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 .
Election/Restrictions
Applicant’s election without traverse of Group I (Claims 1, 3-4, 12-14, 17, 19-23, 26, and 28-31; drawn to a cell overexpressing DUX4) in the reply filed on June 2, 2025, is acknowledged.
Claims 32 and 71 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention (Groups II and III), there being no allowable generic or linking claim.
Applicant further elected the following species:
a. a cell further comprising further modification to increase expression of one or more of CD47, HLA-C, HLA-E, HLAG, PD-Ll, CTLA-4-Ig, Cl-inhibitor, CD46, CD55, CD59, and IL- 35
b. A viral vector as the expression vector
c. SEQ ID NO: 1 as the encoding sequence of DUX4
In light of the Applicant’s elected species, claim 19 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
DETAILED ACTION
The amended claims filed on October 27, 2025, have been acknowledged. Claims 2, 5-11, 15-16, 18, 24-25, 27, 33-70, and 72-88 were cancelled. Claims 1, 3-4, 12, 17, 21, 26, and 30-31 were amended. In light of the Applicant’s elected invention and species, claims 19, 32, and 71 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 1, 3-4, 12-14, 17, 20-23, 26, and 28-31 are pending and examined on the merits.
Priority
The applicant claims domestic priority from U.S. provisional application No. 62/881,840, filed on August 1, 2019. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Claims 1, 3-4, 12-14, 17, 20-23, 26, and 28-31 receive domestic benefit from U.S. provisional application No. 62/881,840, filed on August 1, 2019.
Claim Objections
The prior objection to claim 31 is withdrawn in light of Applicant’s amendments to claim 31 to include an article before each cell type.
Withdrawn Claim Rejections - 35 USC § 112
The prior rejection of claims 1-4, 8-9, 12-14, 17, 20-23, 26, and 28-31 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 in light of Applicant’s amendment to claim 1 to recite that the change in expression is relative to an unmodified cell of the same cell type.
The prior rejection of claim 17 under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends is withdrawn in light of Applicant’s amendments to claim 4 to recite “a modification to increase expression of one or more genes” which is now in line with what is recited in claim 17.
Withdrawn Claim Rejections - 35 USC § 102
The prior rejection of claims 1, 12-14, 20, and 31 under 35 U.S.C. 102(a)(1) as being anticipated by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016; referenced in IDS), as evidenced by Chew et al. (Developmental Cell 50: 658–671. 2019; referenced in IDS) is withdrawn in light of Applicant’s amendments to claim 1 to recite that the cell comprises reduced expression of MHC class II human leukocyte antigens.
Claim Rejections - 35 USC § 103
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 1, 3-4, 12-14, 17, 20, and 30-31 are rejected under 35 U.S.C. 103 as being unpatentable over World Intellectual Property Organization Application No. 2018073787 (Tapscott) further in view of World Intellectual Property Organization Application No. 2018132783 (Schrepfer; referenced in IDS) and Chew et al. (Developmental Cell 50: 658–671. 2019. Published July 2019; referenced in IDS), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016). This is a new rejection made in response to Applicant’s amendments to claim 1 that is substantially similar to a previous rejection. Any aspect of Applicant’s traversal that is relevant to the rejection as newly written is addressed below.
Regarding claims 1 and 3-4, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (Example 3 (pages 109-127), paragraph 00369, and claims 1, 4, and 19-23). Tapscott teaches that they want to use their cell overexpressing DUX4 to treat diseases in humans (paragraphs 0024-0025). Tapscott teaches that allogeneic iPSCs overexpressing DUX4 can be used to treat diseases (claims 1-4, 53, and 55)
Tapscott does not teach a modification to reduce MHC class II HLA expression.
However, Schrepfer teaches that they generated hypoimmune pluripotent stem cells to evade rejection by the host immune cell. As part of this strategy, they eliminated the activity of both alleles of the B2M gene (A B2M knock-out depletes MHC I in mice or HLA-1 in humans) and CIITA genes (A CIITA knockout depletes MHC II or HLA-II expression; a modification to reduce expression of MHC class II), respectively, and increased the expression of CD47. Schrepfer teaches that they used the CRISPR-Cas9 system and gRNAs to inactivate the B2M and CIITA genes and transduced the B2M and CIITA inactivated cells with a lentivirus encoding CD47. As can be seen in Figure 36, the cells have reduced human leukocyte antigens (HLA) I expression and HLA II expression compared to wild type and increased expression of CD47 (through introduction of exogenous CD47) compared to wild type. Schrepfer teaches that immune rejection of iPSCs decreases the likelihood of successful, large-scale engineering of compatible patient-specific tissues for treatment of patients (paragraphs 0003-0013 and 0045, Example 6 (page 60-61), Figure 36, and paragraph 0073). Schrepfer teaches that the benefit of being able to use human allogeneic Hypolmmunogenic Pluripotent ("HIP") cell derivatives in human patients results in significant benefits, including the ability to avoid long-term adjunct immunosuppressive therapy and drug use generally seen in allogeneic transplantations. It also provides significant cost savings as cell therapies can be used without requiring individual treatments for each patient. Recently, it was shown that cell products generated from autologous cell sources may become subject to immune rejection with few or even one single antigeneic mutation. Thus, autologous cell products are not inherently non-immunogenic. Also, cell engineering and quality control is very labor and cost intensive and autologous cells are not available for acute treatment options. Only allogeneic cell products will be able to be used for a bigger patient population if the immune hurdle can be overcome. HIP cells will serve as a universal cell source for the generation of universally acceptable derivatives (paragraph 0075).
