DETAILED ACTION
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 4/27/26 has been entered.
New claims 72-74 have been added. Claims 52-53, 55-65, 67, and 70-74 are now 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 statement (IDS) submitted on 4/27/26 is in compliance with the provisions of 37 CFR 1.97 and 1.98. Accordingly, the information disclosure statement has been considered by the examiner, and an initialed and signed copy of the 1449 is attached to this 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.
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.
Claims 52-53, 55-58, 64-65, 67, 70-72, and 74 are newly 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.
Claim 52, drawn to a method of treating cancer by administering a population of genomically modified primary T cells, has been amended to recite “wherein the first genomic modification and second genomic modification are each made with an efficiency greater than or equal to about 85% in the population of primary T cells when modified by a CRISPR system”. Claim 72 depends on claim 52 and further recites that the efficiency is greater than or equal to about 90%. This limitation is confusing as the method of claim 52 is a method of treating a cancer with a single method step of administering a population of primary T cells. The method as claimed does not contain any method steps in regards to actually making any one or more of the specific genomic modifications that are recited as being present in the T cells. As such, the metes and bounds of the new limitation which states that the first and second genomic modifications “are each made with an efficiency greater than or equal to about 85%” can not be determined as it is unclear whether this limitation is intended to represent an active method step, or is intended to reflect the genetic composition of the T cell population as some undisclosed point in time. It is further noted that the wherein clause additionally recites, “when modified by a CRISPR system”. The use of the word “when” in this context further appears to imply that this potential method step/limitation only applies where CRISPR is used generate the genomic modifications. However, again, the sole method step of the claimed method is for administering primary T cells which have already been genomically modified. Thus, as a whole, the claim is confusing as it is unclear how the conditional limitation relating to a particular method of making the cells relates to the actual method steps as claimed, particularly as the population of primary T cells is not recited to be a population obtained immediately following genomic modification, or to a population which has been modified by any particular means of genomic modification. It is also noted that an “indel” is a term which encompasses any modification to a sequence resulting from any genome editing process, not limited to a CRISPR based process, and reads on various deletions or insertions of nucleotide sequence at the identified genetic loci. Therefore, for the reasons set forth above, the metes and bounds of claim 52 cannot be determined. Claims 53, and 55-58 depend on claim 52 and thus are included in this rejection.
Independent claim 64, similar to claim 59, has also been amended to recite “wherein the first genomic modification and second genomic modification are each made with an efficiency greater than or equal to about 85% in the population of primary T cells when modified by a CRISPR system”. Claim 74 depends on claim 64 and further recites that the efficiency is greater than or equal to about 90%. Claim 64 is a product claim drawn to a population of genomically modified primary T cells. Claim 64 is not a method for making the product, and it is unclear whether the recitation that the genomic modifications “are made” with a particular efficiency is intended to recite this action as a method step as kind of a product by process type claim. Thus, as written, the claim is confusing as it is unclear whether the claim is a product or product by process claim. It is further noted that the wherein clause additionally recites, “when modified by a CRISPR system”. The use of the word “when” in this context further appears to imply that this potential method step/limitation only applies where CRISPR is used generate the genomic modifications. However, again, the claim is drawn to a product and not a process of making. Thus, as a whole, the claim is confusing as it is unclear how the conditional limitation relating to a particular method of making the cells relates to product as claimed, particularly as the population of primary T cells is not clearly recited to be a population obtained by process step, and does not contain any limitations regarding when the claimed population was made, i.e. the population does not appear to be limited to a population of cell generated immediately following genomic modification, or to a population which has been modified by any particular means of genomic modification. Therefore, the metes and bounds of the claimed population of cells cannot be determined. Claims 65-67, and 70-71 depend on claim 64 and thus are included in this rejection.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 52-53, 55-65, 67, and 70-74 are newly rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Independent claims 52, 59, and 64 now recite the limitation, “wherein the first genomic modification and second genomic modification are each made with an efficiency greater than or equal to about 85% in the population of primary T cells when modified by a CRISPR system”. Dependent claims 72-74 further limit the efficiency to greater than or equal to about 90% for the first and second genomic modifications.
