DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 01/28/2026 has been entered.
Claim Status
Claims 3,8,14, and 16 are amended.
Claims 1-2 are cancelled.
Claims 3,8-9,12,12,16, 21, and 24 are under examination.
Rejections Withdrawn
Claim Rejections - 35 USC § 103
The rejection of claims 1,3, 8,9,12,14,16,21,and 24 are under 35 U.S.C. 103 as being unpatentable over by Wu et al (iScience, 2019 ), in view of Rong et al (The Journal of Biological Chemistry, 2012), Valamehr et al ( WO 2017/ 079673 A1), Liang et al (Nature,2018), and Lo et al (Biotechniques,2017), as evidenced by Straathof et al ( Gene therapy, 2005) is withdrawn in view of Applicants claim amendment.
Response to Amendments
Applicant’s arguments have been carefully considered and found persuasive as noted above. The new ground of rejection below addresses the deficiencies raised by Applicant with respect to the amended claims.
New Ground of Rejections
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 16 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claim 16, the claim recites the limitation "the genetically engineered cell " in claim 1. It should be noted that claim 1 is cancelled. Therefore, the limitation lacks antecedent basis.
Claim Interpretation
It should be noted that the optional recitations in claims 9 and 16 is not given patentable weight as they are not required by the subject claim.
Claim Rejections - 35 USC § 103
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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
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 3, 8-9,12,14, 21, and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Rong et al (The Journal of Biological Chemistry, 2012), in view of Straathof et al ( Gene therapy, 2005), and Valamehr et al ( WO 2017/ 079673 A1).
Regarding claims 8 and 14, Rong et al teach a safety switch system encoding the herpes simplex thymidine kinase (TK) suicide gene to specifically eradicate undifferentiated stem cells and prevent teratoma formation of human embryonic stem cells (hESCs). The method of Rong et al involves the in-frame integration of the TK gene expression cassette into the 3’-untranslated region of the endogenous NANOG gene locus of hESCs to allow the normal expression of the NANOG gene in hESCs.(See Fig. 1, A and B). Rong et al state that “NANOG is a critical pluripotency factor specifically expressed in hESCs but rarely in their differentiated derivatives”. (See abstract). Rong et al teach that utilizing the BAC-based strategy for gene targeting enables high efficiency of homologous recombination in hESCs as it prevents random integration. (See the 1st paragraph of the Results section on page 32340). Rong et al also demonstrate that using the BAC-based mediated homologous recombination for gene targeting to the NANOG locus efficiently eliminated the teratoma risk associated with hESCs without affecting their differentiated derivatives. ( See Figs.2-3). Rong et al also state that “ our strategy could be effectively applied to the clinical development of hESCs-based human cell therapy. (See abstract).
Taken together, the system of Rong et al involves the in-frame insertion of a suicide gene into NANOG genomic locus, which is only active during the pluripotent state. However, Rong et al do not teach a first safety switch encoding for an inducible caspase protein lacking native caspase activation domain, nor do they teach a second suicide gene designed to eradicate the entire cell product, with the genomic insertion locus located within a ubiquitously expressed gene.
Straathof et al supplement Rong et al by teaching away from using TK as a safety switch in adoptive T-cell therapy due to unwelcomed side effects. According to Straathof et al, TK is immunogenic, limiting its application in cell therapy, and the use of ganciclovir as a prodrug precludes the use of ganciclovir for the treatment of cytomegalovirus infection. ( See the introduction section-1st column-2nd paragraph- on page 4247). To address these difficulties, Straathof et al developed a safer switch to replace TK, wherein the switch comprises of a fusion protein between caspase 9 lacking the activation domain and the human FKBP containing F36V mutation (iCasp9), with the safety switch being activated by AP1903 (or analogs). It should be noted that Straathof et al referred to this construct as F-Casp9/iCasp9M ,which reads on the safety switch of claims 8 and 14. (See Straathof et al, Fig.2A, Materials and methods “Plasmids”, page 4248, and the first paragraph of the results section on page 4250 ). According to Straathof et al, iCasp9M has several advantages over other safety switches, including TK. First, the iCasp9M has a lower potential immunogenicity as it consists of human gene products. Second, administration of the pro- drug AP1903 (or analogs ) has proven safe at the required dose for optimum deletional effect, and, unlike ganciclovir, has no other biologic effects in vivo. ( See abstract, 1st column-2nd paragraph of the introduction-on page 4247, and the last paragraph of the discussion on page 4253). Therefore, it would have been obvious for a person of ordinary skill in the art to substitute the safety switch of Rong with the safety switch of Straathof et al, because Straathof et al clearly suggest the use of iCasp9M over TK in cell therapy, providing a motivation to a person of ordinary skill in the art to use iCasp9M.
It is submitted that neither Rong nor Straathof teach a genetically engineered cell comprising a second safety switch.