Chew teaches that MB135 human myoblasts transduced with a lentivirus encoding DUX4 exhibited a reduction in MHC Class I expression (Figure 4). Furthermore, Chew teaches that this reduction in MHC Class I expression was also found in other studies using human WS236 myoblasts transfected with DUX4-expressing plasmids and in DUX4+ myoblasts following induction of differentiation for myoblasts that spontaneously express DUX4 (Figure 4). Chew teaches that DUX4 is a cell-intrinsic suppressor of MHC class I expression (page 664, column 1, paragraph 2-page 665, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the allogeneic iPSCs with increased DUX4 expression of Tapscott by including additional modifications to B2M, CIITA, and CD47 to make the iPSC cells hypoimmune, as identified by Schrepfer to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to modify with a reasonable expectation of success because Schrepfer teaches that immune rejection of iPSCs decreases the likelihood of successful, large-scale engineering of compatible patient-specific tissues for treatment of patients. Furthermore, Schrepfer identifies allogeneic HIP cells avoid long-term adjunct immunosuppressive therapy and drug use generally seen in allogeneic transplantations and limit costs compared to autologous transplantations while serving as a universal cell source. Additionally, Chew teaches that DUX4 expression reduces MHC class I expression. Therefore, B2M inactivation and DUX4 overexpression both downregulate MHC class I expression, As such, it would have been obvious to further modify the cell of Tapscott to further decrease MHC class I expression. MPEP 2144.06 states "It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from their having been individually taught in the prior art." In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980) (citations omitted). Therefore, it would have been obvious to make the cells of Tapscott hypoimmune through the additional modifications of Schrepfer to increase the likelihood that they have a therapeutic effect in patients. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding the limitation wherein the increase expression of Dux4 reduces MHC class I HLA expression, as stated supra, Chew teaches that that DUX4 is a cell-intrinsic suppressor of MHC class I expression (page 664, column 1, paragraph 2-page 665, column 1, paragraph 1).
Regarding claims 12-13 and 20, as stated supra, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). Regarding claim 13, the codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
Regarding claim 14, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
Regarding claim 17, as stated supra, Schrepfer teaches that they transduced the B2M and CIITA inactivated cells with a lentivirus encoding CD47 (Example 6).
Regarding claim 30, Tapscott does not teach that the cell comprises an inducible suicide switch.
However, Schrepfer teaches that inducible suicide switches can be included in the hypoimmunogenic pluripotent cells as a safety switch that can cause the death of the hypoimmunogenic pluripotent cells should they grow and divide in an undesired manner. The "suicide gene" ablation approach includes a suicide gene in a gene transfer vector encoding a protein that results in cell killing only when activated by a specific compound (i.e. inducible) (paragraphs 00177-00178).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the hypoimmunogneic iPSCs with increased DUX4 expression of the combined teachings of Tapscott and Schrepfer by including an inducible suicide switch, as identified by Schrepfer to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to modify with a reasonable expectation of success because Schrepfer teaches that inducible suicide switches can be included in the hypoimmunogenic pluripotent cells as a safety switch that can cause the death of the hypoimmunogenic pluripotent cells should they grow and divide in an undesired manner. Therefore, it would have been obvious to include an inducible suicide switch in these cells to improve their safety for treating patients in case of undesired growth and division (i.e. potential cancerous growth). Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 31, as stated supra, Tapscott and Schrepfer teach that they modified iPSCs.
Response to Arguments
Applicant's arguments filed October 27, 2025, are acknowledged.
Applicant argues that it is improper hindsight to make the cells of Tapscott hypoimmune as Tapscott does not suggest making hypoimmune cells for the purpose of immune evasion as there was no need to make the cells hypoimmune as Tapscott discusses using autologous (donor cells obtained from the subject to be treated) and, thus, would obviate the risk of rejection. As such, a skilled artisan would not have had any reason to consider further modifications to make the cells of Tapscott hypoimmune to prevent rejection (page 10, paragraph 3-page 12, paragraph 2).
Applicant's arguments have been fully considered but they are not 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).
It is worth noting that Applicant’s arguments focus on the use of autologous cells which at least partially obviate the risk of rejection. However, this is only one embodiment identifies by Tapscott. As stated in the rejection above, Tapscott specifically identifies that the modified iPSCs can be allogeneic. MPEP 2143.01(I) states that the court stated that "the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed…." Id. In affirming the Board’s obviousness rejection, the court held that the prior art as a whole suggested the desirability of the combination of shoe sole limitations claimed, thus providing a motivation to combine, which need not be supported by a finding that the prior art suggested that the combination claimed by the applicant was the preferred, or most desirable combination over the other alternatives. Id. See also In re Urbanski, 809 F.3d 1237, 1244, 117 USPQ2d 1499, 1504 (Fed. Cir. 2016).
Furthermore, as stated in the rejection above, Schrepfer teaches that, recently, it was shown that cell products generated from autologous cell sources may become subject to immune rejection with few or even one single antigeneic mutation. Thus, autologous cell products are not inherently non-immunogenic. Additionally, Schrepfer identifies multiple benefits associated with using human allogeneic Hypolmmunogenic Pluripotent ("HIP") cell derivatives in human patients, including avoiding long-term adjunct immunosuppressive therapy and drug use generally seen in allogeneic transplantations. It also provides significant cost savings as cell therapies can be used without requiring individual treatments for each patient. Also, cell engineering and quality control is very labor and cost intensive and autologous cells are not available for acute treatment options. Only allogeneic cell products will be able to be used for a bigger patient population if the immune hurdle can be overcome. HIP cells will serve as a universal cell source for the generation of universally acceptable derivatives (paragraph 0075).
Therefore, one of ordinary skill in the art would understand that modified allogeneic iPSCs were a viable, and possibly superior, option compared to autologous cells.
