DETAILED ACTION
Applicant’s amendment and response received on 10/24/25 has been entered. Claims 54, 66, and 68-69 have been canceled. Claims 52-53, 55-65, 67, and 70-71 are currently pending and under examination in this application in view of the elected species of 1) a CAR specific for CD19, and 2) a fourth genomic modification which is either an indel in a PD1 gene or an indel in a TCR beta gene. An action on the merits follows.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . Thos sections of Title 35, US Code, not included in this action can be found in a previous office action.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 10/24/25,, 12/3/25, and 1/7/26
Are compliance with the provisions of 37 CFR 1.97 and 1.98. Accordingly, the information disclosure statements have been considered by the examiner, and initialed and signed copies of the 1449s are attached to this action.
Claim Rejections - 35 USC § 112
The rejection of claims 52-71 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention, is withdrawn in view of applicant’s amendments to the claims which now recite that the population of primary T cells comprises a subset which comprises all three of the recited genomic modifications or all four of the recited genomic modifications.
Claim Interpretation
The following claim interpretation has been applied to claims 52-53, 55-65, 67, and 70-71. The claims as written have been give their broadest reasonable interpretation as encompassing a population of primary T cells that comprising additional subsets of primary T cells which may have only 1 or 2 of the recited modifications. Further, as the claims as amended recite that the first and second genomic modifications are “each present in about 10% to about 80% in the population of primary T cells when modified by a CRISPR system”, the claims have been given their broadest reasonable interpretation of encompassing about 10% to about 80% of each genomic modification in entire population of primary T cells not limited to the subset of primary T cells that comprises all three of the genomic modifications.
Claim Rejections - 35 USC § 103
The rejection of claims 52-71 under 35 U.S.C. 103 as being unpatentable over US Patent Application Publication 2016/0311907 (2016), hereafter referred to as Brogdon et al., with an effective filing date of 12/20/2013, in view of Singh et al. (2008) Cancer Res., Vol. 68(8), 2961-2971, U.S Patent Application Publication 2017/0175128 (2017), hereafter referred to as Welstead et al., with an effective filing date of 4/18/2014, and WO 2016/063264 (2016), hereafter referred to as Naldini et al., with an effective filing date of 10/24/2014, is withdrawn over canceled claims 54, 66, and 68-69, and further withdrawn over amended claims 52-53, 55-65, 67, and 70-71, which are now limited to primary T cells, where a subset of the primary T cells comprises all three genomic modifications recited in claim 52, and where the first 2 modifications, or all three modifications are present in about 10-80% of the population of primary T cells when modified by a CRISPR system.
Applicant’s amendments to the claims have necessitated the following new grounds of rejection.
Claims 52-53, 55-65, 67, and 70-71 are newly rejected under 35 U.S.C. 103 as being unpatentable over US Patent Application Publication 2016/0311907 (2016), hereafter referred to as Brogdon et al., with an effective filing date of 12/20/2013, in view of Singh et al. (2008) Cancer Res., Vol. 68(8), 2961-2971, U.S Patent Application Publication 2017/0175128 (2017), hereafter referred to as Welstead et al., with an effective filing date of 4/18/2014, U.S. Patent Application Publication 2017/0290858 (2017), hereafter referred to as Zhao et al., with an effective filing date of 10/31/14, Ardolino et al. (2014) J. Clin. Invest., Vol. 124(11) 4781-4794, and WO 2016/063264 (2016), hereafter referred to as Naldini et al., with an effective filing date of 10/24/2014.
