DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 12/16/2025 has been entered.
Applicant’s amendments to the claims and arguments filed on December 16, 2025 have been received and entered. Claim 1-12, 14, 16-20, 24-30, 32 have been canceled.
Claims 13, 15, 21-23, 31, 33-40, 48, 50-54 are pending in the instant application.
Election/Restrictions
Applicant’s election without traverse of claims 24-30 (group I) in the reply filed on December 10, 2024 was acknowledged. Claims 13, 15, 21-23 and 31 link invention of group I and II. Additionally, applicant election without traverse of species (1) B2M; (ii) CIITA; (ii) MICA; and (iv) CD47, is also acknowledged. Upon further consideration, previously presented species set forth in withdrawn claims 32-33 were rejoined in view of applicant’s amendments to the claims.
Claim 35-40, 48, 50 and 51 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on December 10, 2024.
Priority
This application is a continuation of 16/495,318 filed on 09/18/2019, which is a 371 of PCT/US2018/023288 filed on 03/30/2018, which claims priority from US provisional application 62/473,564 filed on 03/20/2017.
Claims 13, 15, 21-23, 33-34, 52-53 and 54 are under consideration.
Withdrawn-Claim Rejections - 35 USC § 103
Claim 13, 15, 21-23, 33-34, 52-53 and 54 are rejected under 35 U.S.C. 103 as being unpatentable over Meissner et al (WO/2016/183041, dated 11/17/2016, filed 5/9/2016, EFD5/8/2015, IDS)/ Schrepfer et al (US20190376045, dated 12/12/2019, EFD 1/13/2017 or WO 2018/132783 IDS), Hering (US20200352142, dated 11/12/2020, EFD: 12/10/2015)/Tang et al (WO/2018140890, EFD01/29/2017, IDS) and Valamehr et al (WO 2017/079673, dated 05/112017, filed 11/4/2016, IDS). Upon further consideration, rejection of claims is hereby withdrawn in view of new combination of prior art addressing limitation of an insertion of a nucleic acid encoding an immune evasion factor and a suicide gene. Applicants’ arguments with respect to the withdrawn rejections are thereby rendered moot. The claims are however subject to new rejections over the prior art of record, as set forth below.
New-Claim Rejections - 35 USC § 103-necessiated by amendments
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.
Claim 13, 15, 21-23, 31, 33-34, 52-53 and 54 are rejected under 35 U.S.C. 103 as being unpatentable over Meissner et al (WO/2016/183041, EFD5/8/2015, IDS), Hering (US20200352142, EFD: 12/10/2015)/Tang et al (WO/2018140890, EFD01/29/2017, IDS) and Valamehr et al (WO 2017/079673, dated 05/112017, filed 11/4/2016, IDS) and Luo (Curr Protoc Stem Cell Biol. ; 29: 5A.7.1–5A.7.18, 1-21).
With respect to claims 13, 15, 21, 31, Meissner et al teach a genetically engineered pluripotent stem cell (claim 17 and 18 of ‘041) comprising reducing the expression of the one or more MHC-1 and MHC-11 human leukocyte antigens relative to a wild-type stem cell (see claim 1-3 of ‘041). It is further disclosed that one or more MHC-1 and MHC-11 human leukocyte antigens comprises one or more genes encoding one or more transcriptional regulators ofMHC-1 or MHC-11 being deleted from at least one allele of the cell (see claim 6 of ‘041), wherein n the transcriptional regulator is selected from the group consisting of NLRC5, CIITA and B2M (see claim 7 of ‘041). In certain embodiment, Meissner teaches knocking out expression ofB2M and/or TAP1 (see page 42, line8, page 61, lines) thereby reducing or eliminating surface expression of MHC class I molecules in the cell or population thereof (see page 61, lines 5-18, page 82, 22-25). It is further disclosed that these factors inhibit immune rejection of the stem cell or a differentiated stem cell therefrom (progeny) (see page 3, line 25-26, Fig. 28).
Regarding claims 13, 15, 52, Meissner teaches that the genetically engineered pluripotent stem cells further comprise introduced or increased expression of immune evasion factor selected from group consisting of at least one of HLA-G, and CD47 (page 63, lines 1-2, page 84, lines 11-19, claim 11 and 16 of ‘041). It is disclosed that overexpression of CD47 will assist engraftment of stem cell-derived transplants by protecting cells from macrophage engulfment (see para. 16, lines 14-25). Meissner further teaches that the one or more factors may be inserted into a safe harbor AAVS1 locus of at least one allele to inhibit immune rejection (see page 3, lines 12-16).
