CTNF 18/279,848 CTNF 101118 DETAILED ACTION Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Priority The instant application, filed on 31 August 2023, claims domestic benefit to US provisional application no. 63/155,295, filed on 03/01/2021 and PCT/US2022/018389, filed on 03/01/2022. Information Disclosure Statement The information disclosure statement (IDS) submitted on 02, April 2024 has been considered by the examiner. Status of Application, Amendments, and/or Claims The response filed on 02, April 2024 has been entered in full. These are the amended claims of the original claim set received on 31 August, 2023. In the amendment, claims 2-7, 9, 10, 13, 18-21, and 70 are amended and claims 8, 11, 12, 15-17, 22, 23, 26-52, 54-57, 59-69, and 71-81 are cancelled. Therefore, claims 1-7, 9, 10, 13, 14, 18-21, 24, 25, 53, 58, and 70 are pending and are the subject of this Office Action. 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. Claim 6 is rejected under 35 U.S.C. 112(b) , as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention. Claim 6 recites the method of claim 1 wherein the inhibitor is a polynucleotide encoding an siRNA molecule. This is unclear as an siRNA itself is a polynucleotide and the definition in the specification which states the term includes an RNA molecule that is transcribed from a DNA molecule (pg.16, lines 27-28) does not redefine the term. For the purpose of further examination and in light of the specification the claim will be interpreted to say, the method of claim 1 wherein the inhibitor is an siRNA molecule. Claim 58 is rejected under 35 U.S.C. 112(b) , as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention. Claim 58 recites “wherein the lentiviral particle comprises VSV-g and envelope proteins. This is unclear as VSV-g is an envelope protein, therefore it is unclear if the lentivirus needs to contain one or more envelope proteins. For the purpose of further examination and in light of the specification which says the lentiviral particles may comprise two or more envelope proteins (pg.21 lines 16-18), the claim will be interpreted to say wherein the lentiviral particle comprises VSV-g and one or more additional envelope proteins. Claim Rejections - 35 USC § 102 07-07-aia AIA 07-07 The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action: A person shall be entitled to a patent unless – 07-08-aia AIA (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention. 07-12-aia AIA (a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention. 07-15 AIA Claim s 1, 2, 3, 10, 13, 14, 18, 19, and 70 are rejected under 35 U.S.C. 102( a)(1) and 35 U.S.C. 102(a)(2 ) as being anticipated by Rosen et al. (WO2019/018603) . In regards to claims 1 and 14 Rosen anticipates a method of T cell populations modified towards a central memory T cell phenotype (pg.72, lines 31-33) in which the T cells are isolated from fresh leukopaks and cultured with IL-2 and anti-CD3/anti-CD28 beads (agents that stimulate expansion) (pg.70, lines 3-13) and then further incubating the cells with a list of inhibitors including a JAK inhibitor (an inhibitor of a negative modulator gene of TCF7) (pg.73, lines 14-16/ Figure 1A) before being modified further by a CAR. Rosen also anticipates a sufficient length of time for modulating immune cells to be no less than 30, 42, 54, 66, 78, or 90 hours (pg.14, lines 20-22). In regards to claim 2 Rosen anticipates a sufficient length of time for modulating immune cells to be no less than 30, 42, 54, 66, 78, or 90 hours (pg.14, lines 20-22). In regards to claim 3 Rosen anticipates the inhibitor being a small molecule inhibitor (pg.31 line 29- pg.32 line 1/ Table 1, compounds 16-19). In regards to claims 10, 18, and 19 Rosen anticipates the use of a JAK inhibitor (negative modulator gene JAK2) and further anticipates the use of specific JAK inhibitors ruxolitinib and pacritinib (Table 1). In regards to claim 13 Rosen anticipates the T cells are isolated from fresh leukopaks (ex-vivo) (pg.70, lines 3-5). In regards to claim 70 Rosen anticipates in vivo functionality in a CD19+ xenograft mice model in which the modified CAR-T cells are delivered to NSG mice bearing Nalm-6-luc CD19+ disseminated tumors (pg.79, lines 17-21) . 