Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 06 November 2025 has been entered.
CLAIMS UNDER EXAMINATION
Claims 1, 5-6, 8, 12, 49-52, 54-58 and 60-64 have been examined on their merits.
PRIORITY
Provisional Application 62/432202, filed on 09 December 2016, is acknowledged.
WITHDRAWN REJECTIONS
The previous rejections have been withdrawn due to claim amendment.
REJECTIONS
New grounds of rejection have been necessitated by claim amendment.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 5-6, 8, 12, 49-52, 56-58 and 60-64 are rejected under 35 U.S.C. 101 because the claimed invention is not directed to patent eligible subject matter as evidenced by Kersh et al. (previously cited; Rapid Demethylation of the IFN-γ Gene Occurs in Memory but Not Naïve CD8 T cells. J Immunol (2006) 176 (7): 4083–4093), Abdelsamed (Human memory CD8 T cell effector potential is epigenetically preserved during in vivo homeostasis. J Exp Med (2017) 214 (6): 1593–1606), Scharer et al. (Global DNA methylation remodeling accompanies CD8 T cell effector function. J Immunol. 2013 September 15; 191(6): 3419–342) and Basu et al. (cited as prior art in the rejections below).
Based on the claims as a whole, claims 1, 5-6, 8, 12, 49-52, 56-58 and 60-64 are determined to be directed to a law of nature/natural principle. The rationale for the determination is explained below.
Question 1: Is the claim to a process, machine manufacture or composition of matter? Yes, the invention recited in claim 1 is a process.
Question 2A Prong 1: Is the claim directed to a law of nature, a natural phenomenon, or an abstract idea (judicially recognized exceptions)? Yes, claim 1 is directed to a law of nature and an abstract idea.
(a) The limitations in the claim that set forth the law of nature is:
Claim 1 is directed to a method of producing a population of CAR modified CD8+ T cells having increased activity. The claim recites measuring the methylation level of Tcf7, T-bet and Eomes loci in CD8+ T cells. The claim identifies cells with decreased methylation as having increased T cell activity. The law of nature is a correlation between T cell activity and decreased methylation level.
As evidenced by the published specification of the instant specification the methylation status of the loci of effector cytokines, transcription factors, or regulators of cellular proliferation can be used to predict CD8 T-cell activity ([0017]). As evidenced by the instant specification, the methylation status of genes, promoters, and/or transcription factors of Tcf7, T-bet, eomesodermin (Eomes), IFNγ, granzyme K (GzmK), granzyme B (GzmB), Foxp1, CCR7 and Myc can be used for prediction of T-cell activity ([0017]).
As evidenced by Kersh et al., it is well known in the art that DNA methylation negatively affects gene expression (see page 4083, right column, second paragraph). In mammals, DNA methylation occurs at cytosines within CpG dinucleotide sequences, and coincides with repressed or inactive chromatin.
As evidenced by Abdelsamed, maintenance of human memory CD8 T cell effector potential during in vitro and in vivo homeostatic proliferation is coupled to preservation of acquired DNA methylation programs (Abstract). As evidenced by Abdelsamed, T-bet and Eomes have well-established roles in CD8 T cell effector and memory differentiation. Consistent with the relative level of gene expression, all memory CD8 T cells were generally demethylated at regions downstream of the transcriptional start site of T-bet and Eomes relative to that in naive T cells. (See page 1596, left column, last paragraph). As evidenced by Scharer et al., the transcription factor Tcf7, is essential for lymphocyte development and differentiation (last paragraph of page 5). The promoter region of Tcf7 is constitutively unmethylated (last sentence of page 5 bridging first sentence of page 6).
Therefore claim 1 is based on the natural correlation between decreased methylation and cell activity. The abstract idea is comparing cells with a decreased methylation level at a claimed loci to control cells (a mental process). The abstract idea and natural phenomenon are judicial exceptions.
Question 2A Prong 2: Does the claim recite additional elements that integrate the judicial exception into a practical application? No.
Claim 1 has been amended to recite CAR modified CD8+ T cells. The method steps do not modify cells. The method steps are directed to measuring methylation in a population of cells which have already been modified. A CAR modified CD8+ T cell is a T cell. While the cells are not naturally occurring, the claim is directed to a law of nature: a natural correlation between methylation and T cell activity. Separating cells (e.g., isolating a desired cell type) from a population of cells is well known in the art and does not add significantly more to the judicial exceptions. This step only separates naturally occurring cells with decreased methylation.
