene may be integrated into either one or both loci, preferably in more than 20%, 30% or even more than 40% of the transgene-containing cells within a cell population. The locus may be homozygous and comprise at least two copies of, e.g, SEQ ID NO: 1 or SEQ ID NO: 2 or parts thereof. The locus may be heterozygous and comprise, e.g., both SEQ ID NO: 1 and SEQ ID NO: 2 or parts thereof.
[0014] at least one locus comprising an insertion site of an endogenous retrovirus (ERV) sequence or a LTR-retrotransposon (LTR-RT) sequence, wherein said at least one locus comprise(s): [0015] (i) a) the ERV sequence or the LTR-RT sequence, or b) the insertion site and, optionally, parts of the sequence of a), and/or [0016] (ii) an allelic wild type counterpart sequence of (i).
[0018] Certain embodiments are directed to a cell population comprising engineered cells described herein. The at least one transgene may be integrated into more than 20%, 30% or even more than 40% of (i) and/or (ii) of cells within said cell population. The engineered cells of the cell population may comprise (i) and (ii), above. (1) may comprise: at least nucleotides 29021 to 40247 (or 29521 to 39747) of SEQ ID NO: 1 or a sequence having 95%, 98% or 99% sequence identity with nucleotides 29021 to 40247 (or 29521 to 39747) of SEQ ID NO: 1 and (ii) may comprise at least nucleotides 29020 to 31020 (or 29520 to 30520) of SEQ ID NO: 2 or a sequence having 95% 98%, or 99% sequence identity with nucleotides 29020 to 31020 (or 29520 to 30520) of SEQ ID NO: 2. The engineered cell/cell population in certain preferred embodiments lacks expressed endogenous retroviral sequences (ERV). In certain preferred embodiments there are no detectable viral particles comprised in the cell population culture supernatant.
[0064] An insertion site of an endogenous retrovirus (ERV) sequence or a LTR-retrotransposon (LTR-RT) sequence of a genome of a cell is a nucleic acid sequence having a length of not more than 100 nucleotides, preferably not more than 90, 80, 70, 60, 50, 40, 30, 20, 10, 5, 4, 3, 2 nucleotides: (i) a) comprising an ERV or a LTR-RT sequence, i.e. a ERV or a LTR-RT sequence integrated into the genome of the cell, which is also referred to herein as an integrated ERV/LTR-RT sequence, (i) b) having comprised an ERV or a LTR-RT sequence prior to complete or partial removal of the ERV a LTR-RT sequence or (ii) is the allelic wild type, sometimes referred to herein as ERV-devoid, counterpart locus of (i). (i) a) and b) are referred to herein as “ERV sequence or LTR-RT sequence insertion locus/allele” or “ERV or LTR-RT insertion locus/allele”, (ii) is referred to herein as “allelic wild-type counterpart locus/allele of an ERV sequence insertion locus/allele” or the “allelic wild-type counterpart locus/allele of an LTR-RT sequence insertion locus/allele” or just “allelic wild-type (wt) counterpart sequence” of the above. As a person skilled in the art will readily understand, there will be loci in which: [0065] one allele [0066] (i) a) comprises an ERV or a LTR-RT sequence, or [0067] (i) b) has comprised an ERV or a LTR-RT sequence prior to complete or partial removal of the ERV or LTR-RT sequence, and/or [0068] (ii) is the allelic wild type counterpart of (i).
[0069] A cell that combines at least two distinct alleles of a locus, e.g., (i) a) and (ii), or (i) b) and (ii), is sometimes referred to herein as heterozygous for that locus.
[0070] A cell that combines (i) a) and (ii) is said to be hemizygous for the single copy ERV sequence. A cell having two identical alleles at a locus, e.g. (i) a) and (i) a), is referred to as homozygous for that locus.
[0083] An endogenous retrovirus (ERV) sequence constitutes a left-over of retroviral integration into the genome of a cell and comprise at least parts of a gag gene, a pol gene, and an env gene, and/or at least one, preferably two LTR(s). Functional units or parts thereof that make up a ERV sequences are also referred to as ERV subsequences. Thus, a gag gene, a pol gene, an env gene, an LTR are considered an ERV subsequence. In a preferred embodiment, at least one, preferably two of the gag gene, the pol gene or the env gene expresses the respective protein. In an even more preferred embodiment of ERV selection, the ERV sequence releases VPs (viral particles) or a VLPs (viral like particles). The size of a complete endogenous retrovirus is between 6-12 kb on average and it contains gag, pol and env genes that always occur in the same order. Coding sequences are flanked by two LTRs (Long Terminal Repeat sequences). Most ERVs are defective, as they are carrying a multitude of inactivating mutations. In addition, they can be inactivated (i.e. not transcribed) by epigenetic silencing effects. However, some ERVs still have open reading frames in their genome and/or they may be transcriptionally active. The ERVs of mammals bear strong similarities and may originate from the genus of gammaretroviruses and betaretroviruses, including Intracisternal type-A particle (IAP or IAPS), Feline leukemia virus (FeLV), Mouse Leukemia Virus (MLV), Koala epidemic virus (KoRV), Mouse Mammary Tumor Virus (MMTV). ERVs are maintained in the genomes and may have certain advantages for the cells into whose genome they are integrated, including providing a source of genetic diversity and protection against other viral pathogens. However, they can become infectious and carry risks in in the context of transgene, i.e. protein, expression described elsewhere herein, in particular, as a result of ERV awakening due to cancer, cellular stress and/or epigenetic modifications.