As Tapscott directly identifies that allogeneic iPSCs could be used, it would have been obvious to one of ordinary skill in the art to make the allogeneic iPSCs of Tapscott hypoimmune to increase the likelihood that they have a therapeutic effect in patients, reduce costs, and provide a universal cell source for administering to multiple patients.
Therefore, Applicant’s arguments are considered unpersuasive.
Claims 1, 4, 21-23, 26, and 28-29 are rejected under 35 U.S.C. 103 as being unpatentable over World Intellectual Property Organization Application No. 2018073787 (Tapscott) further in view of World Intellectual Property Organization Application No. 2018132783 (Schrepfer) and Chew et al. (Developmental Cell 50: 658–671. 2019), as applied to claims 1 and 4 above, and further in view of Torres et al. (Gene Therapy 21: 343-352. 2014), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016). This rejection is repeated with regards to the prior rejection in the Non-final office action mailed on July 29, 2025. Applicant’s traversal has been addressed above.
Regarding claims 21, 26, and 28-29, the teachings of Tapscott, Schrepfer, and Chew are as discussed above.
The combined teachings of Tapscott, Schrepfer, and Chew do not teach wherein the modification to increase DUX4 expression and/or CD47 expression comprises introducing a polynucleotide sequence encoding DUX4 and/or CD47 into a selected locus of the cell.
However, Torres teaches that transgenesis procedures in which the position and dosage of the inserted transgene are uncontrolled can lead to unpredictable effects due to disruption of host gene function, compromising data interpretation and placing severe limits on the applicability of this technology. This leads to unpredictable outcomes that compromise data interpretation in research contexts and severely limits the potential clinical application of these technologies. To overcome these problems, procedures for gene gain- or loss-of-function must avoid all genome effects other than the desired modification, such as single-copy insertion at a specific genomic locus. Torres teaches that the ideal sites for transgene insertion are ‘safe harbours’, sites susceptible to disruption and that support transcriptional activity with minimal interference in host gene function. The AAVS1 locus, mapping to chromosome 19 and encoding the PPP1R12C gene, is widely regarded as innocuous for targeting. Disruption of PPP1R12C by zinc-finger nucleases is safe and does not alter the pluripotency of human induced pluripotent stem cells (hiPSCs). The AAVS1 locus thus displays the two essential characteristics of a transgene safe-harbour (page 343, column 1, paragraph 1-page 344, column 1, paragraph 1 and page 349, column 1, paragraphs 3-4).
Torres teaches that they used integrase deficient lentiviruses to yield single site-specific recombination of a selectable donor cassette (TRINA) at the ‘safe-harbour’ AAVS1 locus previously edited by zinc-finger nuclease to contain an acceptor site (KAS2.0). Their method provides an efficient, simple and inexpensive methodology for replacing cassettes in the AAVS1 locus (whole document).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the Lentivirus mediated random integration method of increasing expression of DUX4 and/or CD47 of the combined teachings of Tapscott, Schrepfer, and Chew with the integrase deficient lentivirus mediated method of site specific integration into the AAVS1 safe harbor locus of Torres to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to substitute with a reasonable expectation of success because Torres teaches that random integration methods have the distinct disadvantage of unpredictable effects due to disruption of host gene function due to uncontrolled positioning and dosage of the inserted transgene that severely limits the potential clinical application of these technologies. However, site specific insertion at a specific genomic locus can overcome these problems while maintaining the pluripotency of human induced pluripotent stem cells (hiPSCs). Therefore, it would have been obvious to use the method of Torres to ensure site specific integration into the AAVS1 safe harbor locus to improve clinical applicability of the iPSCs of Tapscott and Schrepfer. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 22, as stated supra, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
Regarding claim 23, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 1, 3-4, 21, 26, and 28-31 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5, 8-10, 22-27 of copending Application No. 17/637789 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other.
‘789 claims an isolated cell comprising reduced expression of MHC class I and/or class II human leukocyte antigens and a modification to increase expression of Dux4 (claims 1-3). The cell is further modified to increase CD47 expression and inactivate B2M and CIITA by a rare-cutting endonuclease including a Cas protein (claims 3, 5, and 8-10). ‘789 claims that the modification to increase Dux4 and CD47 comprises introducing a polynucleotide sequence encoding Dux4 and CD47 into a selected locus of the cell (claims 22-23). The selected locus can be a safe harbor site, such as AAVS1 (claims 24-25). ‘789 claims the cell further comprises an inducible suicide switch (claim 26). ‘789 claims the cell can be an iPSC (claim 27).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 1, 4, 12-14, 17, 20-23 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5, 8-10, 22-27 of copending Application No. 17/637789 (reference application) as applied to claims 1, 4, and 21 and further in view of World Intellectual Property Organization Application No. 2018073787 (Tapscott), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016).
Regarding claims 12, 17, and 20, the teachings of ‘789 are as discussed above.
‘789 is silent as to the method of introducing the transgenes to the cell.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (Example 3 (pages 109-127), paragraph 00369, and claims 1, 4, and 19-23).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used a lentiviral vector to express DUX4 and CD47 in iPSCs as identified by Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use a lentiviral vector with a reasonable expectation of success because Tapscott has successfully reduced to practice that lentiviral vectors can be used to express transgenes in an iPSC cell Therefore, it would have been obvious to use a lentivirus to introduce a DUX4 and CD47 transgene into iPSCs. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claims 13 and 22, the teachings of ‘789 are as discussed above.
‘789 is silent as to the sequence of DUX4 used.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content because this was shown to enhance transgene expression of the hDUX4 vector (paragraph 00326). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the codon altered DUX4 sequence (SEQ ID NO: 82) of Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use SEQ ID NO: 82 with a reasonable expectation of success because Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content and this was shown to enhance transgene expression of the hDUX4 vector. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claims 14 and 23, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
This is a provisional nonstatutory double patenting rejection.