Question 2B: Do the claims recite any additional elements? Yes.
With respect to Step 2B, limitations that were found to be enough to qualify as “significantly more” when recited in a claim with a judicial exception include:
Improvements to another technology or technical field.
Improvements to the functioning of the computer itself.
Applying the judicial exception with, or by use of, a particular machine.
Effecting a transformation or reduction of a particular article to a different state or thing
Adding a specific limitation other than what is well-understood, routine and conventional in the field, or adding unconventional steps that confine the claim to a particular useful application.
Other meaningful limitations beyond generally linking the use of the judicial exception to a particular technological environment.
With respect to Step 2B, limitations that were found not to be enough to qualify as “significantly more” when recited in a claim with a judicial exception include:
Adding the words ‘‘apply it’’ (or an equivalent) with the judicial exception, or mere instructions to implement an abstract idea on a computer
Simply appending well-understood, routine and conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, e.g., a claim to an abstract idea requiring no more than a generic computer to perform generic computer functions that are well understood, routine and conventional activities previously known to the industry
Adding insignificant extrasolution activity to the judicial exception, e.g., mere data gathering in conjunction with a law of nature or abstract idea
Generally linking the use of the judicial exception to a particular technological environment or field of use.
Does the additional element result in the claim amounting to significantly more?
No.
Regarding claim 1: Claim 1 recites a CAR modified CD8+ T cell. This is a CD8+ T cell. The claim encompasses any CAR. The specification discloses CAR modified T cells ([0028]). As evidenced by the published specification, the methylation status of the loci of effector cytokines, transcription factors, or regulators of cellular proliferation can be used to predict CD8 T-cell activity ([0017]). As evidenced by the instant specification, the methylation status of genes, promoters, and/or transcription factors of Tcf7, T-bet, eomesodermin (Eomes), IFNγ, granzyme K (GzmK), granzyme B (GzmB), Foxp1, CCR7 and Myc can be used for prediction of T-cell activity ([0017]). The specification does not indicate the presence of a CAR changes the judicial exception (i.e. the natural correlation between decreased methylation of the claimed loci recited in claim 1 and increased T cell activity). This limitation does not result in significantly more than the correlation between CD8+ T cell methylation and activity.
The separation step recited in claim 1 is interpreted to be an insignificant extra-solution activity that does not add significantly more to the law of nature and abstract idea. While the claims recites comparison to a control population, as evidenced by the evidentiary art, CD8+ T cells are differentially methylated at the loci recited in claim 1. Claim 1 recites “wherein the second population of CD8+T cells has increased expansion potential as compared to the expansion potential of the control cells when exposed to immune checkpoint blockade therapy”. The wherein clause appears to be an observation of the future outcome. Note it appears the exposure to immune blockade does not appear to be a positively recited limitation. Meaning the claim appears to be indicating future intended use, i.e. when exposed. A comparison can be made by visually comparing the number of cells in both populations using a microscope. Comparison is a mental process and a judicial exception
Claim 5 is directed to the methylation of at least one CpG site. As evidenced by Kersh, DNA methylation negatively affects gene expression (supra). In mammals, DNA methylation occurs at cytosines within CpG dinucleotide sequences and often coincides with repressed or inactive chromatin (supra). As evidenced by Kersh above, demethylation at CpG sites is correlated with cell activation and proliferation. Therefore claim 5 recites a naturally occurring phenomenon.
Regarding claim 6: As set forth, demethylation of the of the claimed loci is a naturally occurring phenomenon in CD8+ T cells. Therefore claim 6 reads on a judicial exception.
Regarding claim 8: As evidenced by Scharer, demethylation at loci of
effector molecules, including IFNγ, GZMB, and GZMK is observed in all memory T cell subsets (see page 1596, right column, second paragraph). Therefore claim 8 is directed to the natural correlation between methylation states and CD8+ T cell function. This is a judicial exception.
Regarding claim 12: The claim recites administration at a level of high generality to an unspecified patient. Therefore the claim is not interpreted to be directed something significantly more than the judicial exception.
