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 .
Response to Amendment
The amendment filed 16 July 2026 is acknowledged. Claims 7-8 are canceled. Claim 2 is amended.
Claim Status
Claims 2-6, and 9-21 are pending and under examination in the instant Office Action.
Withdrawal of Objections
The objection to the drawings is withdrawn in view of the replacement drawings filed 16 July 2026.
The objection to the specification for informalities in the abstract is withdrawn in view of the amendments to the specification.
Withdrawal of Rejections
The rejections of claims 7 and 8 are moot in view of the cancellation of the claims.
The rejection of claims under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite is withdrawn in view of the amendments to the claims.
The rejection of claims 2-5, 8, 12, 14-15, and 18 under 35 U.S.C. 102(a)(1) as being anticipated by Hubbard, May 2016, Nuclease-targeted gene-editing of FOXP3 in primary T cells creates a stable and functional T phenotype, PowerPoint presentation (Of record, IDS dated 2/7/2024) is withdrawn in view of the declaration under 37 CFR §1.130(a) submitted 16 July 2026.
The rejection of claims 2-5, 8, and 14-15 under 35 U.S.C. 102(a)(1) as being anticipated by Hubbard et. al. May 1 2016, Nuclease-targeted gene-editing of FOXP3 in primary T cells creates a stable and functional Treg phenotype, Mol. Ther. 24(Suppl. 1):S18 (ASGCT Abstract) (Of record, IDS dated 2/7/2024) is withdrawn in view of the declaration under 37 CFR §1.130(a) submitted 16 July 2026.
The rejection of claims 2-4, 8, 12, and 14-16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Allan et. al. "Generation of potent and stable human CD4+ T regulatory cells by activation-independent expression of FOXP3." Molecular Therapy 16.1 (2008): 194-202 (Of record, IDS dated 2/7/2024) as evidenced by Mitchell R.S., et. al. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2004;2:E234. doi: 10.1371/journal.pbio.0020234 is withdrawn in view of the amendments to the claims.
The rejection of claims 2-4, 6-7, 9, 10, 12, 14-17 under 35 U.S.C. 103 as being unpatentable over WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS dated 2/7/2024) and Torgerson TR, et. al. Severe food allergy as a variant of IPEX syndrome caused by a deletion in a noncoding region of the FOXP3 gene. Gastroenterology. 2007 May;132(5):1705-17. doi: 10.1053/j.gastro.2007.02.044. Epub 2007 Feb 23. PMID: 17484868 is withdrawn in view of the amendments to the claims.
The rejection of claim 11 under 35 U.S.C. 103 as being unpatentable over Allan et. al. "Generation of potent and stable human CD4+ T regulatory cells by activation-independent expression of FOXP3." Molecular Therapy 16.1 (2008): 194-202 (Of record, IDS dated 2/7/2024) as evidenced by Mitchell R.S., et. al. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2004;2:E234. doi: 10.1371/journal.pbio.0020234 as applied to claim 2 above, and further in view of Zhang, Fang, et al. "Lentiviral vectors containing an enhancer-less ubiquitously acting chromatin opening element (UCOE) provide highly reproducible and stable transgene expression in hematopoietic cells." Blood, The Journal of the American Society of Hematology 110.5 (2007): 1448-1457 is withdrawn in view of the amendments to the claims.
The rejection of claims 5 and 18-19 under 35 U.S.C. 103 as being unpatentable over WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS) and Torgerson TR, et. al. Severe food allergy as a variant of IPEX syndrome caused by a deletion in a noncoding region of the FOXP3 gene. Gastroenterology. 2007 May;132(5):1705-17. doi: 10.1053/j.gastro.2007.02.044. Epub 2007 Feb 23. PMID: 17484868 as applied to claim 2 above, and further in view of De Ravin SS, et. al. Targeted gene addition in human CD34(+) hematopoietic cells for correction of X-linked chronic granulomatous disease. Nat Biotechnol. 2016 Apr;34(4):424-9. doi: 10.1038/nbt.3513. Epub 2016 Mar 7 is withdrawn in view of the amendments to the claims.
The rejection of claims 13, 20, and 21 under 35 U.S.C. 103 as being unpatentable over WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS) and Torgerson TR, et. al. Severe food allergy as a variant of IPEX syndrome caused by a deletion in a noncoding region of the FOXP3 gene. Gastroenterology. 2007 May;132(5):1705-17. doi: 10.1053/j.gastro.2007.02.044. Epub 2007 Feb 23. PMID: 17484868. as applied to claim 2 above, and further in view of De Ravin SS, et. al. Targeted gene addition in human CD34(+) hematopoietic cells for correction of X-linked chronic granulomatous disease. Nat Biotechnol. 2016 Apr;34(4):424-9. doi: 10.1038/nbt.3513. Epub 2016 Mar 7 and WO2017042170 to Guillonneau effectively filed 7 September 2015 is withdrawn in view of the amendments to the claims.