With respect to claims 31 and 34, Meissner teaches that the stem cell is a human embryonic or pluripotent stem cell (see claims 17-18 and 20 of ‘041). It is further disclosed that genome editing tools such as TALEN and./or Crispr system in stem cells would be used to reduce expression or knock out the MHC-1 gene and/or MHC-II gene by directly targeting B2M and CIITA (see page 2, lines 14-19, fig. 16, page 28, lines 5-7, 10-20).
Meissner differs from claimed invention by not disclosing said genetically modified cells further comprises (i) one or more genetic modifications in at least one gene encoding a ligand of NKG2D, wherein the one or more genetic modifications reduces or eliminates expression of the ligand of NKG2D relative to a wild-type cell and (ii) an insertion of one or more nucleic acids encoding at least one immune evasion factor and a suicide gene into a safe harbor locus, wherein the at least one immune evasion factor is selected from HLA-E, HLA-G, CD46/Crrv, CD47, CD55, or a combination thereof.
Before the effective filing date of instant application, Hering teaches a cell population that comprises a genetically modified stem cell, wherein said genetically modified stem cell comprises a disruption in a gene encoding a NOD-like receptor family CARD domain containing 5 (NLRC5), wherein said genetically modified stem cell comprises reduced expression of a MHC class I molecule as compared to a corresponding non-genetically modified stem cell, and wherein said genetically modified stem cell is a human stem cell, wherein said genetically modified stem cell further comprises a disruption in a gene encoding a transporter associated with antigen processing 1 (TAP1), a gene encoding a MHC class I polypeptide-related sequence A (MICA), a gene encoding a MHC class I polypeptide-related sequence B (MICB), a gene encoding a class II Major Histocompatibility Complex Transactivator (CIITA), a gene encoding a β-2-microglobulin (B2M), or a combination thereof (see claim 7-9 of ‘142, para.15, 205) (limitation of claims 13, 22 and 23). Hering further teaches that the exogenous polynucleotide encoding CD47 is inserted adjacent to the promoter of or inside one or more of: a safe harbor locus (see claims 10-11 of ‘142) (limitation of claim 13). Likewise, Tang provided guidance with respect to one nucleic acid encoding the immune checkpoint antagonist, which may be a polypeptide or protein that binds or otherwise interferes with the function or expression of an immune checkpoint-associated protein, or its RNA, wherein the immune checkpoint antagonist includes ligand such as MICA or MICAB. It is further disclosed that checkpoint antagonist or inhibitor interacts with the immune checkpoint-associated protein in such a way as to reduce, interfere with, impair, or otherwise eliminate the ability of the checkpoint protein to be expressed or function by gene editing systems, such as CRISPR-Cas9 system. (see page 16, para. 1 and 3, abstract, provisional claims 1-2, 6-7 and 18 of ‘759, limitation of claim 34).
The combination of references differs from claimed invention by not disclosing an insertion of one or more nucleic acids encoding at least one immune evasion factor and a suicide gene into a safe harbor locus.
Valamehr cure the deficiency by teaching a genetically engineered pluripotent stem cell comprising: indel at one or more endogenous genes selected from group consisting of B2M, TAPI, (see claims 22-25, 42-47 of ‘673), to produce engineered stem cells that are HLA class I and class II deficient (see claim 29, 45 of ‘673). Valamehr further teaches that said cells further comprises at least one exogenous polynucleotide that encodes safety switch protein, such as suicide gene including caspase, thymidine kinase, cytosine deaminase and ganciclovir, 5-fluorocytosine (5-FC) respectively at a safe harbor locus such as AAVS1 (see claims 35 and 36 of ‘673 please note claim 36 incorporates cells that are HLA1 and HLA class II deficient). Valamehr provide motivation to include "safety switch protein to prevent potential toxicity or otherwise adverse effects of a cell therapy that may be conditionally controlled to address safety concerns for transplanted engineered cells that have permanently incorporated the gene encoding the safety switch protein into its genome (see para. 131). It is further disclosed that exogenous polynucleotides integrated by the method may be driven by endogenous promoters in the host genome, at the integration site. In one embodiment, the method of the invention is used for targeted integration of one or more exogenous polynucleotides at AAVS I locus in the genome of a cell (see para. 168) (limitation of claim 13, 33, 53). Valamehr further teaches the one or more exogenous polynucleotides in the construct are polycistronic (see para. 198). Luo provide evidence that bicistronic transgene cassettes using 2A based construct design were routinely used in prior art to integrate into the AAVS1 safe harbor locus human cells using TALEN based genome engineering (see fig. 4). Luo teaches AAVS1 gene targeting with AAVS1-CAG-EGFP donor. Puro expression is driven by endogenous promoter of PPP1R12C gene through a splicing acceptor (SA) linked self-cleaving 2A peptide. EGFP expression is driven by CAG (CAGGS) promoter (see fig. 4). It is suggested that AAVS1 locus is a “safe harbor” and has an open chromatin structure that allows insertion and stable expression of inserted transgenes (see abstract).