Regarding claim 49: The claim further comprises decreasing Dnmt3a (DNA methyltransferase 3a) activity prior to measuring methylation level. As evidenced by the instant specification, decreased Dnmt3a activity results in decreased methylation ([0020]). As set forth above, there is a naturally occurring correlation between demethylation and cell activity. Therefore the claim does not recite something markedly different.
Claim 50 further limits the T cell activity recited in claim 1. As set forth above, Kersh teaches activated cells have increased proliferation. Therefore claim 50 recites a naturally occurring phenomenon that occurs in demethylated cells.
Regarding claim 51: The claim further comprises contacting the cells with a DNA methyl transferase inhibitor. As evidenced by the instant specification, decreased DNA methyl transferase activity results in decreased methylation ([0020]). Therefore the claim does not recite something more than the judicial exceptions (i.e. a correlation between decreased methylation and increased cell activity).
Claim 52 recites the contacting occurs in vitro. This limitation does not recite something more than the judicial exceptions (i.e. a correlation between decreased methylation and increased cell activity).
Claim 56 recites a characteristic of cells with decreased methylation. The claim does not recite something markedly different than the recited judicial exception.
Claim 57 recites how decreasing Dnmt3a activity occurs. This limitation is used to make the correlation between methylation and activity. Therefore it does not result in something significantly more.
Claims 58 and 60 further limit the T cell activity recited in claim 1. As set forth above, Kersh teaches activated cells have increased proliferation (hence, increased cell division). As evidenced by Kersh, both the IFN-γ and IL-2 promoters are demethylated in CD8 T cells upon activation (page 4087, right column, third paragraph). Therefore the claims are directed to a naturally occurring phenomenon.
Claim 61 further limits the methyltransferase of claim 51. Therefore the claim does not recite something more than the judicial exceptions (i.e. a correlation between decreased methylation and increased cell activity).
Claim 62 recites assays for measuring the judicial exception (i.e, methylation level). These are interpreted to be insignificant extra-solution activities because the assays are performed as a necessary data gathering step in order to make the assessment. Claim 63 recites the amount of cells with decreased methylation. The recitation of an amount does not amount to something markedly different than the recited natural phenomenon.
Claim 64 encompasses a control population of naturally occurring cells with a methylation profile that has not been modulated. Therefore the claim is directed to a judicial exception that does not recite something markedly different than the natural correlation recited in claim 1.
Therefore claims 1, 5-6, 8, 12, 49-52, 56-58 and 60-64 are not eligible subject matter under 35 USC 101.
APPLICANT’S ARGUMENTS
The arguments made in the response filed on 06 November 2025 are acknowledged.
Argument: The Applicant argues the amended claims are directed to a non-naturally occurring T cell. The Applicant asserts “a natural process would not be expected to involve the recited CAR T cells” (see page 9, first paragraph).
Response to Argument: The rejection is not based on the recitation of a natural product. The rejection is based on a law of nature. The CAR CD8+ T cells recited in claim 1 are still CD8+ T cells. While the Applicant argues a natural process would not be expected to involve CAR T cells, the specification indicates it does. The instant specification does not indicate the presence of a CAR changes the judicial exception (i.e. the natural correlation between decreased methylation of the claimed loci recited in claim 1 and increased T cell activity). The specification discloses CAR modified T cells. As evidenced by the published specification, the methylation status of the loci of effector cytokines, transcription factors, or regulators of cellular proliferation can be used to predict CD8 T-cell activity ([0017]). As evidenced by the instant specification, the methylation status of genes, promoters, and/or transcription factors of Tcf7, T-bet, eomesodermin (Eomes), IFNγ, granzyme K (GzmK), granzyme B (GzmB), Foxp1, CCR7 and Myc can be used for prediction of T-cell activity ([0017]).
The amended limitation does not result in significantly more than the correlation between CD8+ T cell methylation and activity.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1, 5, 6, 8, 12, 50, 54-56, 58, 60, 62 and 64 are rejected under 35 U.S.C. 103 as being unpatentable over Golubovskaya et al. (previously cited; Different subsets of T cells, Memory, Effector Functions and CART-T Immunotherapy. Cancers (Basel). 2016 Mar; 8(3): 36) in view of Scharer et al. (previously cited; Global DNA methylation remodeling accompanies CD8 T cell effector function. J Immunol. 2013 September 15; 191(6): 3419–342), Araki et al. (Histone Acetylation Facilitates Rapid and Robust Memory CD8 T Cell Response through Differential Expression of Effector Molecules. J Immunol. 2008 Jun 15;180(12):8102–8108) and Makar et al. (DNA Methylation Is a Nonredundant Repressor of the Th2 Effector Program. J Immunol 1 October 2004; 173 (7): 4402–4406) as evidenced by Kersh.
