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 .
Restriction/Election
Applicant’s election without traverse of Group I, drawn to a T cell comprising a nucleic acid comprising a sequence encoding an anti-HIV CAR, a sequence encoding a Tat/Rev inhibitor and a sequence encoding a CCR5 inhibitor and corresponding to claims 1, 3-7, 10-14, 29-30, 32, and 72-74 in the reply filed 06/25/2026 is acknowledged.
Claim Status
Claims 1, 3-7, 10-14, 29-30, 32, 36, 40, 57 and 72-74 are pending. Claims 36, 40, and 57 are withdrawn for being directed to a non-elected invention.
Claims 1, 3-7, 10-14, 29-30, 32, and 72-74 are under examination.
Claim Rejections - 35 USC § 112(a)
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 4 and 6 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP § 2163 states that the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. A “representative number of species” means that the species which are adequately described are representative of the entire genus. See, e.g., AbbVie Deutschland GMBH v. Janssen Biotech, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014). Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus to provide a "representative number” of species. The “structural features common to the members of the genus” needed for one of skill in the art to ‘visualize or recognize’ the members of the genus takes into account the state of the art at the time of the invention.
The teachings of the specification and the claimed invention
The claims are directed to a T cell comprising a nucleic acid sequence encoding an anti-HIV CAR, a sequence encoding a Tat/Rev inhibitor and a sequence encoding a CCR5 inhibitor. Claims 3 and 4 recite the Tat/Rev inhibitor is an shRNA wherein the shRNA comprises a sequence having at least 95% sequence identity to SEQ ID NO: 10. Claims 5 and 6 recite the CCR5 inhibitor is an shRNA wherein the shRNA comprises a sequence having at least 95% sequence identity to SEQ ID NO: 9 or 11.
The specification teaches introduction of wobble bases into the shRNA to prevent self-targeting. The specification teaches the term wobble base refers to base pairing between nucleotides that does not follow Watson-Crick base pair rules such as G-U, I-U, I-A and I-C (Pg. 44, [0148]).
As an example, they provide an shRNA for CCR5 set forth in SEQ ID NO: 9 and a wobble base variant set forth in SEQ ID NO: 11 with three G-U wobble base substitutions on the 3’ end of the sense strand (see Fig. 4A), producing reduced self-targeting (Fig. 4B).
The specification does not provide additional embodiments of anti-Tat/Rev or anti-CCR5 shRNA with any other deletions or mutations or provide guidance on how the disclosed shRNA can be modified while still maintaining stability of the hairpin structure and target specificity.
The state of the relevant art
The art teaches that RNA interference is a highly precise method of suppressing gene expression that has been widely used in research settings and has expanded to use in therapeutic settings. RNA interference can be performed by intracellular expression of shRNA that are transported to the cytoplasm by Exportin-5 and processed by Dicer into siRNA (Liu, RNA. 2010 Jul;16(7):1328-39).
Akeju (Biotechniques. 2006 Feb;40(2):154, 156, 158) teaches RNA interference via shRNA/siRNA interference is able to differ-entially suppress genes or variations of genes that differ by even a single nucleotide. Akeju teaches: “an unintended single nucleotide mismatch between an shRNA and its target sequence may be sufficient to abrogate gene suppression. It is imperative therefore for shRNA encoding plasmids to be sequence-verified prior to use” (Pg. 154, Left column, Lines 28-38).
Holen (Nucleic Acids Res. 2005 Aug 19;33(15):4704-10) teaches mutations in siRNA can be well tolerated in vivo and various siRNAs have the ability to cross-react with targets of partial sequence similarity, potentially stimulating or repressing off-target genes (Pg. 4704, Right column, Full paragraph 2, Lines 1-6). Holen teaches bioinformatic approaches are being used for the design of specific and highly active siRNAs, however, such approaches require knowledge of the mutation tolerance of different positions in the siRNA as the position of the mismatch in the siRNA affects the severity of silencing loss (Pg. 4705, Left column, Paragraph 1, entire paragraph). In their study, Holen systematically induced wobble mutations in the siRNA leading to G-U interactions between the siRNA antisense strand and the mRNA target. They showed that while wobble mutations in the central regions of the siRNA are not well tolerated, wobble mutations in the terminal nucleotides in their siRNAs increased the silencing capacity (Pg. 4705, Left column, Full paragraph 3, entire paragraph).