Therefore, it would have been prima facie obvious for a person of ordinary skill to combine the teachings of prior art to modify the genetically engineered pluripotent stem cells of Meissner by further knocking out MIACA and/or MICAB gene a ligand of NKG2D as suggested in Hering /Tang, with a reasonable expectation of success, before the effective filing date of the instant invention. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would be motivated to do so in order to protect stem cell during transplantation. It would have been further obvious to incorporate at least one exogenous suicide gene with immune evasion factor CD47 at a safe harbor locus as suggested individually in Meissner and Valamehr in the genetically modified cell, with a reasonable expectation of success, before the effective filing date of the instant invention. One of ordinary skill in the art would be motivated to do so in order to produce efficient, reliable, and targeted approach for preventing elimination of genetically modified cells by macrophage and eliminate said modified cells in case there is any adverse effect due to administered cells without damaging surrounding cells and tissues for various cellular therapeutics (see page 29 last line to page 30). It is relevant to note that placing both genes into same safe harbor locus AAVS1 would ensure stable expression of both genes (suicide gene and CD47) thereby reducing the risk of random insertion and variable expression of genes elsewhere in the genome. Absent evidence of any unexpected superior, one of ordinary skill in the art would have been expected to have a reasonable expectation of success because prior art successfully reported (i) producing a genetically modified stem cell comprising a disruption in a gene encoding a transporter associated with antigen processing 1 (TAP1), a MICA, a MICB, CIITA, B2M, or a combination thereof as in Hearing and (ii) incorporating polynucleotide encoding CD47 with thymidine kinase in the HLA class I and class II deficient cell as disclosed in Valamehr in view Luo. It should be noted that the KSR case forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness See the recent Board decision Ex parte Smith, —USPQ2d—, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396) (available at http: www.uspto.gov/web/offices/ dcom/bpai/prec/fd071925.pdf).
Response to augments
To the extent that Applicants’ arguments are pertinent to the new rejections, they are addressed as follows:
Applicant disagree with the rejection arguing claim 33 recites one or more polynucleotides that encode a large number of proteins, including safety switch proteins and refers back to claims 22-32, none of which refer to any safe harbor site. Claim 35 refers back to claims 22-34, and whilst claim 34 recites a safe harbor site, claim 35 recites that the at least one exogenous polynucleotide encodes a safety switch protein. Paragraph 131 discusses safety switch proteins. Paragraph 168 discusses safe harbor sites. Whilst paragraph 166 generally discusses targeted integration of polynucleotides encoding a large number of proteins into a safe harbor site, it does not specifically teach integrating an exogenous polynucleotide encoding CD47 and a safety switch into a safe harbor locus. Thus, Valamehr still does not make up for the deficiencies of Meissner, Hering/Tang. Further, the Office has engaged in improper hindsight to combine the references to arrive at the claimed invention. As noted above, there is no disclosure in Valamehr that specifically teaches inserting an exogenous polynucleotide encoding CD47 and a safety switch into a safe harbor locus. This specific combination can only be gleaned from the instant specification itself. Applicants’ arguments have been fully considered, but are not found persuasive.