Golubovskaya is directed to the role of different T cell subsets in CAR-T therapy (Abstract). The art teaches CAR-T therapy includes withdrawal of T cells from cancer patients used for expansion (see page 8, last paragraph). Figure 6 identifies the use of different T cell subsets as an approach to increase the efficacy of CAR-T cell therapy (see text of Figure 6). Golubovskaya teaches the importance of analyzing variations between a T cell subset’s functions (memory and effector) and the individual patient’s T cell profile in the efficacy of CAR-T cell immunotherapy (page 2, first paragraph). The art teaches the importance of specific T cell subset functions for effective adoptive immunotherapy (page 5, first paraph).
Golubovskaya teaches the different subsets of CD8+ T cells (section 4 on page 4). As set forth above, the art teaches cells are withdrawn from a patient for CAR-T therapy. Therefore the cells would comprise the subsets taught by Golubovskaya. Effector function is increased upon CD8+ T cell differentiation, while memory and proliferation are decreased (see section 4 on page 4). The art teaches the effector and memory T cell functions are regulated by genetic profiles of key effector genes and also by epigenetic mechanisms such as chromatin state (see page 6). Figure 4 identifies naïve and memory/effector cells as different CD8+ subsets.
The art teaches memory CD8+ T cells are characterized by more rapid effector function upon infection versus naïve T cells that are dependent on specific transcriptional profiles of the key effector genes, IFNγ, Gzmb (hence, granzyme B) and Prf1. The art teaches infection caused decreased nucelosomal density and less methylation of H3K27 in interferon-gamma and granzyme B chromatin that persisted in the memory stages (see second paragraph of section 6 on page 5).
The art teaches sorted CD8 cell populations and T cell subsets with specific memory markers and epigenetic profiles should be analyzed and used for regulating the efficacy of CAR-T therapy (see last paragraph of page 8 bridging first paragraph of page 9). Therefore the art teaches sorting and analyzing CD8 cell population for efficacy in CAR-T therapy.
Golubovskaya teaches a correlation decreased methylation of effector genes and effector function in CD8+ T cells. The art is silent regarding TCf7, T-bet and Eomes loci.
Scharer teaches during effector CD8 T cell differentiation, DNA methylation is remodeled such that changes in DNA methylation at gene promoter regions negatively correlated with gene expression (Abstract). DNA methylation remodeling accompanies the acquisition of the CD8 T cell effector phenotype and repression of the naïve cell state (see Abstract). Scharer teaches DNA methylation inversely correlates with gene expression (see page 6, third paragraph). Scharer teaches differentially methylated regions (DMRs) occurred at biologically relevant gene promoters that are necessary for effector CD8 T cell function. The art teaches Gzmb is a gene with a demethylated promoter DMR. (Figure 1F). The Gzmb gene encodes the serine protease Granzyme B, which is important for effector CD8 T cell cytotoxic function and in CD8 effectors compared to naïve cells was strongly demethylated in the gene body and almost completely lacked a methyl-DNA signal at its promoter region (see page 5, last paragraph). The art also teaches granzyme k also contained DMRs that become almost completely demethylated in CD8 effectors (see page 6, second paragraph).
Scharer teaches the transcription factor Tcf7, is essential for lymphocyte development and differentiation (last paragraph of page 5). The promoter region of Tcf7 is constitutively unmethylated (last sentence of page 5 bridging first sentence of page 6).
Scharer identifies DMRs at CPG island shores of Tcf7 (first paragraph of page 6). Scharer analyzes methylation of CpG sites (page 3, last paragraph).
To understand the mechanism regulating the effector function of memory CD8 T cells, Araki examined expression and chromatin state of a key transcription factor (eomesodermin, EOMES) and two of its targets: perforin (PRF1) and granzyme B (GZMB) (Abstract). Araki teaches there is an inverse correlation between the methylation of the 5′UTR and EOMES expression (see page 2, second paragraph).