The rejection of claims 2-5 on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of U.S. Patent No. 11713459. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are anticipated by the instant claims is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The rejection of claim 11 on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of U.S. Patent No. 11713459 as applied to claim 2 above, in further view of in view of Zhang, Fang, et al. "Lentiviral vectors containing an enhancer-less ubiquitously acting chromatin opening element (UCOE) provide highly reproducible and stable transgene expression in hematopoietic cells." Blood, The Journal of the American Society of Hematology 110.5 (2007): 1448-1457 is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The rejection of claims 6, 9-10, 12, and 14-19 on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of U.S. Patent No. 11713459 as applied to claim 2 above, in further view of WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS) is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The rejection of claims 13, 20, and 21 on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of U.S. Patent No. 11713459 as applied to claim 2 above, in further view of WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS) as applied to claims 17-19 above, and in further view of WO2017042170 to Guillonneau et. al. effectively filed 7 September 2015 is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The provisional rejection of claims 2-5 on the ground of nonstatutory double patenting as being unpatentable over claims 28-34, 37, 44-46, 48, 50, 52-55, and 57 of co-pending Application No. 16981213 is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The provisional rejection of claim 11 on the ground of nonstatutory double patenting as being unpatentable over claims 28-34, 37, 44-46, 48, 50, 52-55, and 57 of co-pending Application No. 16981213 as applied to claim 2 above, in further view of in view of Zhang, Fang, et al. "Lentiviral vectors containing an enhancer-less ubiquitously acting chromatin opening element (UCOE) provide highly reproducible and stable transgene expression in hematopoietic cells." Blood, The Journal of the American Society of Hematology 110.5 (2007): 1448-1457 is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The provisional rejection of claims 6, 9-10, 12, and 14-19 on the ground of nonstatutory double patenting as being unpatentable over claims 28-34, 37, 44-46, 48, 50, 52-55, and 57 of co-pending Application No. 16981213 as applied to claim 2 above, in further view of WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS) is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The provisional rejection of claims 13, 20, and 21 on the ground of nonstatutory double patenting as being unpatentable over claims 28-34, 37, 44-46, 48, 50, 52-55, and 57 of co-pending Application No. 16981213 as applied to claim 2 above, in further view of WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS) as applied to claims 17-19 above, and in further view of WO2017042170 to Guillonneau et. al. effectively filed 7 September 2015 is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The provisional rejection of claims 2-5 on the ground of nonstatutory double patenting as being unpatentable over claims 2 and 4-23 of co-pending Application No. 18336276 is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The provisional rejection of claim 11 on the ground of nonstatutory double patenting as being unpatentable over claims 2 and 4-23 of co-pending Application No. 18336276 as applied to claim 2 above, in further view of in view of Zhang, Fang, et al. "Lentiviral vectors containing an enhancer-less ubiquitously acting chromatin opening element (UCOE) provide highly reproducible and stable transgene expression in hematopoietic cells." Blood, The Journal of the American Society of Hematology 110.5 (2007): 1448-1457 is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The provisional rejection of claims 6, 9-10, 12, and 14-19 on the ground of nonstatutory double patenting as being unpatentable over 2 and 4-23 of co-pending Application No. 18336276 as applied to claim 2 above, in further view of WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS) is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
The provisional rejection of claims 13, 20, and 21 on the ground of nonstatutory double patenting as being unpatentable over claims 2 and 4-23 of co-pending Application No. 18336276 as applied to claim 2 above, in further view of WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS) as applied to claims 17-19 above, and in further view of WO2017042170 to Guillonneau et. al. effectively filed 7 September 2015 is withdrawn in view of the approved terminal disclaimer filed 30 July 2026.
Claim Rejections - 35 USC § 112(b)- New/Modified - Necessitated by Amendment
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 2- 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 2 recites a genetically modified cell comprising a heterologous promoter operably linked to a first coding exon in an endogenous FOXP3 gene on a nucleic acid in the cell genome, wherein the heterologous promoter is: (i) downstream from a Treg-specific demethylated region (TSDR) of the endogenous FOXP3 gene; and (ii) upstream from the position of the first coding exon of the endogenous FOXP3 gene. This is indefinite because the phrases “downstream from a Treg-specific demethylated region (TSDR) of the endogenous FOXP3 gene” and “upstream from the position of the first coding exon of the endogenous FOXP3 gene” does not clearly set forth a genomic position. First, although the TSDR of the endogenous FOXP3 gene has been described, it is not consistently identified as a region with particular positions in the genome but rather, the position of the endogenous FOXP3 TSDR is loosely defined as an region whose boundaries are set by the particular primers and the genome used in the particular experiment. For example, Polansky et. al. (2008) DNA methylation controls Foxp3 gene expression. Eur J Immuno 38: 1654-1663 (PTO-892 3/23/2026) defines the TSDR as the region demethylated in Tregs defined by amplicons 1 and 2 in mouse (Fig. 2 A and C), and aligns it with the human genome (see Fig. S1). The sequence identified in Polansky Fig. S1 starts at human chrX position 49117758 of hg19 (see UCSC BLAT results) and ends at chrX position 49117032 (726 base pairs long). Although not prior art, Kressler C, et. al. (2021) Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype. Front. Immunol. 11:609891. doi: 10.3389/fimmu.2020.609891 teaches 12 sgRNAs that cover the TSDR; these sgRNAs span from chrX position 49117608 to chrX position 49117124 (484 base pairs long). However, Yue, Xiaojing, et al. "Control of Foxp3 stability through modulation of TET activity." Journal of Experimental Medicine 213.3 (2016): 377-397 Fig. 1 defines the TSDR as a subregion chrX 17,976,082-18,006,181 of the mammalian conservation track, which by the scale of the Fig. 1A is only approximately 350 base pairs long:
Partial reproduction of Yue et. al. Fig. 1a (red lines are the Examiner’s reproduction of the 100 bp scale to determine the length of the CNS2 shown):
PNG
media_image1.png
286
1355
media_image1.png
Greyscale
Thus although the TSDR of an endogenous FOXP3 gene is an approximate region known in the art, a person of ordinary skill in the art would not be able to determine what positions would constitute “downstream” of the endogenous TSDR. It is unclear, for example, if positions included in some definitions but not others, or positions that are downstream of the approximate first residue are in the middle of the TSDR would be considered downstream, and the metes and bounds of the claim are unclear. Regarding the phrase “upstream from the position of the first coding exon of the endogenous FOXP3 gene”, this further is unclear about which position for the promoter is desired. First, “the position of the first coding exon” lacks antecedent basis; it would not be clear to a person of ordinary skill in the art whether it is referring to a particular position within the first coding exon or to what position is referred. Second, the instant specification says “FOXP3 genes contain[] 11 coding exons, with the first coding exon designated exon 2 in a revised nomenclature” [0006] but also states that “ “Coding exon as described herein, refers to any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing” [0057]. In that case, the specification indicates that either exon 1 (which is untranslated, but is included in the mature mRNA) or exon 2 of Foxp3 is considered the first coding exon because a person of ordinary skill in the art reading the specification would consider both definitions taught by the specification. This is additionally unclear because there are additional reports of Foxp3 splice variants lacking exon 2 (e.g. Smith, Emma L., et al. "Splice variants of human FOXP3 are functional inhibitors of human CD4+ T‐cell activation." Immunology 119.2 (2006): 203-211). However, because the instantly amended claims now read “a heterologous promoter operably linked to a first coding exon in an endogenous FOXP3 gene” and “upstream from the position of the first coding exon of the endogenous FOXP3 gene” (emphasis in the Examiner’s), it is unclear how the exogenous promoter may be operably linked to the first coding exon, wherein the coding exon is exon 1, when the claims also requires the promoter to be downstream of the endogenous TSDR, which is downstream from exon 1 of the endogenous FOXP3 gene. Therefore, although Applicant has clarified that the promoter is interacting with the endogenous FOXP3 gene, the endogenous TSDR, and the endogenous first coding exon, the precise position of the heterologous promoter and the meanings of “upstream” and “downstream” remain unclear. The Examiner suggests amending the claim to recite particular genomic locations or distances to further specify the location of the heterologous promoter that is considered to be the invention.
Dependent claims are rejected for failing to resolve the deficiency as described.
Response to Arguments
Applicant’s arguments filed 16 July 2026 have been fully considered but are not persuasive.
Applicant argues that it is not clear how the presence of 2 copies of the FOXP3 gene would make the position of the promoter indefinite. To clarify this point, the Examiner intended to describe that the presence of additional, non-endogenous copies can be at any location, and therefore in cells with more than 2n, or with mutations such as translocations, etc. there is no definite genomic position of the insertion specified. Applicant argues that claim 2 has been amended to recite the endogenous FOXP3 gene, which obviates the rejection (Remarks p. 7 ¶1). This is not persuasive as described by the new rejection, necessitated by amendment, above. The position of the inserted promoter is not clear because it is indefinite what positions are considered downstream of the TSDR because there is no precise definition of the location in the art or the specification; the position of the first coding exon is not clear because there are contradictory definitions in the specifications, and further because endogenous the first coding may change depending on whether there are mutations in the FOXP3 gene.
Applicant also argues that the terms “upstream” and “downstream” are clear because a skilled artisan considering Fig. 3 of the specification would understand the recited order and that the order makes technical sense only when considering an orientation in which the TSDR is upstream from the position of the first coding exon. This is not persuasive, as described in the new 112(b) rejection, necessitated by amendment, above. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Additionally, in view of Applicant’s contradictory definitions of first coding exon as described above, a person of ordinary skill in the art would not be able to determine whether an insertion between the TSDR and exon 1 of Fig. 3 would read on the instant claims; the Examiner notes that although the amended claims now recite that the promoter is “operably linked to a first coding exon in an endogenous FOXP3 gene”, the previous claim set merely required that the promoter is “operably linked to a FOXP3 gene on a nucleic acid in the cell genome”; which reads therefore previously read on positions both upstream and downstream of the TSDR on the coding strand of FOXP3.
Claim Rejections - 35 USC §103- New, necessitated by amendment
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 2-4, 6, 9, 10, 12, 14-17 are rejected under 35 U.S.C. 103 as being unpatentable over WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS dated 2/7/2024) in view of Floess, Stefan, et al. "Epigenetic control of the foxp3 locus in regulatory T cells." PLoS biology 5.2 (2007): e38 and Myers, A. K., et al. "Clinical and molecular findings in IPEX syndrome." Archives of disease in childhood 91.1 (2006): 63-64.