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). In the instant case, Meissner explicitly teaches a genetically engineered pluripotent stem cells comprise introduced or increased expression of immune evasion factor selected from group consisting of at least one of HLA-G, and CD47 (page 63, lines 1-2, page 84, lines 11-19, claim 11 and 16 of ‘041), wherein the one or more factors may be inserted into a safe harbor AAVS1 locus of at least one allele to inhibit immune rejection (see page 3, lines 12-16).It is further disclosed that overexpression of CD47 will assist engraftment of stem cell-derived transplants by protecting cells from macrophage engulfment (see para. 16, lines 14-25). Applicant in part agree that Valamehr teaches a genetically engineered pluripotent stem cell comprising: indel at one or more endogenous genes selected from group consisting of B2M, TAPI, (see claims 22-25, 42-47 of ‘673), to produce engineered stem cells that are HLA class I and class II deficient (see claim 29, 45 of ‘673). Valamehr further teaches that said cells further comprises at least one exogenous polynucleotide that encodes safety switch protein, such as suicide gene including caspase, thymidine kinase, cytosine deaminase and ganciclovir, 5-fluorocytosine (5-FC) respectively at a safe harbor locus such as AAVS1 (see claims 35 and 36 of ‘673). Additionally, Valamehr provide explicit motivation to include "safety switch protein to prevent potential toxicity or otherwise adverse effects of a cell therapy that may be conditionally controlled to address safety concerns for transplanted engineered cells that have permanently incorporated the gene encoding the safety switch protein into its genome (see para. 131).
In view of foregoing, it is apparent that suicide gene (HSV-TK) and immune evasion factors (CD47) were individually taught to be inserted at safe harbor locus. It would have been prima facie obvious to insert each of these two gene at a safe harbor locus using a bicistronic vector as suggested in prior art to produce cell that could prevent genetically modified cell from macrophage engulfment and at the same time prevent potential toxicity or otherwise adverse effects of the genetically modified cell therapy. Further, insertion of these genes at the same safe harbor locus AAVS1 would ensure stable expression of both genes (suicide gene and CD47) thereby reducing the risk of random insertion and variable expression of genes elsewhere in the genome (supra). Absent evidence of any unexpected results, one of ordinary skill in the art would have reasonable expectation of success in expressing both gene from the safe harbor locus in cells of Meissner and Hering /Tang because prior art successfully reported inserting bicistronic constrict to express two gene inserted at safe harbor locus AAVS1 as evident from the teaching of Luo.
Therefore, in view of the fact patterns of the instant case, and the ground of rejection outlined by the examiner, applicants’ arguments are not compelling and do not overcome the rejection of record.
Conclusion
No claims allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Schrepfer et al (US20190376045, dated 12/12/2019, EFD 1/13/2017 or WO 2018/132783 art of record) teaches Schrepfer et al teach hypoimmunogenic pluripotent stem cell comprises a gene encoding B2M and CIITA that is knocked out to reduce the expression of HLA-1 and HLA-II respectively (see claims 15-23 of '045). With respect to claims 13, Schrepfer et al teach hypoimmunogenic pluripotent stem cell comprising an immune evasion CD47 gene, wherein said reduced susceptibility to NK cell killing is caused by an increased expression of a CD47 protein, wherein said increased CD47 protein expression results from a modification to an endogenous CD47 gene locus, wherein said increased CD47 protein expression results from a CD47 transgene (see claim 33-35 of '045). It is further disclosed that gene CD47 may be under control of an inducible promoter (see para. 186, 188).
Sims (US patent 5955441, 9/21/1999). teach protecting transfused cells and transplanted organs from the effects of activated complement proteins generated in blood serum or plasma by expressing in the cells the gene for CD59 and/or administering with the cells the product of expression of the gene. In the preferred embodiment, the gene for CD59, ligated to a vector suitable for high level expression of the gene in the target cells (see col. 4, lines 54-57 to col. 5), wherein the cells may be hematopoietic progenitor cells (see claims in 441). Sims further teaches that CD59 is expressed in conjunction with CD46 and/or CD55 by transfection or infection with a vector containing the gene for each protein. The co-expression of these genes will serve to limit the amount of C5b-9 that can be generated at the cell surface (through the inhibitory effects of CD46 and/or CD55 on the conversion of C5 to C5b by the complement enzymes) and to protect from the cytolytic and cell-stimulatory effects of the residual C5b-9 that is formed through conversion of C5 to C5b by plasmin and other enzymes that are not inhibited by the action of CD46 and/or CD55 (col. 18).
Soland et al (PLoS One, 2013, 8(3) e60461, 1-8, IDS).
Russell et al (WO/2013/158292, IDS) teaches isolated human cells comprising genetically engineered disruption in a beta-2 microglobulin (B2M) gene, which results in HLA class Uclass II deficiency.
Lanier et al. (WO 2005/097160, international publication date: 10/20/2005, IDS) teach that various agents may be used to inhibit NKG2D signaling, including 1) antibodies, nucleic acids, or small molecules that inhibit NKG2D.
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/ANOOP K SINGH/ Primary Examiner, Art Unit 1632
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