Makar teaches T-bet is a “master regulator” transcription factor (last paragraph right column, page 4403). Markar et al. analyze the contribution of DNA methylation and DNA methyltransferase 1 (Dnmt1) in the regulation of T cell effector functions using T cells from CD4CreDnmt12lox mice in which the Dnmt1 gene is efficiently deleted. T cells from these mice do not express Dnmt1 and have markedly reduced levels of DNA methylation, both globally and at several specific loci (see page 4402, last paragraph of left column bridging first paragraph of right column). Figure 3 illustrates cells with reduced levels of DNA methylation have decreased T-bet expression (see Figure 3, comparing Dnmt-/- CD8 to WT CD8).
It would have been obvious to measure the methylation level of Tcf7, T-bet and Eomes in CAR CD8+ T cells. One would have been motivated to do so since Golubovskaya analyzes the methylation state of CD8+ T cell effector genes and Scharer, Araki and Makar teaches hypomethylation of these loci is associated with increased function. One would separate these cells with decreased methylation at these loci to obtain a population with increased effector function for therapeutic use. One would be further motivated to do so since Golubovskaya teaches use of different subsets to increase efficacy of CAR-T cell therapy. One would have had a reasonable expectation of success since Golubovskaya teaches sorted CD8 cell populations and T cell subsets with specific memory markers and epigenetic profiles should be analyzed and used for regulating the efficacy of CAR-T therapy. One would have expected similar results since each reference analyzes methylation state and effector function in the same cell type. Because cells with decreased methylation at the claimed loci are rendered obvious, they would be expected to have increased expansion potential as compared to the expansion potential of the control cells when exposed to immune checkpoint blockade therapy. Therefore claim 1 is rendered obvious
As evidenced by Kersh, in mammals, DNA methylation occurs at cytosines within CpG dinucleotide sequences and often coincides with repressed or inactive chromatin (supra). Therefore claim 5 is included in this rejection.
Golubovskaya is silent regarding whether the CpG site is located within a promoter or coding sequence (claim 6).
The teachings of Scharer are reiterated. Scharer analyzes methylation of CpG sites (page 3, last paragraph). Scharer analyzes methylation using MeDIP-seq Analysis (see page 3, last paragraph).
It would have been obvious to analyze a CpG site within a promoter sequence of granzyme B. One would have been motivated to do so since Golubovskaya teaches analyzing the methylation status of granzyme B and Scharer teaches Gzmb is a gene with a demethylated promoter DMR (supra). One would have had a reasonable expectation of success since Scharer teaches methylation occurs at CpG sites within the promoter. One would have expected similar results since both references are directed to methylation of the same gene. Therefore claim 6 is rendered obvious.
Golubovskaya teaches CD8+ T cells with less granzyme B methylation have a greater effector function relative to naïve cells (supra). Therefore claim 8 is rendered obvious.
One would administer the cells to a subject since Golubovskaya teaches memory/effector cells can be used for CAR T therapy. Therefore claim 12 is included in this rejection.
Claim 50 recites the activity upon T cell receptor engagement. The claim is interpreted to mean the cells with increased activity recited in claim 1 have one of the characteristics when the receptor is engaged. The art teaches decreased methylation is associated with memory (supra; page 5, paragraph four). Therefore claim 50 is included in this rejection.
Golubovskaya teaches inhibition of immune checkpoints such as PD-1 and CTLA-4 as an potential approach to increase efficacy of CAR-T cell therapy (text of Figure 6; page 8, first paragraph). Golubovskaya teaches sorted CD8 cell populations and T cell subsets with specific memory or stem cell memory markers and genetic, epigenetic, and metabolic profiles in combination with immune checkpoint inhibitors (hence, Immune checkpoint blockade) should be analyzed and used for regulating the efficacy of CAR-T therapy. Therefore claim 54 is included in this rejection.
Because the art teaches administration of cells and ICB, the method would be expected to have the properties recited in claim 55.
The art teaches a subset of CD8+T cells that reads on claim 1. Therefore it would be expected to have the properties recited in claim 56.
Because the claimed method is rendered obvious, it would be expected to result in the T cell activities recited in claims 58 and 60.
Golubovskaya is silent regarding the method used to measure methylation (claim 62).