Claim interpretation: Claim 2 is directed towards a genetically modified cell comprising a heterologous promoter operably linked to a first coding exon in an endogenous FOXP3 gene on a nucleic acid in the cell genome. The Examiner notes that the word phrase “heterologous promoter” is not defined in the claims or the specification. The instant specification defines “a promoter” as “a nucleotide sequence that directs the transcription of a structural gene” [0062]. Floess, Stefan, et al. "Epigenetic control of the foxp3 locus in regulatory T cells." PLoS biology 5.2 (2007): e38 describes teaches “The human FOXP3 promoter has recently been mapped to the putative 5′ end of exon-2b, 6.1 kb upstream from the first coding exon [6]. However, other studies have reported promoter activity upstream from exon-1 close to the differentially methylated region analyzed in the current study [26,27] corresponding to the Foxp3 mRNA species AY357712 and AY357713. We could show here by performing luciferase assays that the differentially methylated region itself possesses transcriptional activity. Together these data suggest that the evolutionarily conserved element might belong to an alternative TATA-less promoter, which contributes to the regulation of Foxp3 expression” (Discussion ¶4). Examples of the heterologous promoters EF-1ɑ, MND, and PGK (claim 4) are used; EF-1ɑ and PGK promoters are both promoters to mammalian genes, and therefore an artisan would not understand “heterologous” to be heterologous to the species of the cell. Therefore, the broadest reasonable interpretation of “heterologous promoter” is that the promoter is heterologous to the specific FOXP3 gene to which it is linked. The Examiner notes, therefore, that this could include editing events that fix a mutated TSDR gene back to an endogenous FOXP3 promoter; or that fix an mutation in endogenous FOXP3 back to wild-type because in that event the “wild-type” promoter or FOXP3 would be heterologous to the endogenous copy of the FOXP3 gene in that cell.
Regarding the position of the promoter, as described in the 112(b) rejection above, the position as claimed is indefinite. For the purposes of expedited prosecution, the claim will be interpreted to refer to wherein the heterologous promoter downstream of the approximate starting position of the TSDR e.g. downstream of approximately human hg19 chrX 49117716 and upstream of the first coding exon of endogenous FOXP3, wherein the first coding exon is the first exon comprising mRNA sequence that is translated.
Marson et al. describes targeted editing a genome in a cell (paragraph [0003]), the method comprising introducing into the cell: (a) a first nucleic acid comprising a heterologous regulatory element (template nucleic acid encodes a sequence that, although adjacent to or flanked by a sufficient region of homology, is entirely orthogonal to the endogenous sequence. For example, the template nucleic acid can encode an inducible promoter; paragraph [0107]); and (b) a nuclease or a second nucleic acid encoding the nuclease (cas9 nuclease; paragraph [0003]), wherein the nuclease is capable of cleaving a targeted locus within or upstream from the first coding exon of a FOXP3 gene in the cell genome, wherein the heterologous regulatory element is inserted into the cell genome, and is operably linked to the FOXP3 gene, thereby producing an engineered cell (template nucleic acid can encode a sequence for rescuing the expression level or activity of a target endogenous gene or protein. For instance, T cells containing a mutation in the FoxP3 gene, or a promoter region thereof can be rescued to treat X-linked IPEX or SLE; paragraph [0105]) (claim 2); The promoter can be inducible or constitutive. The promoter can be tissue specific. In some cases, the promoter is a U6, H1, or spleen focus-forming virus (SFFV) long terminal repeat promoter. In some cases, the promoter is a weak mammalian promoter as compared to the human elongation factor 1 promoter (EF1A). In some cases, the weak mammalian promoter is a ubiquitin C promoter or a phosphoglycerate kinase 1 promoter (PGK) (paragraph [0131])(claims 3-4) wherein the heterologous regulatory element is a heterologous promoter or a heterologous transcriptional enhancer (template nucleic acid encodes a sequence that, although adjacent to or flanked by a sufficient region of homology, is entirely orthogonal to the endogenous sequence. For example, the template nucleic acid can encode an inducible promoter; paragraph [0107]) (claim 6); wherein the heterologous promoter is an inducible promoter (template nucleic acid encodes a sequence that, although adjacent to or flanked by a sufficient region of homology, is entirely orthogonal to the endogenous sequence. For example, the template nucleic acid can encode an inducible promoter; paragraph [0107]) (claim 6); wherein the cell is a hematopoietic stem cell, a CD4+ T cell, or a T regulatory (Treg) cell (the primary hematopoietic cell is an immune cell. In some cases, the immune cell is a T cell. In some cases, the T cell is a regulatory T cell. In some cases, the regulatory T cell is a CD4+ cell; paragraph [0010]) (claims 12, 14, 18); wherein the cell is a CD25hiCD127lo regulatory T cell (paragraph [0010]) wherein the heterologous promoter is inserted upstream from a natural first coding exon of the FOXP3 gene (template nucleic acid can encode a sequence for rescuing the expression level or activity of a target endogenous gene or protein. For instance, T cells containing a mutation in the FoxP3 gene promoter region; paragraph [0105]); further comprising inserting a heterologous enhancer domain into the cell genome, wherein the heterologous enhancer domain is inserted upstream or downstream from one or more regulatory elements of the FOXP3 gene (a promoter is defined as an array of nucleic acid control sequences that direct transcription of a nucleic acid. As used herein, a promoter includes distal enhancer elements; paragraph [0023]) (claim 9); further comprising inserting a heterologous transcriptional activation domain into the cell genome (a promoter is defined as an array of nucleic acid control sequences that direct transcription of a nucleic acid. As used herein, a promoter includes distal enhancer elements; paragraph [0023]) (claim 10); wherein the cell expresses a chimeric antigen receptor (CAR) (the primary hematopoietic cell or a primary hematopoietic stem cell is modified to express a heterologous protein before the genome of the cell is edited. In some embodiments, the heterologous protein is a chimeric antigen receptor (CAR) protein or a heterologous T-cell Receptor (TCR), including but not limited to a rearranged TCR; paragraph [0003]) (claims 16-17, 18-19); wherein the cell expresses a T cell receptor (TCR) (the primary hematopoietic cell or a primary hematopoietic stem cell is modified to express a heterologous protein before the genome of the cell is edited. In some embodiments, the heterologous protein is a chimeric antigen receptor (CAR) protein or a heterologous T-cell Receptor (TCR), including but not limited to a rearranged TCR; paragraph [0003]).