As example, Holen teaches they performed a series of mild wobble mutations at positions 3, 7 and 10 in the context of anti-Fen1 siRNA (Figure 1B). Whereas no significant loss of activity was found after wobble mutations at position 7 and 3, a single wobble mutation in position 10 resulted in a dramatic loss of activity (Figure 2) (Pg. 4706, Left column, Full paragraph 4, entire paragraph). They found that wobble mutations, relative to the mRNA target, not only can be tolerated, but can also enhance activity when the mutations are in specific places. The mechanistic basis of this phenomenon is unknown, but might reflect the preferences and structural characteristics of the RISC complex (Pg. 4709, Right column, Full paragraph 2, entire paragraph).
In all, the art teaches even a single substitution in shRNA and resulting siRNA can abrogate binding. While some mutations in shRNA, particularly “wobble” mutations can be tolerated, they are not tolerated in every location and the ability to retain specificity and prevent off-target gene silencing requires verification.
Claim analysis
In light of the guidance taught in the specification and the state of the relevant art, the claims have the following written description issues:
Claim 4 recites the anti-Tat/Rev shRNA comprises a sequence having at least 95% sequence identity to SEQ ID NO:10 which allows for any substitutions, deletions and additions at any location. The specification does not define what locations can be mutated while still retaining stability and specificity.
Claim 5 recites the anti-CCR5 shRNA comprises a sequence having at least 95% sequence identity to SEQ ID NO:9 or 11 which allows for any substitutions, deletions and additions at any location. The specification does not define what locations can be mutated while still retaining stability and specificity.
In light of the claim language that encompasses any substitution, deletion, and addition to the shRNA one would neither expect nor predict the appropriate functioning of the shRNA and resulting siRNA as broadly as is claimed. There is no disclosure of a correlation between structure and function that would allow those of skill in the art to recognize other members of the claimed genus from the disclosure.
Given the lack of shared structural properties that provide the claimed function, the limited number of species described, and the fact that the species that were described cannot be considered representative of the broad genus, Applicant was not in possession of the invention as claimed.
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.
Claims 1, 3, 5, 11-14, 29-30, and 72-74 are rejected under 35 U.S.C. 103 as being unpatentable over Zaia (WO2019/084018A1, published 02 May 2019, effectively filed 10/23/2017, cited in IDS 11/17/2025) in view of Junghans (US2013/0183276A1, published 07/18/2013, effectively filed 04/14/2010).
The disclosure of Zaia is directed to methods for treating HIV comprising T cells expressing HIV-specific chimeric antigen receptors (see Abstract).
Regarding claims 1, 11, 12 and 72, pertaining to a T cell comprising a nucleic acid composition encoding an anti-HIV chimeric antigen receptor (CAR), wherein the anti-HIV CAR comprises: (i) an antibody region capable of binding an HIV envelope protein; and (ii) a transmembrane domain (claim 11), wherein the HIV envelope protein is gp120 or gp41 (claim 12), and wherein the antibody region is an scFv (claim 72), Zaia discloses a human T cell expressing a CAR comprising an antigen binding domain that binds to an epitope on HIV gp120, a spacer, a transmembrane domain, a co-stimulatory domain, and a CD3 zeta signaling domain (Pg. 41, claim 1). Zaia discloses the antigen binding domain is an scFv (Pg. 41, claim 2) and provides known gp120-specific neutralizing antibodies whose light chain and heavy chain variable regions could be used in the CAR (Fig. 3 and 5).