It would have been obvious to analyze gene methylation using MeDIP. One would have been motivated to do so since Golubovskaya teaches analyzing the methylation status of the granzyme B gene and Scharer analyzes methylation using MeDIP-seq Analysis.
The skilled artisan would use a technique known in the art for analyzing granzyme B gene. One would have had a reasonable expectation of success since Scharer teaches MeDIP can be used to analyze granzyme B gene methylation status. Therefore claim 62 is included in this rejection.
The art teaches naïve CD8+ T cells (supra). Therefore claim 64 is included in this rejection.
Therefore Applicant’s Invention is rendered obvious as claimed.
Claims 51-52 and 61 are rejected under 35 U.S.C. 103 as being unpatentable over Golubovskaya in view of Scharer et al., Araki et al. and Makar as applied to claim 1 above, and further in view of Stresemann et al. (previously cited; Azacytidine causes complex DNA methylation responses in myeloid leukemia. Mol Cancer Ther. 2008 Sep;7(9):2998-3005).
Claim 1 is rejected on the ground set forth above. The teachings of Golubovskaya Scharer, Araki and Makar are reiterated. Golubovskaya is directed to CAR-T therapy for cancer patients. The art measures CD8+ T cell methylation. The art does not teach the use of a DNA methyltransferase inhibitor prior to measuring.
Stresemann teaches aberrant DNA methylation patterns play an important role in the pathogenesis of hematologic malignancies. The DNA methyltransferase inhibitors azacytidine and decitabine have shown significant clinical benefits in the treatment of myelodysplastic syndrome (MDS), but their precise mode of action remains to be established. Both drugs have been shown the ability to deplete DNA methyltransferase enzymes and to induce DNA demethylation and epigenetic reprogramming in vitro.
It would have been obvious to treat cells with a DNA methyltransferase inhibitors prior to measuring. One would have been motivated to do so since Golubovskaya teaches demethylation of CD8+T cells and Stresemann treatment with said inhibitors results in DNA demethylation. One would do so to produce CD8+T cells with increased effector function. One would have had a reasonable expectation of success since Stresemann teaches the inhibitors can be used in vitro or in vivo. One would have expected similar results since both references are directed to DNA demethylation. Therefore claim 51 is rendered obvious. Stresemann teaches cells can be contacted in vitro (supra). Therefore claim 52 is included in this rejection. Stresemann teaches azacytidine (supra). Therefore claim 61 is included in this rejection.
Therefore Applicant’s Invention is rendered obvious.
Claims 49 and 57 are rejected under 35 U.S.C. 103 as being unpatentable over Golubovskaya in view of Scharer et al., Araki et al. and Makar as applied to claim 1 above, and further in view of Youngblood (previously cited; Dnmt3a mediated de novo DNA methylation programming enforces T cell exhaustion. May 2015).
Claim 1 is rejected on the grounds set forth above. The teachings of Golubovskaya Scharer, Araki and Makar are reiterated. Makar teaches methylation in CD8 T cells can be reduced by eliminating Dnmt1 function.
The art does not teach decreasing Dnmt3a activity prior to measuring.
The art does not teach decreasing comprising mutagenesis of the gene encoding Dnmt3a.
Youngblood teaches CD8 T cells progressively lose their function during prolonged antigen exposure (first sentence). Repression of CD8 T cell effector functions, commonly referred to as T cell exhaustion limits the ability of the immune system. The art teaches deletion of Dnmt3a in activated CD8T cells blocked said cells from becoming exhausted (sixth line from bottom).
It would have been obvious to combine the teachings of the prior art by decreasing Dnmt3a activity in the CD8 T cells taught by Golubovskaya. One would have been motivated to do so since Golubovskaya is directed to active CD8 T cells used for therapy and Youngblood teaches decreasing Dnmt3a activity in the CD8 T. One would do so to prevent exhaustion of the CD8 T cells taught by Golubovskaya. One would have had a reasonable expectation of success since Youngblood teaches Dnmt3a can be decreased in activated CD8T cells. One would have expected similar results since both references are directed to active CD8+ T cells. Therefore claim 49 is rendered obvious. Youngblood teaches Dnmt3a deletion (mutagenesis; supra). Therefore claim 57 is included in this rejection.
Therefore Applicant’s Invention is rendered obvious as claimed.