Marson et. al. teaches “a target genomic region at or near the gene encoding FOXP3 can be targeted to increase or rescue FOXP3 function and thereby treat patients suffering from an autoimmune disease such as IPEX” (paragraph [0114]).
Marson et. al. additionally teaches an sgRNA sequence for targeting FOXP3 comprising at FoxP3 target sequence in Exon 2 (See Fig. 3A, [0166]), which is in the same region as the instant promoter insertion as shown in instant Fig. 3.
Marson et. al. does not explicitly teach the genetically modified cell wherein the heterologous promoter operably linked to the first coding exon of an endogenous FOXP3 gene on a nucleic acid in the cell genome is (i) downstream from a Treg-specific demethylated region of the endogenous FOXP3 gene; and (ii) upstream from the position of the first coding exon of the endogenous FOXP3 gene.
This deficiency is resolved by Floess et. al., and Myers et. al.
Floess et. al. teaches that the lymphoproliferative disorder of scurfy mice “is completely resuced by transgenic complementation with a 30.8-kilobase (kb) genomic fragment containing the foxp3 gene from wild-type mice. This indicates that most key regulatory elements required for proper Foxp3 expression are located within the transgene including the entire gene, as well as 12.5 kb and 2.8 kb of 5′ and 3′ flanking sequences, respectively” (p. 0170 left column ¶3). Floess et. al. teaches that a CpG-dense region upstream from exon-1 correlates with CD25+CD4+ Tregs compared to CD25-CD4+ conventional T cells (p. 0170 right column ¶3, Fig. 2C) and that the region is conserved and possesses transcriptional activity when cloned in front of a minimal SV40 promoter that is responsive to PMA activation (p. 0170 right column ¶5, Fig. 3). Floess et. al. teaches “The human FOXP3 promoter has recently been mapped to the putative 59 end of exon-2b, 6.1 kb upstream from the first coding exon [6]. However, other studies have reported promoter activity upstream from exon-1 close to the differ entially methylated region analyzed in the current study [26,27] corresponding to the Foxp3 mRNA species AY357712 and AY357713. We could show here by performing luciferase assays that the differentially methylated region itself possesses transcriptional activity. Together these data suggest that the evolutionarily conserved element might belong to an alter native TATA-less promoter, which contributes to the regulation of Foxp3 expression”.
Myers et. al. teaches a variant of IPEX syndrome caused by a G>T substitution in the first coding exon at -7 from the translational start site (p. 63 left column “Case 1; Fig. 1) that cause a new ATG and new reading frame, causing an early stop codon.
It would have been obvious, at the time of filing, for a person of ordinary skill in the art to genetically alter the hematopoietic stem cells or T cells of the patient of Myers et. al. in the manner suggested by Marson et. al. by using homology dependent repair to restore exon 1 to wildtype and to insert an exogenous promoter to benefit from alternative transcriptional control of the endogenous FOXP3 gene and to repair the FOXP3 gene in IPEX condition as taught by Marson et. al and using the FOXP3 target 1 site of Marson et. al. A person of ordinary skill in the art would place the insertion downstream of the TSDR because 1) Marson et. al. teaches placing an exogenous promoter within or downstream of existing promoter/enhancer elements; 2) Floess et. al. teaches that the TSDR acts with transcriptional activity (e.g. is a promoter/enhancer region of Foxp3); 3) Floess et. al. teaches that the TSDR upstream of a constitutive promoter is sufficient to drive transcription; 4) the TSDR element is in closer proximity the start site mutation as taught by Myers et. al. and therefore would readily lead itself to homology-dependent repair and insertion of the promoter with a single template, while the other promoter of Foxp3 at the -2 exon is far enough away that it may require a separate construct or editing event; and 5) Marson et. al teaches a specific sgRNA sequence for targeting a PAM site that is proximal to the described region and the mutation of Myers. This would have a reasonable expectation of success because a person of ordinary skill in the art reading Marson et. al. would understand that the exogenous promoter could be placed downstream of any promoter or enhancer element and Floess et. al. teaches that the TSDR acts as a transcriptional promoter/enhancer.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS dated 2/7/2024) in view of Floess, Stefan, et al. "Epigenetic control of the foxp3 locus in regulatory T cells." PLoS biology 5.2 (2007): e38 and Myers, A. K., et al. "Clinical and molecular findings in IPEX syndrome." Archives of disease in childhood 91.1 (2006): 63-64 as applied to claim 2 above, and further in view of Allan et. al. "Generation of potent and stable human CD4+ T regulatory cells by activation-independent expression of FOXP3." Molecular Therapy 16.1 (2008): 194-202 (Of record, IDS dated 2/7/2024) and Zhang, Fang, et al. "Lentiviral vectors containing an enhancer-less ubiquitously acting chromatin opening element (UCOE) provide highly reproducible and stable transgene expression in hematopoietic cells." Blood, The Journal of the American Society of Hematology 110.5 (2007): 1448-1457 (PTO-892 3/23/2026).