Claims 1, 3-4, 12-14, 17, 20, and 30-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 333-334 and 349-350 of copending Application No. 18/579300 in view of World Intellectual Property Organization Application No. 2018073787 (Tapscott), World Intellectual Property Organization Application No. 2018132783 (Schrepfer), and Chew et al. (Developmental Cell 50: 658–671. 2019; referenced in IDS), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016).
Regarding claims 1 and 3-4, ‘300 claims a cell comprising a polycistronic vector encoding DUX4 (claims 333, 334, and 350).
‘300 is silent as to the cell type of the cell.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (Example 3 (pages 109-127), paragraph 00369, and claims 1, 4, and 19-23). Tapscott teaches that they want to use their cell overexpressing DUX4 to treat diseases in humans (paragraphs 0024-0025).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used an iPSC as the cell with increased expression of DUX4 as identified by Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use an iPSC as the cell with increased expression of DUX4 with a reasonable expectation of success because Tapscott has successfully reduced to practice that iPSCs can be transduced to increase DUX4 expression and identifies that these cells may be useful in treating diseases. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
‘300 and Tapscott do not teach a modification for reducing expression of MHC class II HLA.
However, Schrepfer teaches that they generated hypoimmune pluripotent stem cells to evade rejection by the host immune cell. As part of this strategy, they eliminated the activity of both alleles of the B2M gene and CIITA genes, respectively, and increased the expression of CD47. Schrepfer teaches that they used the CRISPR-Cas9 system and gRNAs to inactivate the B2M and CIITA genes and transduced the B2M and CIITA inactivated cells with a lentivirus encoding CD47. As can be seen in Figure 36, the cells have reduced human leukocyte antigens (HLA) I expression and HLA II expression compared to wild type and increased expression of CD47 compared to wild type. Schrepfer teaches that immune rejection of iPSCs decreases the likelihood of successful, large-scale engineering of compatible patient-specific tissues for treatment of patients (paragraphs 0003-0013, Example 6 (page 60-61), Figure 36, and paragraph 0073).
Chew teaches that MB135 human myoblasts transduced with a lentivirus encoding DUX4 exhibited a reduction in MHC Class I expression (Figure 4). Furthermore, Chew teaches that this reduction in MHC Class I expression was also found in other studies using human WS236 myoblasts transfected with DUX4-expressing plasmids and in DUX4+ myoblasts following induction of differentiation for myoblasts that spontaneously express DUX4 (Figure 4). Chew teaches that DUX4 is a cell-intrinsic suppressor of MHC class I expression (page 664, column 1, paragraph 2-page 665, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the iPSCs with increased DUX4 expression of the combined teachings of ‘300 and Tapscott by including additional modifications to B2M, CIITA, and CD47 to make the iPSC cells hypoimmune, as identified by Schrepfer to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to modify with a reasonable expectation of success because Schrepfer teaches that immune rejection of iPSCs decreases the likelihood of successful, large-scale engineering of compatible patient-specific tissues for treatment of patients. Furthermore, Chew teaches that DUX4 expression reduces MHC class I expression. Therefore, B2M inactivation and DUX4 overexpression both downregulate MHC class I expression, As such, it would have been obvious to further modify the cell of Tapscott to further decrease MHC class I expression. MPEP 2144.06 states "It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from their having been individually taught in the prior art." In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980) (citations omitted). Therefore, it would have been obvious to make the cells of Tapscott hypoimmune through the additional modifications of Schrepfer to increase the likelihood that they have a therapeutic effect in patients. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding the limitation wherein the increase expression of Dux4 reduces MHC class I HLA expression, as stated supra, Chew teaches that that DUX4 is a cell-intrinsic suppressor of MHC class I expression (page 664, column 1, paragraph 2-page 665, column 1, paragraph 1).
Regarding claims 12 and 20, as stated supra, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369) and ‘300 claims a virus containing the polycistronic vector includes lentiviral vectors.
Regarding claim 13, ‘300 is silent as to the sequence of DUX4 used.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content because this was shown to enhance transgene expression of the hDUX4 vector (paragraph 00326). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the codon altered DUX4 sequence (SEQ ID NO: 82) of Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use SEQ ID NO: 82 with a reasonable expectation of success because Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content and this was shown to enhance transgene expression of the hDUX4 vector. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
Regarding claim 14, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
Regarding claim 17, as stated supra, Schrepfer teaches that they transduced the B2M and CIITA inactivated cells with a lentivirus encoding CD47 (Example 6).
Regarding claim 30, ‘300, Tapscott, and Chew do not teach that the cell comprises an inducible suicide switch.
However, Schrepfer teaches that inducible suicide switches can be included in the hypoimmunogenic pluripotent cells as a safety switch that can cause the death of the hypoimmunogenic pluripotent cells should they grow and divide in an undesired manner. The "suicide gene" ablation approach includes a suicide gene in a gene transfer vector encoding a protein that results in cell killing only when activated by a specific compound (i.e. inducible) (paragraphs 00177-00178).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the hypoimmunogneic iPSCs with increased DUX4 expression of the combined teachings of ‘300, Tapscott, Schrepfer, and Chew by including an inducible suicide switch, as identified by Schrepfer to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to modify with a reasonable expectation of success because Schrepfer teaches that inducible suicide switches can be included in the hypoimmunogenic pluripotent cells as a safety switch that can cause the death of the hypoimmunogenic pluripotent cells should they grow and divide in an undesired manner. Therefore, it would have been obvious to include an inducible suicide switch in these cells to improve their safety for treating patients in case of undesired growth and division (i.e. potential cancerous growth). Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 31, as stated supra, ‘300 is silent as to the cell type but Tapscott and Schrepfer teach that they modified iPSCs.
