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 .
Claims 104-123 are pending and being examined.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
2. Claim(s) 104, 117, and 123 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kato et al (Oncotarget, 2018, 9:11009-11019).
With regard to claim 104, Kato teaches:
providing a cancer cell line (C1R) expressing exogenous HLA (MHC) molecule, wherein the cells were transfected to express HLA-A*24:02 or HLA-A*02:01 genes; further providing cancer cell lines expressing HLA-A*24:02 (TE-8 and TE-11) (Materials And Methods, p. 11015, col. 1);
identifying somatic mutations in the TE-8 cancer cell lines (HLA-A*24:02), all as potential neoantigens;
predicting binding affinity of the neoantigens to HLA-A2402 by computer algorithm, selecting high affinity neoantigens, then confirming expression of the neoantigens by RNA sequencing;
utilizing peripheral blood from healthy donors to produce neoantigen-specific CD8+ T cells, and identify neoantigen-reactive T cells, wherein T cells were reactive against neoantigen derived from DPY19L4; and
perform TCR sequencing to determine the entire TCRA and TCRB chains in the FACS sorted T cells p. 11011, col. 1-2, figure 2B);
transducing T cells derived from peripheral blood of a healthy donor with the TCRA and TCRB sequences specific for DPY19L4 neoantigen (p. 11012, col. 1-2);
demonstrating the TCR-engineered T cells showed binding of specific dextramers loaded with the mutant but not with wild-type DPY19L4 peptide (Figure 3);
co-culturing the TCR-engineered cells with the C1R cancer cells stably expressing exogenous HLA-A*24:02 or HLA-A*02:01 and loaded with mutant or wild-type DPY19L4 peptide (i.e., cancer cell line expressing the endogenous antigen and exogenous MHC molecule) (p. 11012, col. 1);
identifying activated TCR-engineered cells by IFNγ ELISPOT assay, by ELISA, and by FACS sorting utilizing the CD137 marker (p. 11012, col. 1); wherein C1R cells were only recognized by the engineered T cells when C1R cells expressed HLA-A*24:02 and were loaded with the mutant DPY19L4 peptide (p. 11012, col. 2; Figure 3).
Kato further teach testing endogenously processed antigen recognition by engineered T cells comprising:
incubating DPY19L4 neoantigen-reactive TCR-engineered T cells with TE-8 cancer cells endogenously expressing the DPY19L4 neoantigen and expressing exogenous HLA-A*24:02 allele (TE-8 cancer cells were transfected to express HLA-A*24:02);
determining the DPY19L4 neoantigen-reactive TCR-engineered T cells were reactive against the TE-8 cancer cells expressing the DPY19L4 neoantigen and HLA-A*24:02 allele, but not reactive with mock-transfected TE-8 cells (p. 11012, col. 2; Figure 3); and
incubating DPY19L4 neoantigen-reactive TCR-engineered T cells with TE-11 cancer cells endogenously expressing the DPY19L4 neoantigen in a HLA-A*24:02 -restricted manner, and determining the T cells showed cytotoxic activity against the TE-11 cancer cells (p. 11013, col. 1; Figure 3).
With regard to claim 117, Kato teaches an isolated cancer sample from an ovarian cancer patient obtained before conducting the assays (p. 11011, col. 1-2).
With regard to claim 123, Kato teaches the TE-8 cell line expressing endogenous antigen and exogenous MHC molecule (HLA-A*24:02) that is expressed by a subject, as well as a T cell expressing a TCR that recognizes the antigen presented by the same MHC molecule. It is noted that claim 123 recites the “natively paired TCR” is “derived from the subject” however, this is a product by process situation. The instantly claimed TCR cannot be distinguished from the TCR of Kato, or distinguished from TCRs “derived from” any other subject.
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.
3. Claim(s) 104-120 and 123 are rejected under 35 U.S.C. 103 as being unpatentable over Kato et al (Oncotarget, 2018, 9:11009-11019); in view of Cafri et al (Nature Communications, 2019, 10:449, internet pages 1-9).