The teachings of Marson et. al. in view of Floess et. al. and Myers et. al. in regard to claim 2 are in the 103 rejection above.
Marson et. al. in view of Floess and Myers does not teach the genetically modified cells wherein the nucleic acid further comprises a ubiquitous chromatin opening element (UCOE).
This deficiency is resolved by Allan et. al. and Zhang et. al.
Allan et. al. teaches design of a FOXP3 lentiviral vector under the control of the constitutive EF1a promoter “pCCLFP3” (Fig. 1a) that is upstream of the first coding exon of FOXP3 that is transduced into cells (Fig. 2a, see Methods “Retroviral and lentiviral transduction of primary and Jurkat T cells section” p. 200 right column). Allan et. al. teaches that the promoter is the constitutive EF1a promoter. Allan et. al. teaches that the cells are CD4+ T cells (p. 196, right column). Allan teaches that the cells are regulatory T cells (“EF1a-driven FOXP3 expression induce a stable population of suppressive T cells” p. 199 left column) and that they are CD25+, CD127-, and CTLA4+ (Fig. 3a). Allan et. al. teaches the cells express a TCR (“Expression of FOXP3 does not affect TCR diversity” p. 199 right column; Tables S1 and S2).
Zhang et. al. teaches the use of a HNRPA2B1-CBX3 UCOE within the context of a self-inactivating lentiviral therapy for restoring immunodeficiency by overexpressing IL2RG in HSCs (Abstract) and teaches that the UCOE constructs resulted in 2.5 to 6.2-fold higher GFP expression that SFFV and CMV vector constructs, respectively. The overexpression of IL2RG in the HSCs resulted in restoration of all lineages including T cells and restored T cell proliferation (Fig. 7, Table 3). Zhang et. al. teaches that “The efficacy of gene transfer in vivo has in many cases been compromised by instability (high variability, silencing) of transgene expression from viral promoters.17,18 Furthermore, potentially mutagenic enhancer activity may be maintained even when linked promoters are silenced by DNA methylation […] We show for the first time that A2UCOE-regulated transgenes within lentiviral vectors produce a high, consistent, and homogeneous population of expressing cells that is not prone to gene silencing both in vitro (Figure 3) and more importantly within either HSCs or their progeny in vivo (Figure 4).” (Discussion, p. 1454).
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to add the UCOE regulatory element to the inserted promoter of modified Marson et. al. in order to benefit from high, consistent, and homogenous expression in hematopoietic stem cell lineages (such as T cells) as taught by Zhang et. al. in order to make a more stable Treg with consistently high FOXP3 expression as taught by Allan et. al. This would have a reasonable expectation of success because both Allan and Zhang show stabilization of gene expression in T cells and therefore an artisan would have a reasonable expectation that the FOXP3 expression of Allan et. al. could be stabilized by using the UCOE regulatory element of Zhang et. al and a person of ordinary skill in the art would expect to be able to modify the in situ promoter of Marson et. al. in a similar manner to Allan et. al. and Zhang et. al. to achieve the desired expression levels.
Claims 5 and 18-19 are rejected under 35 U.S.C. 103 as being unpatentable over WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS dated 2/7/2024) in view of Floess, Stefan, et al. "Epigenetic control of the foxp3 locus in regulatory T cells." PLoS biology 5.2 (2007): e38 and Myers, A. K., et al. "Clinical and molecular findings in IPEX syndrome." Archives of disease in childhood 91.1 (2006): 63-64 as applied to claim 2 above, and further in view of De Ravin SS, et. al. Targeted gene addition in human CD34(+) hematopoietic cells for correction of X-linked chronic granulomatous disease. Nat Biotechnol. 2016 Apr;34(4):424-9. doi: 10.1038/nbt.3513. Epub 2016 Mar 7 (PTO-892 3/23/2026).
The teachings of Marson et. al., Floess et. al., and Myers et. al. in regard to claim 2 are in the 103 rejection above.
Marson et. al. in view of Floess and Myers et. al. does not explicitly teach wherein the promoter is an MND promoter; wherein the cell is a CD4+ Treg expressing a TCR or a CAR wherein the heterologous promoter is an MND promoter; wherein the cell is a CD8+ Treg expressing a TCR or a CAR wherein the heterologous promoter is an MND promoter.
This deficiency is resolved by De Ravin et. al.
De Ravin et. al. teaches a method of gene therapy to modify human CD34+ hematopoietic stem and progenitor cells (HPSCs) using targeted integration into the human genome and a vector with an MND promoter operably linked to gp91 phox cDNA (target cDNA). De Ravin et. al. teaches “The MND (Myeloproliferative sarcoma virus MPSV enhancer, negative control region NCR deleted, d1587rev primer-binging site substituted) promoter has been shown to be suitable to drive high levels of transgene expression in HSCs19, 20. Further optimization of AAV6-donor delivery into HSCs from CGD patients to balance effects on cell growth and transfection efficiency achieved 15% gp91phox protein expression in vitro (Fig. 4a) from both the MND-gp91 donor and the SA-2A-gp91 donor [...] Despite similar TI efficiencies with both MND-91phox and SA-2A-gp91 donors, corrected cells produce significantly more gp91 from the MND promoter (MFI 107) versus from the captured PPP1R12C promoter (MFI 49)” () and that the higher levels driven by the MND promoter approached normal function. De Ravin et. al. teaches that the edited HSCs engrafted and produced engrafted progenitors (Fig. 1e).