This is a provisional nonstatutory double patenting rejection.
Claims 1, 4, 21-23, 26, and 28-29 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 333-334 and 349-350 of copending Application No. 18/579300, World Intellectual Property Organization Application No. 2018073787 (Tapscott), World Intellectual Property Organization Application No. 2018132783 (Schrepfer), and Chew et al. (Developmental Cell 50: 658–671. 2019 as applied to claims 1 and 4 above, and further in view of Torres et al. (Gene Therapy 21: 343-352. 2014).
Regarding claims 21, 26, and 28-29, the teachings of ‘300, Tapscott, Schrepfer, and Chew are as discussed above.
The combined teachings of ‘300, Tapscott, Schrepfer, and Chew do not teach wherein the modification to increase DUX4 expression and/or CD47 expression comprises introducing a polynucleotide sequence encoding DUX4 and/or CD47 into a selected locus of the cell.
However, Torres teaches that transgenesis procedures in which the position and dosage of the inserted transgene are uncontrolled can lead to unpredictable effects due to disruption of host gene function, compromising data interpretation and placing severe limits on the applicability of this technology. This leads to unpredictable outcomes that compromise data interpretation in research contexts and severely limits the potential clinical application of these technologies. To overcome these problems, procedures for gene gain- or loss-of-function must avoid all genome effects other than the desired modification, such as single-copy insertion at a specific genomic locus. Torres teaches that the ideal sites for transgene insertion are ‘safe harbours’, sites susceptible to disruption and that support transcriptional activity with minimal interference in host gene function. The AAVS1 locus, mapping to chromosome 19 and encoding the PPP1R12C gene, is widely regarded as innocuous for targeting. Disruption of PPP1R12C by zinc-finger nucleases is safe and does not alter the pluripotency of human induced pluripotent stem cells (hiPSCs). The AAVS1 locus thus displays the two essential characteristics of a transgene safe-harbour (page 343, column 1, paragraph 1-page 344, column 1, paragraph 1 and page 349, column 1, paragraphs 3-4).
Torres teaches that they used integrase deficient lentiviruses to yield single site-specific recombination of a selectable donor cassette (TRINA) at the ‘safe-harbour’ AAVS1 locus previously edited by zinc-finger nuclease to contain an acceptor site (KAS2.0). Their method provides an efficient, simple and inexpensive methodology for replacing cassettes in the AAVS1 locus (whole document).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the Lentivirus mediated random integration method of increasing expression of DUX4 and/or CD47 of the combined teachings of ‘300, Tapscott, Schrepfer, and Chew with the integrase deficient lentivirus mediated method of site specific integration into the AAVS1 safe harbor locus of Torres to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to substitute with a reasonable expectation of success because Torres teaches that random integration methods have the distinct disadvantage of unpredictable effects due to disruption of host gene function due to uncontrolled positioning and dosage of the inserted transgene that severely limits the potential clinical application of these technologies. However, site specific insertion at a specific genomic locus can overcome these problems while maintaining the pluripotency of human induced pluripotent stem cells (hiPSCs). Therefore, it would have been obvious to use the method of Torres to ensure site specific integration into the AAVS1 safe harbor locus to improve clinical applicability of the iPSCs of Tapscott and Schrepfer. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 22, as stated supra, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
Regarding claim 23, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
This is a provisional nonstatutory double patenting rejection.
Claims 1, 3-4 and 31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 9, 38, 76, 117, and 313 of copending Application No. 18/682798 (reference application) as evidenced by Chew et al. (Developmental Cell 50: 658–671. 2019). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding claims 1 and 3-4, ‘798 claims an engineered cell with reduced MHC class I and MHC class II expression and increased DUX4 expression, wherein the modifications to reduce cell surface expression of MHC class I is by inactivation of B2M gene activity, wherein the modifications to reduce cell surface expression of MHC class II molecules is by inactivating expression of CIITA, and CD47 expression is increased (claims 1, 9, 38, and 76).
Chew evidences that MB135 human myoblasts transduced with a lentivirus encoding DUX4 exhibited a reduction in MHC Class I expression (Figure 4). Furthermore, Chew evidences that this reduction MHC Class I expression was also found in other studies using human WS236 myoblasts transfected with DUX4-expressing plasmids and in DUX4+ myoblasts following induction of differentiation for myoblasts that spontaneously express DUX4 (Figure 4). Additionally, the Applicant’s specification discloses that exogenous expression of DUX4 in iPSCs led to reduced MHC class I expression. Therefore, although ‘798 is silent regarding DUX4 causing reduced expression of MHC class I in their transduced cells, it naturally flows that the cells of ‘798 with increased expression of DUX4 would also have reduced MHC class I expression caused by the increased DUX4 expression.
Regarding claim 31, ‘798 claims that the engineered cell can be a differentiated cell (claims 117 and 313).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1, 12-14, 17, 20, and 31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 9, 38, 76, 117, and 313 of copending Application No. 18/682798 (reference application) as applied to claim 1 above and further in view of World Intellectual Property Organization Application No. 2018073787 (Tapscott), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016).
‘798 is silent as to the cell type of the engineered cell.
Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (Example 3 (pages 109-127), paragraph 00369, and claims 1, 4, and 19-23). Tapscott teaches that they want to use their cell overexpressing DUX4 to treat diseases in humans (paragraphs 0024-0025).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used an iPSC as the cell with increased expression of DUX4 as identified by Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use an iPSC as the cell with increased expression of DUX4 with a reasonable expectation of success because Tapscott has successfully reduced to practice that iPSCs can be transduced to increase DUX4 expression and identifies that these cells may be useful in treating diseases. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claims 12 and 20, the teachings of ‘798 are as discussed above.