Valamehr et al supplement Rong et al and Straathof et al by teaching methods for producing genetically engineered iPSCs containing at least two safety switches integrated into the genome and operably linked to any of the following endogenous promoters: AAVS 1, CCR5, ROSA26, collagen, HTRP, HI 1, beta-2 microglobulin, GAPDH, TCR or RUNXl. (See claims 1,10-11, and paragraphs [000161], [000164], [000204]). According to Valamehr et al, the selected site for in-frame insertion can be a safe harbor locus, a highly expressive locus, or a temporally expressed locus. (See claim 7). According to Valamehr et al, potential safety switches that can be used include, but are not limited to, caspase 9 and API 903; thymidine kinase (TK) and ganciclovir (GCV); or cytosine deaminase (CD) and 5-fluorocytosine (5-FC). (See paragraph [000166]. Taken together, Valamehr et al teach methods for producing genetically engineered iPSCs containing at least two safety switches integrated at a designated genomic locus. It is submitted that Valamehr et al do not specifically teach that the first locus of integration is at a locus that selectively expressed in pluripotent state or the second is at ubiquitously expressed locus; however, the teachings that state the site of integration is at “highly expressive locus” or “ temporally expressed locus” should read on the ubiquitously and selectively expressed terms, respectively.
Therefore, claim 1 would have been obvious to one of ordinary skill in the art, as there was some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. One with ordinary skill in the art at the time the invention was filed would be motivated to combine the teachings of Rong, Straathof, and Valamehr to utilize a dual safety system in which the first safety switch enables for the killing of the undifferentiated stem cells while the second safety switch allows for the eradication of all cell products in the event of an awry scenario. Because Rong et al in view of Straathof et al render obvious a safety switch that can be utilized to eradicate undifferentiated stem cells, reducing the danger of teratoma formation. Valamehr et al teach methods for producing genetically engineered iPSCs containing at least two safety switches integrated at specific sites, and clearly suggest that the site of integration could be at a highly expressive locus, or a temporally expressed locus. Thus one would have been motivated to combine the teachings of prior arts and utilize a dual safety system for the control and prompt eradication of cell products. There is a reasonable expectation of success in selecting a first integration locus at a selectively expressed genomic locus such as NANOG, as disclosed by Rong, and a second integration locus at a ubiquitously or highly expressed locus, as suggested by Valamehr et al, because doing so would allow for the timely and controlled eradication of stem cells and their products in the event of awry scenario occurring at different differentiation state. A double suicide system for each differentiation level is preferable since single suicide gene has the potential to induce incomplete cell elimination. See MPEP 2143 (I)(G).
Regarding claim 3, following the discussion of claim 8 above, the combined teachings of Rong, Straathof, and Valamehr render obvious claim 8. None of the cited prior arts teach the exact killing ratio recited in instant claim; however based on the discussion above, the claimed outcome is presumed to be inherent in the combined teachings of Rong et al, Straathof, and Valamehr as this advantage would flow naturally from following the combined teachings of prior arts. As per the MPEP “(The recitation of an additional advantage associated with doing what the prior art suggests does not lend patentability to an otherwise unpatentable invention.)"
Regarding claims 9 and 12, following the discussion above, the teachings of Rong et al in view of Valamehr et al render obvious the use of dual safety system in cell therapy. Valamehr et al suggest several locus at which the safety switches can be integrated, one of which is collagen, which is a cytoskeleton protein, this reads on claim 9. ( See claims 7-8). Valamehr et al also teach the use of a linker sequence encoding a self-cleaving peptide, where the self-cleaving peptide is 2A, which allows for the production of two distinct proteins to be produced from a single transcript, this reads on claim 12. ( See claims 2-3).
Regarding claims 21 and 24, following the discussion of claim 8, the combined teachings of Rong, Straathof, and Valamehr render obvious the use of a dual safety system in cell therapy to control cell fate at different differentiation states. As discussed above, the teachings of Rong et al in view of Straathof et render obvious the utilization of NANOG locus for the in-frame integration of a suicide gene system comprising caspase 9 lacking the activation domain and fused to the FKBPF36V, whereas the teachings of Rong et al in view of Valamehr et al render obvious a genetically engineer cell comprising dual safety-switches, wherein one of the safety switches could be thymidine kinase (TK) and ganciclovir. (See paragraph [000166]. It is submitted that Valamehr et al do not specifically teach that the first locus of integration is at a locus that selectively expressed in pluripotent state or the second is at ubiquitously expressed locus; however, the teachings that state the site of integration is at “highly expressive locus” or “ temporally expressed locus” should read on the ubiquitously and selectively expressed terms, respectively. It is also submitted that Valamehr et al do not specify the type of the first or second switches. However, Valamehr et al provides a list of safety switches that one with ordinary skill in the art can choose from when making a genetically engineered cell comprising a dual safety system, wherein one of the safety switches could be TK.