Brogdon et al. teaches genetically modified T cells, preferably primary T cells, comprising and expressing a nucleic acid encoding a chimeric antigen receptor (CAR) capable of recognizing a tumor-associated antigen, where the T cells are derived from peripheral blood, such as from an immunocompromised patient or patient with leukemia, or where the T cells are tumor-infiltrating lymphocytes (Brogdon et al., paragraphs 1666, 2131-2138, 2190, and claims 1-71). Brogdon et al. teaches that the CAR comprise an scFv, a hinge region, a transmembrane domain, and one or more intracellular signaling domains, where in certain embodiments the scFv recognizes CD19, the hinge domain is a CD8 hinge sequence, the transmembrane domain is derived from CD8 or CD28, and the intracellular domains includes 4-1BB and CD3 zeta (Brogdon et al., Table 11, and paragraphs 26, 74, 187, 1730, 1765, and 2545). Brogdon et al. also teaches where the CAR comprises two scFv binding domains specific for two different tumor antigens selected from a list comprising CD19 and CD22 (Brogdon et al., paragraphs 182, 1730, and 1736). Brogdon et al. further teaches methods of using regulatable CAR (RCAR) T cells for adoptive immunotherapy of cancer, particularly leukemia, where either autologous or allogeneic RCAR T cells are administered to a patient with cancer (Brogdon et al., paragraphs 2, and 2202-2207, and claims 34-52). In addition, Brogdon et al. teaches in certain embodiments to use CAR T cells genetically engineered to not express any functional TCR or functional HLA class I on the cell surface (Brogdon et al., paragraphs 2140-2144). In particular, Brogdon et al. teaches that T cells can be engineered to not express the TCR subunits and/or HLA components using various methods of gene editing, including CRISPR/cas (Brogdon et al., paragraphs 2149-2157). Brogdon et al. also teaches that the CAR T cell function can be optimized by engineering the T cells using CRISPR/cas to further lack expression of an inhibitory molecules such as PD1 or CTLA4, and in particular PD1 (Brogdon et al., paragraphs 1890 and 2144).
While Brogdon et al. teaches to introduce an exogenous nucleic acid encoding a CAR specific for CD19 to a population of T cells such as primary T cells, Brogdon et al. does not specifically teach a method of genomic integration of the exogenous nucleic acid encoding the anti-CD19 CAR. Singh et al. supplements Brogdon et al. by teaching an efficient method of introducing an exogenous nucleic acid encoding an anti-CD19 CAR into the genome of a population of primary T cells using a sleeping beauty transposon (Singh et al., pages 2961 and Figure 1). Singh et al. teaches a population of T cells where greater than 10% and less than 80% of the T cells express the CAR, and further reports efficiency of sleeping beauty transposon mediated introduction of the nucleic acid encoding the anti-CD19 CAR to the T cell genome of greater than 10% and less than 80% (Singh et al., Figures 2 and 3). Thus, based on the efficiency of integration and expression of an nucleic acid encoding an anti-CD19 CAR in a population of primary T cells made using the transposon methodology taught by Singh et al., it would have been prima facie obvious to the skilled artisan at the time of filing to generate the therapeutic population of primary T cells expressing an anti-CD19 CAR as taught by Brogdon et al. using the methodology of Singh et al. with a reasonable expectation of generating anti-CD19 CAR T cells with greater than 10% and less than 80% efficiency and further of producing a population of T cells where greater than 10% and less than 80% of the cells comprise the insertion of the exogenous nucleic acid encoding the anti-CD19 CAR.