07-15 AIA Claim s 1, 9, 20 and 21 are rejected under 35 U.S.C. 102( a)(1) and 35 U.S.C. 102(a)(2 ) as being anticipated by Rosen et al. (US2019/0125795, of record, IDS 04/02/2024, hereafter Rosen(US)) as evidenced by Kim and Lee (2007) STAT1 as a key modulator of cell death Cellular Signaling (19) 454-465 (hereafter Kim and Lee) . In regards to claim 1 Rosen(US) anticipates a method of modifying T cell populations towards a central memory T cell phenotype (pg.29, col 1, lines 5-9) in which the T cells are isolated from fresh leukopaks and cultured with IL-2 and anti-CD3/anti-CD28 beads (agents that stimulate expansion) (pg.27, col 2, 49-60) and then further incubating the cells with a list of inhibitors including a STAT1 inhibitor (an inhibitor of a negative modulator gene of TCF7) (pg.29, col 1, lines 16-21). Rosen also anticipates a sufficient length of time for modulating immune cells to be no less than 30, 42, 54, 66, 78, or 90 hours (pg.14, col 2, lines 12-14). In regards to claims 20 and 21 Rosen teaches the use of a STAT1 inhibitor and further where the STAT1 inhibitor is Fludarabine (pg.29, col 1, lines 16-21/ Table 1). In regards to claim 9 Rosen teaches the use of a STAT1 inhibitor. The STAT1 gene encodes the STAT1 protein which is a transcription factor as evidenced by Kim and Lee which states STAT factors were originally discovered as latent transcriptional factors in the cytoplasm (pg.455, col 1, lines 1-3). Thus, Rosen’s use of a STAT1 inhibitor is the inhibition of a gene which encodes a transcription factor . Claim Rejections - 35 USC § 103 07-20-aia AIA 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. 07-22-aia AIA Claim s 4 and 6 are rejected under 35 U.S.C. 103 as being unpatentable over Rosen as applied to claim 1 above, and further in view of Kurreck (2006) siRNA Efficiency: Structure or Sequence- That is the Question Journal of Biomedicine and Biotechnology (83757) 1-7 (hereafter Kurreck) . Rosen teaches a method of modifying T cell populations towards a central memory T cell phenotype (pg.72, lines 31-33) in which the T cells are isolated, cultured with a stimulating agent, and incubated with a JAK inhibitor (negative modulator gene of TCF7) as outlined above. Further Rosen teaches the JAK inhibitor can be an siRNA (short interfering RNA) (pg.40, lines 7-8). Rosen fails to teach an siRNA sequences comprising at least 10 contiguous nucleotides that is complementary to a genomic sequence of claim 4. Kurreck, however, teaches that siRNAs can be between 19-27 nucleotides and that length has a significant impact on siRNA efficiency (pg.5 col 2 line 16- pg.6 col 1, line 3) and further teaches that siRNA works by binding to the complementary of the target gene RNA in order to disrupt translation of the protein (pg.1 col 1, lines 10-16). Thus, Rosen discloses a method of developing modified T cells wherein T cells are isolated stimulated and contacted with an inhibitor of a negative modulator gene of TCF7 and further teaches this inhibitor can be an siRNA. Kurreck teaches that siRNAs have been studied between 19-27 nucleotides long and that the length of the siRNA impacts its efficiency, further Kurreck teaches the siRNA much be complementary to a target gene in order to interrupt translation of the target protein. Therefore, a person of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to combine the teachings of Rosen with the teachings of Kurreck to use an siRNA inhibitor informed by the teachings of Kurreck to be longer than 10 nucleotides and complementary to the target gene with a reasonable expectation of success to develop an expanded modified T cell population with increased TCF7 expression . 07-22-aia AIA Claim s 5 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Rosen as applied to claim 1 above, and further in view of Seki and Rutz (2018) Optimized RNP transfection for highly efficient CRISPR/Cas9 – mediated gene knockout in primary T cells J. Exp. Med. (215)3 985-997 (hereafter Seki and Rutz) . Rosen teaches a method of modifying T cell populations towards a central memory T cell phenotype (pg.72, lines 31-33) in which the T cells are isolated, cultured with a stimulating agent, and incubated with a JAK inhibitor (negative modulator gene of TCF7) as outlined above. Rosen fails to teach the inhibitor as a complex comprising a CRISPR-associated protein and a guide RNA of a least 10 contiguous and complementary nucleotides of claim 5. Rosen further fails to teach the use of a polynucleotide encoding the complex of claim 7. Seki and Rutz however teach an optimized method of inducing gene knockout using a polynucleotide encoding Cas9 and guide RNA (pg.995, col 2, lines 22-36) with electroporation for higher transfection rates (pg.986, col 2, lines 29-54). Seki and Rutz further teach guide RNAs which are more than ten nucleotide long that encode compliments to target genes (Table S1). Thus, Rosen discloses a method of developing modified T cell populations towards a central memory T cell phenotype in which the T cells are isolated, cultured with IL-2 and anti-CD3/anti-CD28 beads and then incubating the cells with an inhibitor of a negative modulator gene of TCF7. Rosen also teaches a sufficient length of time for modulating immune cells to be no less than 30, 42, 54, 66, 78, or 90 hours. Seki and Rutz teach an optimized method of transfection using Cas9 and guide RNA. Therefore, a person of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to combine the teachings of Rosen with the teachings of Seki and Rutz with a reasonable expectation of success to develop a method of expanding and modifying naïve T cells using a Cas9 and guide RNA complex to knock out gene expression of a target gene for higher transfection rate and a larger yield of modified T cells . 