While the specification does generally recite an editing efficiency of greater than or equal to 85% or 90% using CRISPR, see for examples paragraph 23 of the instant specification, the specification fails to provide the requisite guidance for achieving such high levels of gene editing using a CRISPR system for any target genomic locus, including the B2M and TRAC loci as claimed, in any cell and more particularly in a primary T cell as claimed. The specification provides guidance for elements of a CRISPR system useful for genome editing of various genes including TRAC and B2M, and provides a number of gRNA sequences for specifically targeting each gene loci, which can be used individually as a single gRNA, or preferably in pairs, in combination with a CAS protein such as Cas9 or Cpf1. The specification further teaches that these systems and the specifically disclosed gRNA can be used to genetically modify primary T cells in vitro. The specification also provides three working examples. The first example discloses that gRNA specific for TCR alpha or TCR beta were tested for their on-target efficiency in HEK293T cells, Jurkat T cells, and primary human T cells. Figure 12 provides the only data regarding genomic modification of primary human T cells and shows a FACs expression analysis of CD3 surface expression on the cells as an indirect means of identifying loss of TCR alpha or beta expression. Figure 12, however, only appears to show an increase in CD3- in the primary T cells from 2.44% to 46% following CRISPR. While the reduction in CD3 surface expression does demonstrate genome modification, the data does not demonstrate 85-90% genome editing efficiency of the TCR alpha loci. At best, the results obtained and depicted in Figure 12 show an approximate 43% reduction in CD3 surface expression which does not correlate to genomic modification efficiency of 85%-90%. Neither working example 2 or 3 disclose genomic modification of primary T cells. It is also noted that the only disclosure of genomic modification to the B2M locus involved the use of TALEN, not CRISPR. As such, the working examples do not disclose the achievement of genomic modifications efficiencies to the TCR alpha loci or the B2M locus in primary T cells of greater than or equal to 85% or 90%, encompassing up to 100% genomic modification.
Turning to the state of the prior art at the time of filing, the efficiency of genomic modification of target loci in primary T cells using CRISPR/CAS systems was still under improvement. Zhao et al., for example, 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 (U.S. Patent Application Publication 2017/0290858 (2017), hereafter referred to as Zhao et al., with an effective filing date of 10/31/14, see paragraphs 33 and 434 and Figure 4A, 4B, and 4C). Chen et al., and Schumann et al. further show that even month after the effective filing date, the efficiency of genomic modification in primary T cells using CRISPR/Cas9 had yet to approach 85%. Schumann et al. teaches that CRISPR/Cas9 genomic modification of the CXCR4 locus in primary CD4+ T cells only reached approximately 60% (Schumann et al. (2015) PNAS, Vol. 112(33), 10437-10442, see page 10439 and Figure 2). Chen et al. in a review of CRISPR based gene editing of primary T cells teaches that attempts to genomically modify the PD-1 loci using CRISPR in primary T cells resulted in approximately 55% indel formation, and that attempts to genomically modify the CCR5 locus in primary T cells resulted in approximately 49% frequency (Chen et al., (2015) Trends in Immunol., Vol. 36(11), 667-669, see page 669). Chen et al. concludes on page 669:
Many T-cell engineering applications thus far do not require 100% efficiency in gene modification. For example, adoptive cell therapy trials regularly use unsorted CAR–T-cell products that contain a frac-tion of unmodified T cells. However, applications such as suicide-gene integra-tion or the production of ‘off-the-shelf’ T cells lacking antigens responsible for GVHD will require complete editing of the T-cell population to achieve their desired purpose. Further advancements in methods to edit primary T cells, and subsequently isolate and expand edited cells, will greatly increase the safety and efficacy of engineered T cells for diverse applications.
Thus, both at the time of filing and months thereafter, the skilled artisan had yet to achieve editing efficiencies of any gene target sequence in primary T cells of greater than 85% using a CRIPSR/Cas system, and that further advancements were needed to improve editing efficiencies.
Therefore, in view of the lack of specific guidance in the specification for methods capable of achieving greater than 85% genomic editing using a CRISPR system in primary T cells, the lack of evidence in the working examples for anything greater than perhaps a 43% editing efficiency of the TCR alpha locus in primary human T cells, the failure in the art both prior to and even after the effective filing date for achieving 85-90% or greater editing of any gene in a primary T cell using a CRISPR system, and the breadth of the claims, it would have required undue experimentation to make and use the invention as claimed.
Claim Interpretation
The following claim interpretation has been applied to claims 52-53, 55-65, 67, and 70-74. Based on the “when” clause discussed in the rejection of the claims under 35 U.S.C. 112(b) above, the claims as written have been give their broadest reasonable interpretation as encompassing genomic modifications to the primary T cells which have not been made or are not being made by a CRISPR system. As such, the % efficiency recited in the claims, “when modified by a CRISPR system” has been interpreted to only apply to an embodiment of the claims where CRIPSR has been used, and does not apply to genomic modifications made using other means of genome editing.