Further, while Brogdon et al. teaches to inhibit the expression of both TCR subunits, HLA components, and inhibitory molecules such as PD1 and CTLA4 in CAR T cells using CRISPR/cas to optimize the function of the T cell, Brogdon et al. does not provide any specific details as to the use of CRISPR/cas to introduce deletions or “indels” in these genes in a T cell, or more specifically a primary T cell. However, at the time of filing, Welstead et al. teaches similar methods of genetically modifying human T cells to optimize their function and most specifically teaches to introduce a mutation into each of the human FAS, BID, CTLA4, PDCD1, CBLB, PTPN6, TRAC and TRBC genes in a human T cell or engineered CAR T cell, where the mutations are introduced using CRISPR/Cas9 and wherein the mutations knockdown the expression of each of the targeted genes (Welstead et al. paragraphs 216, and 218-226). Note that PDCD1 is another name of PD1, TRAC refers to a TCR alpha chain gene, and TRBC refers to a TCR beta chain gene. Welstead teaches a number of gRNA encoded targeting sequences for human TRAC, TRBC, and PDCD1 genes (Welstead et al., paragraphs 41-53). Welstead et al. teaches to provide one gRNA complementary to a target domain in the TRAC gene, TRBC gene, or PDCD1 gene, or two or more different gRNA, such as one targeting the TRAC gene, one targeting the TRBC gene, and one targeting PDCD1, in combination with Cas9 to alter the sequence of the target genes in a T cell by producing indels (Welstead et al., paragraphs 41-53, 67, and 167-181). Welstead et al. also provides a large number of specific gRNA for targeting and introducing indels into the human TRAC gene (Table 29), the human TRBC gene (Table 27), and the human PDCD1 gene (Table 31). Welstead et al. also provides working examples demonstrating the efficacy of CRISPR/Cas 9 in genetically modifying genes in T cells (Welstead, examples 5-7). Welstead et al. shows that the percentage of NHEJ varies based on the gRNA used and provides a number of examples of gRNA which produced greater than 10% and less than 80% NHEJ indel formation for each of the TRAC gene, the TRBC gene, and the PDCD1 gene (Welstead et al., Figures 11-16). Welstead et al. also shows that percent indel formation in the TRAC and/or TRBC gene correlates with a decrease in CD3 expression in the human T cells (Welstead et al., Figures 17B and 18B). Ardolino et al. and Naldini et al. further supplements Brogdon et al. by teaching methods of knocking down expression of B2M using CRISPR/Cas 9 using specific gRNA targeting B2M. Ardolino et al. demonstrates the successful inactivation of B2M in cells using CRISPR/Cas9 using specific gRNA targeting the mouse B2M gene (Ardolino et al., page 4792). Naldini et al. teaches gRNA capable of successfully targeting the B2M gene on human chromosome 15 (Naldini et al., pages 51-52 and 103-104, and Figure 14E). In addition, Zhao et al. teaches that CRISPR/Cas9 is also effective in generating indels in a target gene in primary human T cells. Zhao et al. teaches an optimized method for knocking out both the TRAC and TRBC genes in primary human T cells using CRISPR/Cas9 and specific gRNA where the efficiency of indel formation as measured by loss of gene expression in the TRAC and TRBC genes in the primary T cells was 64.5% and 57.5% respectively (Zhao et al., paragraphs 33 and 434 and Figure 4A, 4B, and 4C).
Therefore, in view of teachings of Singh et al. for an efficient method of introducing a nucleic acid encoding an anti-CD19 CAR to population of primary T cells, the detailed teachings of both Welstead, Ardolino, and Naldini et al. for methods of deleting specific portions of each of the human TCR alpha, TCR beta, PD1, and B2M genes using a gRNA targeting each of these genes, the specific teachings of Brogdon et al., Welstead et al., and Zhao et al. to knockdown the TCR alpha, TCR beta, PD1, and B2M genes in a T cell, the evidence provided in Welstead for an efficiency of indel formation in each gene targeted by CRISPR of between 10%-80%, which translated to a reduction in gene expression of each gene by 10%-80% in the targeted cell population, and the evidence provided by Zhao et al. for efficient indel formation in genes such as TCR alpha and TCR beta targeted by CRISPR using an optimized CRISPR protocol in human primary T cells where efficiency of gene targeting leading to loss of gene expression was between 54.5%-64.5%, it would have been prima facie obvious to the skilled artisan at the time of filing to use the specific gRNAs and CRISPR/Cas technology taught by Welstead et al., Zhao et al., and Naldini et al. to make a population of therapeutic primary human T cells capable of treating leukemia where the primary human T cells have been genetically modified to comprise an exogenous nucleic acid encoding a CAR specific for CD19 as taught by Brogdon et al. in view of Singh et al., an indel in the human TRAC gene, an indel in the human B2M gene, and an indel in human PD1 with a reasonable expectation of success, and further to use the specific gRNA targeting sequences disclosed in Welstead et al., Zhao et al., and Naldini et al. to knockout each of the TRAC, B2M, and PD1 genes using CRISPR/Cas9 as taught by Brogdon et al., Welstead et al., and Zhao et al. in population of primary human T cells with between 10%-80% efficiency with a reasonable expectation of success.