Regarding claims 13 and 73, wherein the antibody region according to claim 11 comprises a heavy chain variable domain comprising the sequence of SEQ ID NO: 4 and a light chain variable domain comprising the sequence of SEQ ID NO: 5 (claim 13) and wherein the antibody region of the T cell of claim 11 comprises the CDR sequences of N6 (claim 73), Zaia discloses possession of a CAR T cell comprising the scFv of antibody clone N6 (Fig. 7) and discloses the heavy and light chain variable domains set forth in SEQ ID NO: 100 and 99, identical to instant SEQ ID NO: 4 and 5. The alignment is shown below:
Instant SEQ ID NO: 4 and Saia SEQ ID NO: 100, clone N6
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Instant SEQ ID NO: 5 and Saia SEQ ID NO: 99, clone N6
Regarding claim 14 and 74, wherein the antibody region according to claim 11 comprises a heavy chain variable domain comprising the sequence of SEQ ID NO: 6 and a light chain variable domain comprising the sequence of SEQ ID NO:7 (claim 14) and wherein the antibody region of the T cell of claim 11 comprises the CDR sequences of NIH-45-46 (claim 74), Zaia discloses possession of a CAR T cell comprising the scFv of antibody clone NIH-45-46 (Fig. 7) and discloses the heavy and light chain variable domains set forth in SEQ ID NO: 94 and 93, identical to instant SEQ ID NO: 6 and 7. The alignment is shown below:
Instant SEQ ID NO: 6 and Saia SEQ ID NO: 94, clone NIH-45-46
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Instant SEQ ID NO: 7 and Saia SEQ ID NO: 93, clone NIH-45-46
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Regarding claim 29, pertaining to a pharmaceutical composition comprising the T cell of claim 1 and a pharmaceutically acceptable excipient, Saia describes IV infusion of anti-gp120 CAR T cells into mice ([00118), Lines 1-9 and Fig. 30). This reasonably providing the limitation of a “pharmaceutically excipient” because the CAR T cells needed to be suspended in pharmaceutically acceptable liquid carrier in order for delivery via IV infusion.
Regarding claim 30, pertaining to a nucleic acid comprising a sequence encoding an anti-HIV CAR, Saia teaches the CAR of the disclosed invention is produced by recombinant DNA techniques, specifically, nucleic acids encoding the several regions of the chimeric receptor ([0058], Lines 1-6).
Zaia does not teach: the T cell comprises (1) a sequence encoding a Tat/Rev inhibitor or (2) a sequence encoding a CCR5 inhibitor.
These deficiencies are taught by Junghans.
The disclosure of Junghans is directed to nucleic acid constructs encoding chimeric receptors comprising an extracellular domain that targets HIV and host cells expressing the chimeric receptor (see Abstract). In contrast to the scFv of Zaia, the exemplary gp120-binding extracellular domain of the disclosure is CD4. Junghans teaches that the therapeutic T cells of the disclosure were susceptible to HIV infection resulting in fratricide and loss of effector cells, pointing to the need for eliminating the ability of HIV to infect and reproduce within the engineered therapeutic cells. ([0067], full paragraph).
Regarding claims 1 and 30, pertaining to the limitations wherein the T cell comprises nucleic acid comprising a sequence encoding a Tat/Rev inhibitor and a sequence comprising a CCR5 inhibitor, Junghans Fig. 2 teaches an exemplary construct encoding a chimeric receptor that binds gp120 (Myc-CD4-CD28-seta) and both anti-CCR5 shRNA and anti-Tat/Rev shRNA with a shared promoter.
Regarding claim 3, wherein the Tat/Rev inhibitor of the T cell of claim 1 is an anti-Tat/Rev shRNA, Junghans discloses exemplary Tat/Rev shRNA sense strand (bottom of Pg. 4).
Regarding claim 5, wherein the CCR5 inhibitor of the T cell of claim 1 is an anti-CCR5 shRNA, Junghans discloses exemplary CCR5 shRNA sense strand (top of Pg. 5).
It would have been prima facie obvious to one having ordinary skill in the art at the time of filing to modify the anti-HIV CAR T cells of Zaia with the addition of anti-Tat/Rev shRNA and anti-CCR5 shRNA as taught by Junghans. One would have been motivated to do so because Junghans teaches the engineered cells are susceptible to HIV infection and subsequence fratricide from other anti-HIV engineered cells. Junghans teaches blocking of Tat/Rev and CCR5, would prevent the engineered cells from becoming infected by HIV. There would be an expectation of success in modifying the engineered T cells by incorporating a sequence encoding a Tat/Rev inhibitor and a CCR5 inhibitor into a recombinant nucleic acid in a T cell because shRNA for the two targets were known at the time of filing and the ability to transduce T cells with vectors encoding these shRNA was readily performed at the time of filing.