Claim 63 is rejected under 35 U.S.C. 103 as being unpatentable over Golubovskaya in view of Scharer et al., Araki et al. and Makar as applied to claim 1 above, and further in view of Basu et al. (previously cited; Purification of Specific Cell Population by Fluorescence Activated Cell Sorting (FACS). J Vis Exp. 2010; (41): 1546).
Claim 1 is rejected on the grounds set forth above. The teachings of Golubovskaya Scharer, Araki and Makar are reiterated Golubovskaya teaches obtaining a population of sorted cells.
The art is silent regarding the amount of cells in the sorted population.
Basu teaches experimental and clinical studies often require highly purified cell populations (page 1, abstract). The art teaches cells can be sorted using fluorescence (FACS) to purify cell populations of known phenotype. Other bulk methods of purification include panning, complement depletion and magnetic bead separation. FACS is the preferred method when very high purity of the desired population is required (Abstract). Basu teaches sorting can be used to produce cell populations with greater than 97% purity (page 2, last paragraph).
It would have been obvious to sort cells to obtain a population of CD8+T with the decreased Tcf7, T-bet and Eomes in at least 30% of cells. One would have been motivated to do so since Golubovskaya teaches sorting cells to obtain a specific subset (population of cells) ad Basu teaches cells can be sorted to obtain cell populations with greater than 97% purity. One would have had a reasonable expectation of success since Basu teaches FACS can be used to sort cells to obtain a purity that reads on claim 63. One would have expected similar results since both references are directed to cell sorting. Therefore claim 63 is included in this rejection.
Therefore Applicant’s invention is rendered obvious as claimed.
APPLICANT’S ARGUMENTS
The arguments made in the response filed on 06 November 2025 are acknowledged.
Argument 1: The Applicant argues the Office has not identified any reference that teaches methylation levels of genomic loci comprising TCf7, T-bet and eomesodermin impacts response to ICB therapy in CD8+ CAR T cells, let alone whether or how such methylation levels correlate with CD8+ CAR T cell exhaustion potential in response to ICB therapy.
Response to Argument 1: Claim 1 is not directed to a method of treatment. The claims are directed to a method of producing a population of T cells with increased activity. Claim 1 recites “wherein the second population of CD8+T cells has increased expansion potential as compared to the expansion potential of the control cells when exposed to immune checkpoint blockade therapy”. The wherein clause appears to be an observation of the future outcome. The exposure to immune blockade does not appear to be a positively recited limitation. Meaning the claim appears to be indicating future intended use, i.e. when exposed.
Golubovskaya teaches the use of different T cell subsets as an approach to increase the efficacy of CAR-T cell therapy. The art teaches the effector and memory T cell functions are regulated by genetic profiles of key effector genes and also by epigenetic mechanisms such as chromatin state (see page 6). The art teaches memory CD8+ T cells are characterized by more rapid effector function upon infection versus naïve T cells that are dependent on specific transcriptional profiles of the key effector genes. Decreased methylation in key effector genes is associated with T cell function. The art teaches sorted CD8 cell populations and T cell subsets with specific memory markers and epigenetic profiles should be analyzed and used for regulating the efficacy of CAR-T therapy
While Golubovskaya is silent regarding methylation analysis of TCf7, T-bet and Eomes loci, Scharer et al., Araki et al. and Makar teach decreased methylation of genes is associated with CD8 T cell function.
Argument 2: The Applicant argues Zediak, which is not relied upon as prior art, teaches LCMV infection leads to reduced methylation through two effector gene loci (-IFNγ and Gzmb-) in CD8 T cells that persist into the memory phase of cells. The Arguments state the art teaches transcription occurs at the IFNγ locus but not the Gzmb locus.
Response to Argument 2: Claim 1 recites Tcf7, T-bet and Eomes. The arguments are directed to different loci (IFNγ and granzyme B). The arguments are not commensurate with the scope of the claim. As set forth above, Golubovskaya teaches CD8+ T cells with less granzyme B methylation have a greater effector function relative to naïve cells. The arguments are not persuasive.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NATALIE MOSS whose telephone number is (571) 270-7439. The examiner can normally be reached on Monday-Friday, 8am-5pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila Landau can be reached on (571) 272-0614. The fax phone number for the organization where this application or proceeding is assigned is (571) 270-8439.
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/NATALIE M MOSS/ Examiner, Art Unit 1653
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