‘798 is silent as to the method of introducing the transgenes to the cell.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (Example 3 (pages 109-127), paragraph 00369, and claims 1, 4, and 19-23).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used a lentiviral vector to express DUX4 in iPSCs as identified by Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use a lentiviral vector with a reasonable expectation of success because Tapscott has successfully reduced to practice that lentiviral vectors can be used to express transgenes in an iPSC cell Therefore, it would have been obvious to use a lentivirus to introduce a DUX4 transgene into iPSCs. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 13, ‘798 is silent as to the sequence of DUX4 used.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content because this was shown to enhance transgene expression of the hDUX4 vector (paragraph 00326). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the codon altered DUX4 sequence (SEQ ID NO: 82) of Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use SEQ ID NO: 82 with a reasonable expectation of success because Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content and this was shown to enhance transgene expression of the hDUX4 vector. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
Regarding claim 14, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
Regrading claim 31, Tapscott teach that they used iPSCs
This is a provisional nonstatutory double patenting rejection.
Claims 1, 4, 17, and 30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 9, 38, 76, 117, and 313 of copending Application No. 18/682798 (reference application) as applied to claims 1 and 4 above and further in view of World Intellectual Property Organization Application No. 2018132783 (Schrepfer).
Regarding claim 17, as stated supra, Schrepfer teaches that they transduced the B2M and CIITA inactivated cells with a lentivirus encoding CD47 (Example 6).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used a lentiviral vector to express CD47 as identified by Schrepfer to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use a lentiviral vector with a reasonable expectation of success because Schrepfer has successfully reduced to practice that lentiviral vectors can be used to express transgenes in cells Therefore, it would have been obvious to use a lentivirus to introduce a CD47 transgene into cells. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 30, ‘798 does not teach that the cell comprises an inducible suicide switch.
However, Schrepfer teaches that inducible suicide switches can be included in the hypoimmunogenic pluripotent cells as a safety switch that can cause the death of the hypoimmunogenic pluripotent cells should they grow and divide in an undesired manner. The "suicide gene" ablation approach includes a suicide gene in a gene transfer vector encoding a protein that results in cell killing only when activated by a specific compound (i.e. inducible) (paragraphs 00177-00178).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the cells of ‘798 by including an inducible suicide switch, as identified by Schrepfer to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to modify with a reasonable expectation of success because Schrepfer teaches that inducible suicide switches can be included in cells as a safety switch that can cause the death of the cells should they grow and divide in an undesired manner. Therefore, it would have been obvious to include an inducible suicide switch in these cells to improve their safety for treating patients in case of undesired growth and division (i.e. potential cancerous growth). Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 31, as stated supra, ‘798 is silent as to the cell type but Schrepfer teaches that they modified iPSCs.
This is a provisional nonstatutory double patenting rejection.
Claims 1,4, 21, 26, and 28-29 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 9, 38, 76, 117, and 313 of copending Application No. 18/682798 (reference application) as applied to claims 1 and 4 above and further in view of Torres et al. (Gene Therapy 21: 343-352. 2014).
The teachings of ‘798 are as discussed above.
‘798 does not teach wherein the modification to increase DUX4 expression and/or CD47 expression comprises introducing a polynucleotide sequence encoding DUX4 and/or CD47 into a selected locus of the cell.
However, Torres teaches that transgenesis procedures in which the position and dosage of the inserted transgene are uncontrolled can lead to unpredictable effects due to disruption of host gene function, compromising data interpretation and placing severe limits on the applicability of this technology. This leads to unpredictable outcomes that compromise data interpretation in research contexts and severely limits the potential clinical application of these technologies. To overcome these problems, procedures for gene gain- or loss-of-function must avoid all genome effects other than the desired modification, such as single-copy insertion at a specific genomic locus. Torres teaches that the ideal sites for transgene insertion are ‘safe harbours’, sites susceptible to disruption and that support transcriptional activity with minimal interference in host gene function. The AAVS1 locus, mapping to chromosome 19 and encoding the PPP1R12C gene, is widely regarded as innocuous for targeting. Disruption of PPP1R12C by zinc-finger nucleases is safe and does not alter the pluripotency of human induced pluripotent stem cells (hiPSCs). The AAVS1 locus thus displays the two essential characteristics of a transgene safe-harbour (page 343, column 1, paragraph 1-page 344, column 1, paragraph 1 and page 349, column 1, paragraphs 3-4).
Torres teaches that they used integrase deficient lentiviruses to yield single site-specific recombination of a selectable donor cassette (TRINA) at the ‘safe-harbour’ AAVS1 locus previously edited by zinc-finger nuclease to contain an acceptor site (KAS2.0). Their method provides an efficient, simple and inexpensive methodology for replacing cassettes in the AAVS1 locus (whole document).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the Lentivirus mediated random integration method of increasing expression of DUX4 and/or CD47 of’798 with the integrase deficient lentivirus mediated method of site specific integration into the AAVS1 safe harbor locus of Torres to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to substitute with a reasonable expectation of success because Torres teaches that random integration methods have the distinct disadvantage of unpredictable effects due to disruption of host gene function due to uncontrolled positioning and dosage of the inserted transgene that severely limits the potential clinical application of these technologies. However, site specific insertion at a specific genomic locus can overcome these problems. Therefore, it would have been obvious to use the method of Torres to ensure site specific integration into the AAVS1 safe harbor locus to improve clinical applicability of the cells. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1 and 21-23 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 9, 38, 76, 117, and 313 of copending Application No. 18/682798 (reference application) and Torres et al. (Gene Therapy 21: 343-352. 2014) as applied to claims 1 and 21 above and further in view of World Intellectual Property Organization Application No. 2018073787 (Tapscott), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016).