Claims 1, 3-5, 11-14, 29-30, and 72-74 are rejected under 35 U.S.C. 103 as being unpatentable over Zaia (WO2019/084018A1, published 02 May 2019, effectively filed 10/23/2017) in view of Junghans (US2013/0183276A1, published 07/18/2013, effectively filed 04/14/2010) as applied to claims 1, 3, 5, 11-14, 29-30, and 72-74 above, and further in view of Rossi (US2015/0072347A1, published 03/12/2015, effectively filed 08/01/2002, cited in IDS filed 11/17/2025).
The combined teachings of Zaia and Junghans teach a T cell comprising a nucleic acid comprising a sequence encoding and anti-HIV CAR, a sequence encoding a Tat/Rev inhibitor, and a sequence encoding a CCR5 inhibitor. Junghans specifically teaches the Tat/Rev inhibitor is an anti-Tat/Rev siRNA derived from anti-Tat/Rev shRNA construct.
The combined teachings of Zaia and Junghans do not teach the anti-Tat/Rev shRNA comprises a sequence having at least 95% sequence identity to SEQ ID NO: 10.
This deficiency is taught by Rossi.
The disclosure of Rossi is directed to methods and kits for producing siRNA expression cassettes and expressing amplified expression cassettes in cells (see Abstract). Rossi teaches the use of hairpin precursors (i.e. shRNA, see Fig. 6).
Regarding claim 4, wherein the anti-Tat/Rev shRNA according to claim 3 comprises a sequence having at least 95% sequence identity to SEQ ID NO: 10, Rossi teaches SEQ ID NO: 20, which comprises SEQ ID NO: 10. The construct of Rossi’s SEQ ID NO: 20 was used a positive control for screening variant Tat/Rev shRNA constructs and as seen in Fig. 6 has proven HIV-inhibition activity. The alignment is shown below:
Instant SEQ ID NO: 10 and Rossi SEQ ID NO: 20
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It would have been prima facie obvious to one having ordinary skill in the art at the time of filing to use the anti-Tat/Rev shRNA sequence of Rossi in the engineered T cell of Zaia and Junghans comprising an anti-Tat/Rev shRNA. One would have been motivated to do so because Rossi provides the sequence for a shRNA comprising a Tat/Rev specific anti-sense hairpin RNA, nucleotide loop, and sense hairpin RNA. This construct is used in the reference as a positive control, with proven ability to bind the Tat/Rev target. The use of the anti-Tat/Rev shRNA of Rossi constitutes a simple substitution of one known element for another to obtain predictable results. There would be an expectation of success in using the anti-Tat/Rev shRNA of Rossi in the engineered cell of Zaia and Junghans because Rossi demonstrates the anti-Tat/Rev shRNA has proven Tat/Rev inhibition and the construct could readily be incorporated into CAR T cells at the time of filing.
Claims 1, 3, 5, 7, 11-14, 29-30, 32, and 72-74 are rejected under 35 U.S.C. 103 as being unpatentable over Zaia (WO2019/084018A1, published 02 May 2019, effectively filed 10/23/2017) in view of Junghans (US2013/0183276A1, published 07/18/2013, effectively filed 04/14/2010) as applied to claims 1, 3, 5, 11-14, 29-30, and 72-74 above, and further in view of Alma (US2019/00541119A1, published 02/21/2019, effectively filed 07/18/2017, cited in IDS filed 11/17/2025).
The combined teachings of Zaia and Junghans teach a T cell comprising a nucleic acid comprising a sequence encoding and anti-HIV CAR, a sequence encoding a Tat/Rev inhibitor, and a sequence encoding a CCR5 inhibitor.
The combined teachings of Zaia and Junghans do not teach the nucleic acid further comprises a sequence encoding a hypoxanthine phophoribosyltransferase (HPRT) inhibitor.