Working Examples:
[0044] FIG. 1 is a schematic representation of a locus with integration site, showing one integration site comprising an ERV sequence, here the ERV C 109F (SEQ ID NO: 3) containing allele, and one wild-type counterpart allele thereof.
[0045] FIGS. 2A and 2B show a double CRISPR-based approach for targeting transgene integration in the ERV C 109F locus, in the wild type allele (FIG. 2A) and in the ERV C 109F allele (FIG. 2B).
As such, from the specification, one of ordinary skill could envision the relevant characteristics of the ERV sequence are sequences that are remanent sequences that have integrate into a cells genome after retroviral integration. The artisan can envision that the ERV sequence comprises subsequences and also genetically engineered subsequences. While the specification does specification describe the recited SEQ ID NOS:1 and 2 and sequences recite the genus of sequence with sequence identity thereto for the designated nucleotides, the specification only generically states, “part of the sequence a)” and does not describe any structural species example for “part of the sequence a)”. Further, the ERV sequence in the engineered cell serves as an integration site for a transgene. Essentially any nucleotide base can be an insertion site as functionally described. As such, the specification does not describe any functional characteristics or traits to the part of the ERV sequence that would be further limiting to the claimed genus structure.
State of the Art: While any nucleotide sequence in the genome can function as an integration site, both the specification and prior art describe that insertion of a transgene and its desired expression in highly variable depending upon that insertion site in the genome. Some insertion sites in the genome provide robust expression, some result in week expression, some result in transient expression, and some provide no expression or a loss of the transgene all together (see paragraph [0001] of the instant application; See Chaturvedi et al. Gene Therapy (2018) 25:376-391; Roberts et al. Development (2014) 141, 715-724; Yin et al (2012) Genetics and Molecular Research 11 (1): 355-369).
The abstract of the instant application states, “Disclosed are cells that have stably integrated into their genomes exogenous nucleic acid sequences, such as transgenes, within or proximal to the integration site of a sequence comprising at least part of an endogenous retrovirus (ERV) or a LTR-retrotransposon (LTR-RT), or instead of a sequence encompassing an ERV or a LTR-RT that is part or was part of the genome of the cell, as well as method of producing and using such cells. Advantageously, a high level and/or stable production of the transgene expression product(s) can be achieved.”. As such, the specification describes the invention of the application as one that overcome the unpredictabilites in the art. However, the specification does not describe but only genetically describes a genus of “parts of the sequence a” or parts of the ERV sequence that predictably have the described advantage as discussed above.
In conclusion, the breadth of the claimed parts of the ERV sequence is almost infinitely broad with an almost unfathomable number of possible divergent species. The specification much more narrowly describes a subgenus of complete ERV sequences comprising the recite nucleotides of SEQ ID NO:1 and 2. The specification also describes one ERV109C variant species which is also a complete ERV sequence. The specification however fails to describe any species sequences that would be considered “part of” the ERV sequence subgenus described in the specification that have the advantageous function of stabled integration and high level of transgene expression. As such, the specification fails to adequately describe the complete structure of the vastly broad genus “part of the sequence of a)” by a representative number of species and relevant characteristics and traits. Further the prior art, reinforced by the specification, describes the integration sites that result in stable integration of a transgene are unpredictable. As such, the prior art fails to supplement the shortcoming of the description by the disclosure of the application. Given the great breadth of the genus, “a part of the sequence a” as claimed, the much narrower species description by this application of this genus, and the described unpredictabilites in the art, one of ordinary skill could not envision the complete structure of the claimed genus and would conclusion that the application was not in possession of the claimed genus at the time of effective filing. As such, the claimed genus, “parts of the sequence a)” lack adequate written description.
Because of the great breadth of the genes, “parts of the sequence a)” as describe above, the previously made prior art rejection in prosecution is being reinstated:
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.
Claim(s) 1 and 14-15 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Mermod (WO2017/109177).
Regarding claims 1 and 14, Mermod discloses a CHO cell comprising in its genome an ERV element with a transgene (e.g. GFP transgene) inserted in said ERV element, the breadth of a part of the ERV sequence as claimed encompasses any ERV sequence because part includes at least one nucleic acid in common and Mermod’s ERV has at least one nucleic acid in common with a part of the sequence of a). Mermod discloses a CHO cell comprising in its genome an ERV element with a transgene (e.g. GFP transgene) inserted in said ERV element (p. 42, claim 6).
Regarding claim 15, Mermod discloses a CHO cell.
Examiner’s Comment
Searches for the claimed nucleotide sequences of SEQ ID NOS:1 and 2 and sequences with 95%, 98%, or 99% did not provide any prior art. As such, these sequences appear to be free of the prior art.
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARCIA STEPHENS NOBLE whose telephone number is (571)272-5545. The examiner can normally be reached M-F 9-5:30.
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MARCIA S. NOBLE
Primary Examiner
Art Unit 1632
/MARCIA S NOBLE/ Primary Examiner, Art Unit 1632
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