Regarding claim 22, ‘798 is silent as to the sequence of DUX4 used.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content because this was shown to enhance transgene expression of the hDUX4 vector (paragraph 00326). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the codon altered DUX4 sequence (SEQ ID NO: 82) of Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use SEQ ID NO: 82 with a reasonable expectation of success because Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content and this was shown to enhance transgene expression of the hDUX4 vector. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
Regarding claim 23, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1, 3-4, 12, 17, 20-21, 26, and 28-31 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1, 10-11, 19, 29-30, 53-55, 58, 67-68, 84-86, 89, 95-98, 163, and 167 of copending Application No. 18/845742 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other.
‘742 claims an engineered cell comprising reduced expression of MHC class I and/or class II human leukocyte antigens and a modification to increase expression of Dux4 (claims 1, 19, 29-30, 58, 67-68, and 89). The cell is further modified to increase CD47 expression and inactivate B2M and CIITA by a rare-cutting endonuclease including a Cas protein (claims 29-30, 53-55, 58, 67-68, 84-86, and 89). ‘742 claims that the modification to increase Dux4 and CD47 can integrated into the genome using lentiviruses (claims 89 and 95). ‘742 claims that the modification to increase Dux4 and CD47 comprises introducing a polynucleotide sequence encoding Dux4 and CD47 into a selected locus of the cell (claims 96-98). The selected locus can be a safe harbor site, such as AAVS1 (claims 98). ‘742 claims the cell further comprises an inducible suicide switch (claims 163 and 167). ‘742 claims the cell can be an iPSC (claims 10-11).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 1, 12-14, and 21-23 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5, 8-10, 22-27 of copending Application No. 18/845742 (reference application) as applied to claims 1 and 21 and further in view of World Intellectual Property Organization Application No. 2018073787 (Tapscott), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016).
Regarding claims 13 and 22, the teachings of ‘742 are as discussed above.
‘742 is silent as to the sequence of DUX4 used.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content because this was shown to enhance transgene expression of the hDUX4 vector (paragraph 00326). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the codon altered DUX4 sequence (SEQ ID NO: 82) of Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use SEQ ID NO: 82 with a reasonable expectation of success because Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content and this was shown to enhance transgene expression of the hDUX4 vector. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claims 14 and 23, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1 and 3-4 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 144-150 of copending Application No. 18/945839 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other.
‘839 claims an engineered cell comprising reduced expression of MHC class I and/or MHC class II molecules, wherein the engineered cell does not express B2M and CIITA, and wherein the cell has increased expression of DUX4 and CD47 (claims 144-150).
Claims 1, 12-14, 20, and 31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 144-150 of copending Application No. 18/945839 (reference application) as applied to claim 1 above and further in view of World Intellectual Property Organization Application No. 2018073787 (Tapscott), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016).
‘839 is silent as to the cell type of the engineered cell.
Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (Example 3 (pages 109-127), paragraph 00369, and claims 1, 4, and 19-23). Tapscott teaches that they want to use their cell overexpressing DUX4 to treat diseases in humans (paragraphs 0024-0025).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used an iPSC as the cell with increased expression of DUX4 as identified by Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use an iPSC as the cell with increased expression of DUX4 with a reasonable expectation of success because Tapscott has successfully reduced to practice that iPSCs can be transduced to increase DUX4 expression and identifies that these cells may be useful in treating diseases. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claims 12 and 20, the teachings of ‘839 are as discussed above.
‘839 is silent as to the method of introducing the transgenes to the cell.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (Example 3 (pages 109-127), paragraph 00369, and claims 1, 4, and 19-23).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used a lentiviral vector to express DUX4 in iPSCs as identified by Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use a lentiviral vector with a reasonable expectation of success because Tapscott has successfully reduced to practice that lentiviral vectors can be used to express transgenes in an iPSC cell Therefore, it would have been obvious to use a lentivirus to introduce a DUX4 transgene into iPSCs. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 13, ‘839 is silent as to the sequence of DUX4 used.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content because this was shown to enhance transgene expression of the hDUX4 vector (paragraph 00326). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the codon altered DUX4 sequence (SEQ ID NO: 82) of Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use SEQ ID NO: 82 with a reasonable expectation of success because Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content and this was shown to enhance transgene expression of the hDUX4 vector. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
Regarding claim 14, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
Regrading claim 31, Tapscott teach that they used iPSCs
This is a provisional nonstatutory double patenting rejection.
Claims 1, 4, 17, and 30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 144-150 of copending Application No. 18/945839 (reference application) as applied to claims 1 and 4 above and further in view of World Intellectual Property Organization Application No. 2018132783 (Schrepfer).
Regarding claim 17, as stated supra, Schrepfer teaches that they transduced the B2M and CIITA inactivated cells with a lentivirus encoding CD47 (Example 6).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used a lentiviral vector to express CD47 as identified by Schrepfer to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use a lentiviral vector with a reasonable expectation of success because Schrepfer has successfully reduced to practice that lentiviral vectors can be used to express transgenes in cells Therefore, it would have been obvious to use a lentivirus to introduce a CD47 transgene into cells. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 30, ‘839 does not teach that the cell comprises an inducible suicide switch.
However, Schrepfer teaches that inducible suicide switches can be included in the hypoimmunogenic pluripotent cells as a safety switch that can cause the death of the hypoimmunogenic pluripotent cells should they grow and divide in an undesired manner. The "suicide gene" ablation approach includes a suicide gene in a gene transfer vector encoding a protein that results in cell killing only when activated by a specific compound (i.e. inducible) (paragraphs 00177-00178).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the cells of ‘839 by including an inducible suicide switch, as identified by Schrepfer to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to modify with a reasonable expectation of success because Schrepfer teaches that inducible suicide switches can be included in cells as a safety switch that can cause the death of the cells should they grow and divide in an undesired manner. Therefore, it would have been obvious to include an inducible suicide switch in these cells to improve their safety for treating patients in case of undesired growth and division (i.e. potential cancerous growth). Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding claim 31, as stated supra, ‘839 is silent as to the cell type but Schrepfer teaches that they modified iPSCs.