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to use the MND promoter of De Ravin et. al. in the place of the heterologous constitutive promoter such as EF1a as taught by modified Marson et. al. in view of in order to benefit from the higher levels of expression in HSCs and the higher likelihood of restoration of gene function; this would further result in progenitor cells such as the CD4+ Tregs of Marson et. al. comprising the modification via maturation of the progenitors as taught by De Ravin. This would have a predictable effect because an artisan would expect to have similar expression benefits with a different genes expressed with the same promoter in the same cell type, and both Marson et. al. and De Ravin et. al. teach targeting the promoter to a particular locus for gene therapy. It would additionally be obvious, as taught by Marson et. al., to further modify the cells with a TCR or a CAR in order to induce antigen-specific tolerance for improvement of the outcomes in the Myers et. al patient (e.g. tolerance to self antigens related to diabetes). This would have a reasonable expectation of success because an artisan would expect to be able to express a CAR or TCR in the constitutive promoter-FOXP3 cell as taught by Marson et. al. in view of Floess and Myers; and would expect improved FOXP3 expression from the teachings of De Ravin et. al. as described.
Claims 13, 20, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over WO2016123578 to Marson et. al. published 4 August 2016 (Of record, cited in IDS dated 2/7/2024) in view of Floess, Stefan, et al. "Epigenetic control of the foxp3 locus in regulatory T cells." PLoS biology 5.2 (2007): e38 and Myers, A. K., et al. "Clinical and molecular findings in IPEX syndrome." Archives of disease in childhood 91.1 (2006): 63-64 as applied to claim 2 above, and further in view of De Ravin SS, et. al. Targeted gene addition in human CD34(+) hematopoietic cells for correction of X-linked chronic granulomatous disease. Nat Biotechnol. 2016 Apr;34(4):424-9. doi: 10.1038/nbt.3513. Epub 2016 Mar 7 (PTO-892 3/23/2026) and WO2017042170 to Guillonneau effectively filed 7 September 2015 (PTO-892 3/23/2026).
The teachings of Marson et. al., Floess et. al., and Myers et. al. in regard to claim 2 are in the 103 rejection above.
Marson et. al. in view of Floess and Myers does not teach wherein the T cell is a CD8 T cell, and wherein the cell is a CD8+ regulatory T cell expressing a CAR, and wherein the heterologous promoter is an MND promoter; or a pharmaceutical composition comprising the cells a pharmaceutically acceptable excipient.
This deficiency is resolved by Guillonneau and De Ravin.
De Ravin et. al. teaches a method of gene therapy to modify human CD34+ hematopoietic stem and progenitor cells (HPSCs) using targeted integration into the human genome and a vector with an MND promoter operably linked to gp91 phox cDNA (target cDNA). De Ravin et. al. teaches “The MND (Myeloproliferative sarcoma virus MPSV enhancer, negative control region NCR deleted, d1587rev primer-binging site substituted) promoter has been shown to be suitable to drive high levels of transgene expression in HSCs19, 20. Further optimization of AAV6-donor delivery into HSCs from CGD patients to balance effects on cell growth and transfection efficiency achieved 15% gp91phox protein expression in vitro (Fig. 4a) from both the MND-gp91 donor and the SA-2A-gp91 donor [...] Despite similar TI efficiencies with both MND-91phox and SA-2A-gp91 donors, corrected cells produce significantly more gp91 from the MND promoter (MFI 107) versus from the captured PPP1R12C promoter (MFI 49)” (p. 427 right column) and that the higher levels driven by the MND promoter approached normal function. De Ravin et. al. teaches that the edited HSCs engrafted and produced engrafted progenitors (Fig. 1e).
Guillonneau et. al. teaches a new subpopulation of CD8+CD45RLOW Tregs and teaches “Indeed, the highly suppressive isolated Tregs may then be expanded and pulsed with antigens of interest or genetically modified (e.g. in order to express a given chimeric antibody receptor also referred to as CAR or to express a chimeric T cell receptor (TCR)) or other types of chimeric antigen receptors in order to efficiently induce antigen- specific immune tolerance. Such expanded populations of Treg cells are of particular interest in the fields of chronic inflammation, autoimmunity, allergy, transplantation, treatment with therapeutic protein and gene therapy, to avoid degradation of self or therapeutic molecules/tissues by the immune system” (p. 1 lines 28-p. 2 line 2). Guillonneau teaches that this highly suppressive Treg population expresses FoxP3 (p. 3 lines 21-32). Regarding claim 21, Guillonneau teaches pharmaceutical compositions comprising the CD8+CD45LOW Tregs of the invention and a pharmaceutically acceptable additives, diluents or stabilizers (reads on excipient; p. 34 line 33-p. 35 line 8).