07-21-aia AIA Claim s 24 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Shifrut et al (2018) Genome-Wide CRIPSR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function Cell (175) 1958-1971 (hereafter Shifrut) in view of Siddiqui et al. (2019) (of record, IDS 04/02/2024) In regards to claims 24 and 25 Shifrut teaches a method of genetic screening which includes contacting a T cell populations with a lentivirus containing single guide RNAs and then further contacting the T cells with a Cas9 proteins with electroporation (pg.1959, col 1, lines 21-42). The T cells are stimulated with anti-CD28, anti-CD3, and IL-2 before contacting with the lentiviral and Cas9 protein (pg.e2, lines 15-17) and maintained in culture with IL-2 after (pg.e3, lines 12-14). Shifrut also teaches guide RNAs which are longer than 10 nucleotides complementary to the target sequence (Table S1). Further, Shifrut teaches separation of the cell with increased proliferation after treatment with the lentivirus and Cas9 protein and analyzing the guide RNA abundance to identify target sequences for the RNA (pg.1960, col 2, lines 1-8). Shifrut uses this method to identify targets within the T cells which modulate the proliferation of the T cells and further T cell activation compared to WT cells and finds sequences which increase proliferation by more than 10% (Figure 3). Shifrut fails to teach the use of this method to measure the change in TCF7 expression to determine target sequences to modulate TCF7 expression. Siddiqui, however, teaches that TCF7 expression is essential for the function of the intertumoral stem-cell like cells to produce differentiated progeny and to maintain themselves as tumor infiltrating lymphocytes and further that finding TCF-1 dependent target is essential to maintain the stem-like function of these TILs (pg.208, col 2, lines 15-19). Thus, Shifrut discloses a method of genetic screening using lentiviral particles containing guide RNA and electroporation of Cas9 protein with RNAs longer than 10 nucleotides complementary to a target sequence, and Siddiqui teaches that TCF7 is an important gene for the maintenance of a stem-like cell for tumor infiltration and control. Therefore, a person of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to use the method of Shifrut with the substitution of measuring TCF7 activity as informed in Siddiqui with a reasonable expectation of success to find targets in which TCF7 expression is increased for the purpose of preparing a modified T cell with maintained stem like properties for tumor control . 07-21-aia AIA Claim s 53 and 58 are rejected under 35 U.S.C. 103 as being unpatentable over Shifrut in view of Wang et al. (2014) CCR5 Gene Disruption via Lentiviral Vectors Expressing Cas9 and Single Guided RNA Renders Cells Resistant to HIV-1 Infection PLoS ONE 9(12): e115987 (hereafter Wang) and Shinohara and Shinohara (2020) Transgenesis and Gnome Editing of Mouse Spermatogonial Stem Cells by Lentivirus Pseudotyped with Sendai Virus F protein Stem Cell Reports (14) 447-461 (hereafter Shinohara and Shinohara) . Shifrut teaches a method of genetic screening which includes contacting a T cell populations with a lentivirus containing a plurality of single guide. Shifrut also teaches guide RNAs which are longer than 10 nucleotides complementary to the target sequence (Table S1). Shifrut fails to teach a method wherein the CRISPR associated protein is encoded into the vector itself, and further where the lentiviral vector comprises VSV-g and an ecotropic envelope protein. Wang, however, teaches the method of silencing a gene (pg.3 lines 16-29) using a lentiviral particle which encodes a Cas9 protein and a guide RNA and further wherein the lentiviral particle was enveloped in VSV-G (pg.4, lines 11-29) for a single round transduction of a target cell. Wang fails to teach the addition of another ecotropic envelope protein; however, Shinohara and Shinohara teach the use of an envelope protein comprised of SVS-G and F protein from the Sendai Virus (SV) for improved transfection efficiency in germline stem cells which more closely mimics SV for gene therapy (pg.457, col 1, lines 4-11). Thus, Shifrut discloses a method of genetic screening in which a T cell is contacted with a lentivirus encoding a plurality of guide RNAs, Wang teaches a method of loading a single lentiviral particle with a polynucleotide encoding Cas9 and the guide RNA for a single round transduction, and Shinohara and Shinohara teach the method of adding an ecotropic envelope protein with an VSV-G envelope protein to work with each other to improve transfection efficiency in the target cell. Therefore, a person of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to combine the teachings of Shifrut, Wang, and Shinohara and Shinohara with a reasonable expectation of success to develop a lentiviral particle encoding a Cas9 protein and a plurality of guide RNAs which is enveloped in SVS-G and another ecotropic protein for a single step, more efficient transduction method to genetically screen a target cell . Double Patenting 08-33 AIA 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. 