Applicant’s arguments presented in their response have been fully considered in so far as they apply to the new grounds of rejection above. The applicant argues that claims 52, 59, and 64 have been amended to recite that the T cells are primary human T cells and that the first and second genomic modifications are present in the population at about 10% to about 80% when modified by CRISPR. The applicant argues that Brogdon et al. is silent regarding genomic modifications of the B2M gene in primary T cells using CRISPR, that Singh et al. uses a Sleeping Beauty system no CRISPR, that Welstead modified cell lines and did not modify primary human T cells, and that Naldini et al. used a nuclease defective Cas in their CRISPR system for inactivating B2M expression in a cell line cells.
In response, it is first noted that claim 59 does not limit the genomic modifications to CRISPR modifications. Claim 59 reads on any type of modification leading to a reduction in B2M gene expression and TCR alpha gene expression. Claim 64 does refer to genomic modifications which are indels in the B2M and TCR alpha genes, but does not limit the indel formation to indels formed by a CRISPR system. In regards to Brogdon et al., Brogdon et al. clearly teaches that the CAR T cells can be engineered to not express the TCR subunits and/or HLA components using various methods of gene editing, including CRISPR/cas (Brogdon et al., paragraphs 2149-2157). B2M, as taught by Ardolino et al. and Naldini et al. is a well known component of MHC class I, referred to as HLA in humans. Further, Brogdon et al. is not read in a vacuum. The rejection of record further cites Singh et al., Welstead et al., Zhao et al., Ardolino et al., and Nalini et al. One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Further, the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). In regards to Singh et al., it is noted that none of the claims require that the genomic modification to introduce a CAR was introduced utilizing a CRISPR system. The claims read on any genetic modification which inserts an exogenous nucleic acid encoding the CAR into the genome of the T cell. Singh et al. teaches a sleeping beauty system for introducing a nucleic acid encoding a CAR into the genome of a cell with high efficiency. Singh et al. was not cited for CRISPR modification of B2M, TCR alpha or beta, or PD1. Further, applicant’s argument that Welstead and Naldini tested CRISPR in cell line cells and not primary T cells is not persuasive as the rejection of record now cites Zhao et al. for teaching an optimized CRISPR methodology for high efficiency knockout of TCR alpha and TCR beta in human primary T cells. Zhao et al. clearly shows that their optimized CRISPR system exhibited an efficiency of gene modification leading to loss of gene expression 64.5% and 57.5% respectively for the TCR alpha gene (TRAC) and TCR beta gene (TRBC) in a population of primary human T cells. Further, in regards to applicant’s argument that the genetic modification of Naldini did not create an indel, this argument do not apply to claim 59 and its dependent claims, as no indel is required for B2M genome modification in these claims. In addition, the rejection of record now cites Ardolino et al. who both teaches and successfully demonstrated CRISPR/Cas9 knockout of B2M expression in cells using a wild type Cas9. Naldini et al. was cited for teaching gRNA which can be used to successfully target the human B2M gene. As such, for the reasons presented in the rejection of record above, it is maintained that the cited references provide both the requisite teachings and motivation to make the population of primary T cells as claimed with a reasonable expectation of success.
No claims are allowed.
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.
Any inquiry concerning this communication from the examiner should be directed to Anne Marie S. Wehbé, Ph.D., whose telephone number is (571) 272-0737. If the examiner is not available, the examiner’s supervisor, Maria Leavitt, can be reached at (571) 272-1085. For all official communications, the technology center fax number is (571) 273-8300. Please note that all official communications and responses sent by fax must be directed to the technology center fax number. For informal, non-official communications only, the examiner’s direct fax number is (571) 273-0737. For any inquiry of a general nature, please call (571) 272-0547.
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Dr. A.M.S. Wehbé
/ANNE MARIE S WEHBE/Primary Examiner, Art Unit 1634