This is a provisional nonstatutory double patenting rejection.
Claims 1,4, 21, 26, and 28-29 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 144-150 of copending Application No. 18/945839 (reference application) as applied to claims 1 and 4 above and further in view of Torres et al. (Gene Therapy 21: 343-352. 2014).
The teachings of ‘839 are as discussed above.
‘839 does not teach wherein the modification to increase DUX4 expression and/or CD47 expression comprises introducing a polynucleotide sequence encoding DUX4 and/or CD47 into a selected locus of the cell.
However, Torres teaches that transgenesis procedures in which the position and dosage of the inserted transgene are uncontrolled can lead to unpredictable effects due to disruption of host gene function, compromising data interpretation and placing severe limits on the applicability of this technology. This leads to unpredictable outcomes that compromise data interpretation in research contexts and severely limits the potential clinical application of these technologies. To overcome these problems, procedures for gene gain- or loss-of-function must avoid all genome effects other than the desired modification, such as single-copy insertion at a specific genomic locus. Torres teaches that the ideal sites for transgene insertion are ‘safe harbours’, sites susceptible to disruption and that support transcriptional activity with minimal interference in host gene function. The AAVS1 locus, mapping to chromosome 19 and encoding the PPP1R12C gene, is widely regarded as innocuous for targeting. Disruption of PPP1R12C by zinc-finger nucleases is safe and does not alter the pluripotency of human induced pluripotent stem cells (hiPSCs). The AAVS1 locus thus displays the two essential characteristics of a transgene safe-harbour (page 343, column 1, paragraph 1-page 344, column 1, paragraph 1 and page 349, column 1, paragraphs 3-4).
Torres teaches that they used integrase deficient lentiviruses to yield single site-specific recombination of a selectable donor cassette (TRINA) at the ‘safe-harbour’ AAVS1 locus previously edited by zinc-finger nuclease to contain an acceptor site (KAS2.0). Their method provides an efficient, simple and inexpensive methodology for replacing cassettes in the AAVS1 locus (whole document).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the Lentivirus mediated random integration method of increasing expression of DUX4 and/or CD47 of ‘839 with the integrase deficient lentivirus mediated method of site specific integration into the AAVS1 safe harbor locus of Torres to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to substitute with a reasonable expectation of success because Torres teaches that random integration methods have the distinct disadvantage of unpredictable effects due to disruption of host gene function due to uncontrolled positioning and dosage of the inserted transgene that severely limits the potential clinical application of these technologies. However, site specific insertion at a specific genomic locus can overcome these problems. Therefore, it would have been obvious to use the method of Torres to ensure site specific integration into the AAVS1 safe harbor locus to improve clinical applicability of the cells. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1 and 21-23 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 144-150 of copending Application No. 18/945839 (reference application) and Torres et al. (Gene Therapy 21: 343-352. 2014) as applied to claims 1 and 21 above and further in view of World Intellectual Property Organization Application No. 2018073787 (Tapscott), as evidenced by Jagannathan et al. (Human Molecular Genetics 25: 4419-4431. 2016).
Regarding claim 22, ‘839 is silent as to the sequence of DUX4 used.
However, Tapscott teaches that they transduced human induced pluripotent stem cells (iPSCs) with a lentivirus encoding codon altered DUX4 (DUX4CA) (paragraph 00369). Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content because this was shown to enhance transgene expression of the hDUX4 vector (paragraph 00326). The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the codon altered DUX4 sequence (SEQ ID NO: 82) of Tapscott to arrive at the instantly claimed invention. One of ordinary skill in the art would have a reason to use SEQ ID NO: 82 with a reasonable expectation of success because Tapscott teaches that the hDUX4 transgenes were codon-altered to decrease overall CpG content and this was shown to enhance transgene expression of the hDUX4 vector. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
The codon altered sequence of Tapscott corresponds to SEQ ID NO: 82 and SEQ ID NO: 82 is 100% identical to the codon altered sequence of Jagannathan (Supplementary Figure 2. Jagannathan evidences that the codon-altered DUX4 encoding sequence was re-coded to reduce the total number of CpG sites while preserving the protein sequence (page 4420, column 1, paragraph 4-column 2, paragraph 2, Figure 1, and page 4427, column 1, paragraph 2-page 4428, column 1, paragraph 1).
Regarding claim 23, the codon altered DUX4 of SEQ ID NO: 82 of Tapscott (paragraphs 00152-00154) is 100% identical to SEQ ID NO: 1 of the instant application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant's arguments filed October 27, 2025, are acknowledged.
Applicant argues that MPEP § 804 (I)(B)(1)(b)(i) states that "[i]f a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earlier patent term filing date, the examiner should withdraw the rejection in the application having the earlier patent term filing date and permit that application to issue as a patent." In view of the amended claims and preceding remarks, the provisional nonstatutory double rejections should be the only remaining rejections in the Application. Therefore, because the present application has the earlier patent term filing date relative to any of the reference applications, the provisional rejections for nonstatutory double patenting should be withdrawn. Accordingly, Applicant respectfully requests that the Office withdraw the rejections.
Applicant's arguments have been fully considered but they are not persuasive.
There remains a 103 rejection. Therefore, the NSDP rejection is not the only rejection and is, accordingly, maintained for each NSDP rejection made above.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/KEENAN A BATES/Examiner, Art Unit 1631
/JAMES D SCHULTZ/Supervisory Patent Examiner, Art Unit 1631