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to use the MND promoter of De Ravin et. al. in the place of the heterologous constitutive promoter such as EF1a as taught by modified Marson et. al. in order to benefit from the higher levels of expression in HSCs and the higher likelihood of restoration of gene function; this would further result in progenitor cells such as the CD4+ Tregs of Marson et. al. comprising the modification via maturation of the progenitors as taught by De Ravin. This would have a predictable effect because an artisan would expect to have similar expression benefits with a different genes expressed with the same promoter in the same cell type, and both Marson et. al. and De Ravin et. al. teach targeting the promoter to a particular locus for gene therapy. It would additionally be obvious, as taught by Marson et. al., to further modify the cells with a TCR or a CAR in order to induce antigen-specific tolerance for improvement of the outcomes in the Torgerson et. al. patients. This would have a reasonable expectation of success because an artisan would expect to be able to express a CAR or TCR in the constitutive promoter-FOXP3 cell as taught by Marson et. al. in view of Torgerson; and would expect improved FOXP3 expression from the teachings of De Ravin et. al. as described.
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to edit the obtain CD8+CD45RLow population as taught by Guillonneau from the HSCs of patients of modified Marson et. al. in view of Torgerson et. al. and De Ravin et. al. in order to benefit from the increased immunosuppressive properties of CD8+CDR45RLow T cells as taught by Marson et. al. to make an improved cell and pharmaceutical composition for treatment; further, an artisan would expect to be able to make an improved T cell composition for reducing the IPEX symptoms as taught by Myers et. al. by inducing antigen-specific tolerance (e.g. diabetes-related antigens) by expressing a CAR as suggested by Marson and Guillonneau et. al. This would have a reasonable expectation of success because an artisan would expect to be able to use an improved type of regulatory T cell in place of the generic regulatory T cell of Marson et. al.
Response to Arguments
Applicant’s arguments have been fully considered but are not persuasive.
In regard to the rejection of Marson et. al. in view of Torgerson et. al., some of the arguments are moot in view of the new rejection, necessitated by amendment, above, which does not rely on Torgerson et. al.
Applicant argues that the TSDR is more than 3000 nucleotides downstream from the first exon of the FOXP3 gene and the deletion of Torgerson et. al. is entirely upstream from the TSDR’s position. This is moot in view of the new rejection, necessitated by amendment, above. However, the Examiner notes that, as described in the 112(b)s in the Non-Final office action, all of the positions of the deletion of Torgerson et. al. would have been considered to be between the TSDR and the first coding exon of FOXP3 because the BRI of the claim would including that either exon 1 or exon 2 of Fig. 3 is the first coding exon of FoxP3 (one is the first exon of the mature mRNA; the other has the translation start site, as defined in the instant specification [0006] and [0057], respectively); therefore all of the positions between exon 1 and the TSDR are also downstream of the TSDR and upstream of exon 1 on the opposing strand, as described in the 112(b) of the Non-Final office action. However, as described in the claim interpretation section above, although the Applicant’s amendments to recite the endogenous TSDR and the endogenous first coding exon require the new rejection, necessitated by amendment.
Applicant argues that Marson et. al. does not disclose inserting a promoter downstream of the TSDR, at best contemplating the endogenous promoter region, which is upstream from the TSDR (Remarks 7/16/2026 p. 10-p. 11 ¶1). First, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). As described in the new 103 rejection, necessitated by amendment, above, a person of ordinary skill in the art would read Marson et. al. as disclosing inserting a promoter in or downstream of any promoter or enhancer region. As described by Floess et. al., a person of ordinary skill in the art would have understood that the TSDR is a promoter/enhancer region of FOXP3 and that it functions to regulate transcription when upstream of an endogenous promoter. Additionally, Marson et. al. teaches method to restore the function of the FOXP3 gene and Myers et. al. teaches a mutation in exon-1 which is downstream of the TSDR and upstream of the first coding exon. Finally, as described in the new 103 rejection, necessitated by amendment, above, Marson et. al. suggests a particular sgRNA and PAM sequence for modifying the FOXP3 gene which is proximal to both the mutation of Myers and is downstream of the TSDR and upstream of exon 2 of the FOXP3 gene. Therefore, as described, it would have been obvious with a reasonable expectation of success to insert a promoter downstream of the TSDR and operably linked to exon 2 of the FOXP3 gene in order to benefit from alternative transcriptional control and repair as taught by Marson, repair of the IPEX mutation as taught by Marson and Myers, and by inserting a promoter downstream of an endogenous promoter/enhancer region as taught by Marson and Floess.
Regarding the arguments over the rejection of claim 11 over Allan as evidenced by Mitchell and further in view of Zhang, these arguments are moot in view of the withdrawal of the rejection and the new rejections, necessitated by amendment, above.
Regarding the rejection of claims 5, 18, and 19 over Marson and Torgerson in further view of De Ravin, these arguments are moot in view of the withdrawal of the rejection and the new rejections, necessitated by amendment, above.
Regarding the rejection of claims 13, 20, and 21, over Marson and Torgerson in further view of De Ravin and Guillonneau, these arguments are moot in view of the withdrawal of the rejection and the new rejections, necessitated by amendment, above
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Kathleen CunningChen whose telephone number is (703)756-1359. The examiner can normally be reached Monday - Friday 11-8:30 ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gregory Emch can be reached at (571) 272-8149. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KATHLEEN CUNNINGCHEN/ Examiner, Art Unit 1646
/GREGORY S EMCH/ Supervisory Patent Examiner, Art Unit 1678
Prosecution Insights