08-36 AIA Claim s 24 and 25 rejected on the ground of nonstatutory double patenting as being unpatentable over claim s 1 and 2 of U.S. Patent No. 11,197,467 in view of Siddiqui and Shifrut . Claims 1 of the U.S. patent recite claim to a method of identifying a gene(s) or genetic element(s) (genetic screening) capable of modulating a leukocyte immune response which comprises obtaining a plurality of a mouse leukocytes modified to contain a Cas9 transgene expression cassette and delivering in vitro vectors containing guide RNA to inhibit expression of target genes, contacting the cells with a stimulatory agent and isolating and sorting the leukocytes according to their expression levels of one or more markers. Claim 2 of the U.S. patent recites claim to further identifying genes or genetic elements by sequencing the nucleic acid present in the isolated or sorted leukocytes. These claims significantly encompass the methods claimed in claims 24 and 25 of the instant application. Claims 1 and 2 of the U.S. patent fail to distinctly teach the use of T cells, the measurement of TCF7, and further wherein the guide RNAs are 10 or more nucleotides long. Siddiqui, however, teaches that TCF7 expression is essential for the function of the intertumoral stem-cell like cells to produce differentiated progeny and to maintain themselves as tumor infiltrating lymphocytes and further that finding TCF-1 dependent target is essential to maintain the stem-like function of these TILs (pg.208, col 2, lines 15-19). Siddiqui fails to teach the guide RNAs being 10 or more nucleotides long. Shifrut, however, teaches guide RNAs which are longer than 10 nucleotides complementary to the target sequence (Table S1) which were successfully used in a genome wide screening of T cells. Thus, the U.S. Patent discloses a method of genetic screening which includes contacting a leukocyte with a Cas9 and guide RNAs and further wherein they are activated, and sorted based on their expression of a target molecule, Siddiqui teaches the importance of TCF7 in T cell ability to maintain their beneficial functions, and Shifrut teaches guide RNAs which are longer than 10 nucleotides complementary to the target sequence. Therefore, a person of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to combine the method of the U.S. Patent with the teachings of Siddiqui and Shifrut with a reasonable expectation of success to adapt the method for use in T cells with the goal of finding target sequences which modulate TCF7 expression. Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to DASIA A ALDARONDO whose telephone number is (571)272-1977. The examiner can normally be reached on Monday - Thursday from 7am to 4pm and Friday 7am to 11am. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Joanne Hama, can be reached at telephone number (571)272-2911. The fax phone number for the organization where this application or proceeding is assigned is (571)273-8300. Information regarding the status of an application may be obtained from Patent Center. Status information for published applications may be obtained from Patent Center. Status information for unpublished applications is available through Patent Center to authorized users only. Should you have questions about access to the USPTO patent electronic filing system, contact the Electronic Business Center (EBC) at (866)217-9197 (toll-free). Examiner interviews are available via a variety of formats. See MPEP § 713.01. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) Form at https://www.uspto.gov/InterviewPractice. /D.A.A/Examiner, Art Unit 1647 /JOANNE HAMA/Supervisory Patent Examiner, Art Unit 1647 Application/Control Number: 18/279,848 Page 2 Art Unit: 1647 Application/Control Number: 18/279,848 Page 3 Art Unit: 1647 Application/Control Number: 18/279,848 Page 4 Art Unit: 1647 Application/Control Number: 18/279,848 Page 5 Art Unit: 1647 Application/Control Number: 18/279,848 Page 6 Art Unit: 1647 Application/Control Number: 18/279,848 Page 7 Art Unit: 1647 Application/Control Number: 18/279,848 Page 8 Art Unit: 1647 Application/Control Number: 18/279,848 Page 9 Art Unit: 1647 Application/Control Number: 18/279,848 Page 10 Art Unit: 1647 Application/Control Number: 18/279,848 Page 11 Art Unit: 1647