Therefore, it would have been prima facie obvious to one with ordinary skill in the art at the time the invention was filed to combine the teachings of Rong, Straathof, and Valamehr to utilize a dual safety system, where the first safety switch protein is induced casp 9 fused to FKBPF36V that is activated by a first activating agent e.g. AP1903, and a second safety switch protein comprises of TK that is activated by a second agent e.g. ganciclovir, to improve the safety of cell-based therapy. Because the combined teachings of Rong and Straathof render obvious the use of NANOG locus for the in-site integration of a safety switch composed of inducible caspase 9 fused to FKBPF36V to eradicate undifferentiated stem cells, reducing the danger of teratoma formation. Valamehr et al teach dual safety-switches and suggest that TK is an acceptable suicide gene for induced cell death. Thus, one of ordinary skill in the art who had reviewed Rong and Straathof, could have come across Valamehr and immediately noticed the strong possibility of using two safety switches, instead of only one, would have the predictable results of generating genetically engineered cell that can be safely used in cell-based therapy. In other words, claim 24 is combining prior art elements according to known methods to yield predictable result, namely the predictable result being the generation of genetically engineered cell comprising dual-safety switches. See MPEP 2143 (I)(A).
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Rong et al (The Journal of Biological Chemistry, 2012), in view of Straathof et al ( Gene therapy, 2005), and Valamehr et al ( WO 2017/ 079673 A1) as applied to claims 3, 8-9,12,14, 21, and 24, and further in view of Stavrou et al ( Molecular Therapy, 2017).
Regarding claim 16, the teachings of Rong, Straathof, and Valamehr are set forth above. Straathof et al teach a safety switch comprising an inducible caspase 9 fused to the human FKBP containing F36V mutation (i.e. iCasp9), which is activated by AP1903. It is submitted that none of the cited prior arts teach an inducible caspase 9 that is fused to FKBP and FRB.
Stavrou et al supplement Rong and Straathof by teaching an obvious variant of a safety switch comprising of an inducible caspase 9 that is fused to FKBP12 and FRB and can be activated with rapamycin, wherein the rapamycin induced activation requires hetero-dimerization of the FRB-caspase 9 fusion and the FKBP-caspase 9 fusion. ( See abstract, and Fig.1B). According to Stavrou et al, a practical limitation of iCasp9 ( i.e. casp9 fused to mutated FKBP) is the requirement for an experimental small molecule that is not a licensed pharmaceutical agent, greatly limiting the broad utility of iCasp9, whereas rapamycin is readily available, and well tolerated dimerizing drug that is licensed for commercial sale worldwide with a good biodistribution. ( See 1st column- 2nd and 4th paragraph- on page 1273). Stavrou et al also state that “ In comparison with iCasp9, rapamycin-induced caspase 9 shows equivalent function to iCasp9 but with the convenience of using an off-the-shelf pharmaceutical agent. ( See the 1st column-1st paragraph-on page 1274). Therefore, it would have been prima facie obvious to one with ordinary skill in the art at the time the invention was filed to substitute the safety switch of Straathof et al with the safety switch of Stavrou, because Stavrou et al clearly suggest utilizing a safety switch comprising rapamycin-induced caspase 9, as rapamycin is readily available pharmaceutical agent. In other words, claim 16 is a substitution of one known element for another known element, the elements having equivalent effect, thus the claim is considered obvious absent showing that the result of the substitution yields more than predictable results.
Response to Arguments
Applicant’s arguments, filed 01/02/2026, with respect to the rejection of claims 1,3, 8,9,12,14,16,21,and 24 under 35 U.S.C. 103 as being unpatentable over Wu et al (iScience, 2019 ), in view of Rong et al (The Journal of Biological Chemistry, 2012), Valamehr et al ( WO 2017/ 079673 A1), Liang et al (Nature,2018), and Lo et al (Biotechniques,2017), as evidenced by Straathof et al ( Gene therapy, 2005) have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made over Rong et al in view of Straathof et al, Valamehr et al, and Stavrou et al. ( See the above rejection).
Conclusion
Here is some additional prior arts that is relevant to the subject matter but was not
discussed above.
Qadir et al “ A Double Fail-Safe Approach to Prevent Tumorigenesis and Select Pancreatic β Cells from Human Embryonic Stem Cells” Stem Cell Reports, 2019. Qadir et al teach the generation of a genetically engineered cells harboring two suicide gene cassettes, whose expression results in cell death in the presence of specific pro-drugs. ( See abstract).
Lo et al “Generating stable cell lines with quantifiable protein production using CRISPR/Cas9-mediated knock-in”, Reports,2017. Lo provide a proof-of principal experiment using beta actin (ACBT) gene for locus-specific integration and physiological expression of gene of interest under the control of the ACBT gene promoter. (See abstract, and Fig.2).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FATIMAH KHALAF MATALKAH whose telephone number is (703)756-5652. The examiner can normally be reached Monday-Friday,7:30 am-4:30 pm EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Tracy Vivlemore can be reached on 571-272-2914. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/FATIMAH KHALAF MATALKAH/Examiner, Art Unit 1638
/Tracy Vivlemore/Supervisory Primary Examiner, Art Unit 1638