Claim Rejections - 35 USC § 103
The rejection of claims 52-53, 55-65, 67, and 70-71 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, 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, is withdrawn in view of new grounds of rejection set forth below.
Claims 52-53, 55-65, 67, and 70-74 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, Berdien et al. (2014) Gene Therapy, Vol. 21, 539-548, and U.S. Patent No. 11,820,996 (2023), hereafter referred to as Poirot et al., with an effective filing date of March 11, 2014.
Please refer to the claim interpretation section set forth above, and the rejections of the claims under 35 U.S.C. 112(b) for a discussion of how the newly added limitations to the independent claims has been interpreted. Most specifically, note that the claims as amended have been give their broadest reasonable interpretation as encompassing genomic modifications to the primary T cells which have not been made or are not being made by a CRISPR system. As such, the % efficiency recited in the claims, “when modified by a CRISPR system” has been interpreted to only apply to an embodiment of the claims where CRIPSR has been used, and does not apply to genomic modifications made using other means of genome editing.
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 TALENS, or ZFNs (Brogdon et al., paragraphs 2149-2172). Brogdon et al. also teaches that the CAR T cell function can be optimized by engineering the T cells using gene editing 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% 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% (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 a population of primary anti-CD19 CAR T cells where greater than 10% 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 ZFN or TALENs, to introduce deletions (indels) in these genes in a T cell, or more specifically a primary T cell. However, at the time of filing, Berdien et al. teaches an efficient and precise method to introduce a deletion into both the human TCR alpha and beta genes in primary human T cells using specific TALENS (Berdien et al., pages 540, 543, 546-547, and Figure 4). Note that genomic modification of TCR beta is one of the alternatives recited as a fourth genomic modification in the claims. Berdien et al. further teaches that their TALEN based knockout of TCR alpha and beta chains in primary human T cells can be used to further produce re-directed T cells comprising an exogenous CAR for adoptive therapy of disease including cancer (Berdien et al., page 539). Poirot et al. further supplements Brogdon et al. by teaching an efficient and precise method to introduce a deletion into the beta-2-microglobulin (B2M) gene in primary human T cells using specific TALENS where the resulting cell population was 80% negative for B2M expression (Poirot et al., paragraph 223, Figure 10, and claims 1-14).
Thus, based on the specific teachings and motivation provided by Brogdon et al. for making and using CAR T cells genetically engineered using a TALEN to lack expression of both TCR subunits and functional HLA class I on the cell surface, the 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 Berdien et al. and Poirot et al. for using TALENs to introduce deletions into the TCR alpha gene, the TCR beta gene, and the B2M gene in primary human T cells, and the further motivation provided by Berdien et al. to combine the deletion in the TCR subunits with the introduction of an exogenous CAR, it would have been prima facie obvious to the skilled artisan at the time of filing to use the specific TALENs taught by Berdien et al. and Poirot 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., and to further comprise genomic modifications comprising indels in the TCR alpha, TCR beta, and B2M gene 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 “wherein the first genomic modification and second genomic modification are each made with an efficiency greater than or equal to about 85% in the population of primary T cells when modified by a CRISPR system”. The applicant argues that none of the previously cited references teach CRISPR genomic modifications to primary T cells with this level of efficiency.
In response, it is first noted that applicant’s arguments regarding the teachings of references which are not cited in this new grounds of rejection are considered moot. Second, as discussed in detail in both the rejections of the claims under 35 U.S.C. 112(b) and the claim interpretation section provided above, the claims are not limited to the introduction of indels using a CRISPR system. The claims read broadly on using any type of gene editing system to generate the recited genomic modifications/indels. The newly introduced limitation only states that a particular efficiency of editing is achieved “when modified by a CRISPR system”. The 85% or 90% gene modification efficiency is thus only required when the gene modification system is a CRISPR system. The rejection set forth above is based on TALEN mediated genomic modification to the TCR alpha, TCR beta, and B2M genes, which is clearly encompassed by the claims as written. As such, applicant’s arguments regarding the lack of teachings for a CRISPR system capable of achieving a gene editing efficiency of 85% or greater in primary T lymphocytes is not found persuasive.
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
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