The disclosure of Alma is directed to a method of generating lymphocytes for adoptive transfer comprising generating HPRT-deficient lymphocytes from a donor sample and positively selecting for the HPRT-deficient lymphocytes ex vivo to isolate the population of modified lymphocytes (Fig. 1 and Pg. 20, claim 1).
Regarding claims 7 and 32, wherein said nucleic acid of claim 1 and the nucleic acid of claim 30 further comprise a sequence encoding an HPRT inhibitor, Alma teaches production of CAR T cells comprising a CAR construct and HPRT shRNA construct on a single lentiviral vector ([0142], Lines 1-5). Alma further teaches expanding the CAR T/ HPRT shRNA cells with 6TG, a purine analog that causes cell death when incorporated into the DNA and RNA in the cell ([0143], Lines 1-4). HPRT is required for incorporation of the purine analog, therefore HPRT-deficient T cells are resistant to cell death (rationale diagramed in Alma Fig. 7). Alma distills to practice HPRT inhibition for positive selection of engineered cells (Results in Fig. 9A and 9B).
It would have been prima facie obvious to one having ordinary skill in the art at the time of filing to modify the CAR T cell of Saia and Junghans by inhibiting HPRT as taught by Alma. One would have been motivated to do so because Alma distills to practice the use of HPRT knockdown or knockout for “chemoselection” of engineered cells based on their resistance to 6TG and provides evidence that this method does indeed allow for positive selection of modified T cells. There would be an expectation of success in incorporating HPRT inhibition into the T cell of Saia and Junghans because Alma demonstrates using techniques known at the time of filing that HPRT inhibition facilitates positive selection of engineered cells in the presence of 6TG.
Claims 1, 3, 5, 10-14, 29-30, and 72-74 are rejected under 35 U.S.C. 103 as being unpatentable over Zaia (WO2019/084018A1, published 02 May 2019, effectively filed 10/23/2017) in view of Junghans (US2013/0183276A1, published 07/18/2013, effectively filed 04/14/2010) as applied to claims 1, 3, 5, 11-14, 29-30, and 72-74 above, and further in view of Holen (Nucleic Acids Res. 2005 Aug 19;33(15):4704-10).
The combined teachings of Zaia and Junghans teach a T cell comprising a nucleic acid comprising a sequence encoding and anti-HIV CAR, a sequence encoding a Tat/Rev inhibitor, and a sequence encoding a CCR5 inhibitor.
The combined teaching of Zaia and Junghans do not teach the anti-CCR5 shRNA comprises a wobble base.
The disclosure of Holen is directed to RNA interference and investigating the factors that determine the specificity and activity of the active product- the siRNA. In their study they investigated the in vivo toleration of wobble G:U mutations in high activity siRNAs (see Abstract). Holen teaches wobble mutations in the terminal nucleotide in a series of low and high activity siRNA increased the silencing capacity. Holen was the first to demonstrate the enhancing effect in mammalian cells in vivo (Pg. 4705, Left column, Full paragraph 3, entire paragraph).
Regarding claim 10, wherein the anti-CCR5 shRNA of the T cell of claim comprises a wobble base, Holen teaches wobble base insertion in their siRNA, demonstrating that a wobble mutation in the 5’ terminal region improved activity compared with the wild-type siRNA (Pg. 4708, Left column, Lines 1-4, and Fig. 5C).
It would have been prima facie obvious to one having ordinary skill in the art at the time of filing to optimize the CCR5 shRNA of Saia and Junghans with the introduction of wobble bases. One would have been motivated to do so because Holen teaches insertion of wobble mutations in the target-binding siRNA can enhance their inhibitory activity. There would be an expectation of success in inserting certain wobble mutations into the CCR5 shRNA of Zaia and Junghans because Holen teaches that locations of wobble mutations can readily be assayed to determine which wobble mutations are tolerated and produce enhanced inhibitory activity.
Allowable Subject Matter
A search of the prior art did not identify prior art for SEQ ID NOs: 9 and 11.
Conclusion
No claims are allowed.
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/CAROL ANN CHASE/Examiner, Art Unit 1646
/HONG SANG/Primary Examiner, Art Unit 1646
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