Kato teaches a set forth above:
providing a cancer cell line (C1R) expressing exogenous HLA (MHC) molecule, wherein the cells were transfected to express HLA-A*24:02 or HLA-A*02:01 genes because their endogenous MHC molecule is inactivated; further providing cancer cell lines expressing HLA-A*24:02 (TE-8 and TE-11) (Materials And Methods, p. 11015, col. 1);
identifying somatic mutations in the TE-8 cancer cell lines (HLA-A*24:02), all as potential neoantigens;
predicting binding affinity of the neoantigens to HLA-A2402 by computer algorithm, selecting high affinity neoantigens, then confirming expression of the neoantigens by RNA sequencing;
utilizing peripheral blood from healthy donors to produce neoantigen-specific CD8+ T cells, and identify neoantigen-reactive T cells, wherein T cells were reactive against neoantigen derived from DPY19L4; and
perform TCR sequencing to determine the entire TCRA and TCRB chains in the FACS sorted T cells p. 11011, col. 1-2, figure 2B);
transducing T cells derived from peripheral blood of a healthy donor with the TCRA and TCRB sequences specific for DPY19L4 neoantigen (p. 11012, col. 1-2);
demonstrating the TCR-engineered T cells showed binding of specific dextramers loaded with the mutant but not with wild-type DPY19L4 peptide (Figure 3);
co-culturing the TCR-engineered cells with the C1R cancer cells stably expressing exogenous HLA-A*24:02 or HLA-A*02:01 and loaded with mutant or wild-type DPY19L4 peptide (i.e., cancer cell line expressing the endogenous antigen and exogenous MHC molecule) (p. 11012, col. 1);
identifying activated TCR-engineered cells by IFNγ ELISPOT assay, by ELISA, and by FACS sorting utilizing the CD137 marker (p. 11012, col. 1); wherein C1R cells were only recognized by the engineered T cells when C1R cells expressed HLA-A*24:02 and were loaded with the mutant DPY19L4 peptide (p. 11012, col. 2; Figure 3).
Kato further teach testing endogenously processed antigen recognition by engineered T cells comprising:
incubating DPY19L4 neoantigen-reactive TCR-engineered T cells with TE-8 cancer cells endogenously expressing the DPY19L4 neoantigen and expressing exogenous HLA-A*24:02 allele (TE-8 cancer cells were transfected to express HLA-A*24:02);
determining the DPY19L4 neoantigen-reactive TCR-engineered T cells were reactive against the TE-8 cancer cells expressing the DPY19L4 neoantigen and HLA-A*24:02 allele, but not reactive with mock-transfected TE-8 cells (p. 11012, col. 2; Figure 3);
incubating DPY19L4 neoantigen-reactive TCR-engineered T cells with TE-11 cancer cells endogenously expressing the DPY19L4 neoantigen in a HLA-A*24:02 -restricted manner, and determining the T cells showed cytotoxic activity against the TE-11 cancer cells (p. 11013, col. 1; Figure 3).
Kato also teaches another method of identifying neoantigen-reactive T cells for higher clinical relevance comprising:
providing an ovarian cancer sample that is HLA-A*02:01 (thereby isolating a primary cancer cell before conducting the assays);
conducting whole exome sequencing on the ovarian cancer sample (HLA-A*02:01) to identify somatic mutations, as potential neoantigens;
predicting binding affinity of the neoantigens to HLA-A0201 by computer algorithm, selecting high affinity neoantigens;
utilizing peripheral blood from healthy donors to produce neoantigen-specific CD8+ T cells, identify neoantigen-reactive T cells, wherein one T cells was reactive against neoantigen peptide derived from RNF19B; and
performing TCR sequencing to determine the entire TCRS and TCRB chains in the neoantigen-reactive T cell (p. 11011, col. 1-2).
Kato teaches performing these methods to identify TCRs that are reactive to a patient’s tumor neoantigens, wherein the antigen-reactive T cells can be isolated from the patient’s peripheral blood, Preclinical studies show that adoptive transfer of neoantigen-specific TCR-engineered T cells can be effective against large and long-established solid tumors. Kato teaches their method allows for rapid identification of cancer neoantigen-specific TCRs using T cells derived from blood of HLA-matched healthy donors. Kato teaches patient-derived mutation-specific T cells might be functionally impaired because the cells are epigenetically imprinted to revert into an inactive state even after transient activation. Kato teaches using their pipeline for the efficient generation of neoantigen-specific T cells and the identification of their TCRs to develop personalized and cancer-specific adoptive immunotherapies using TCR-engineered T cells especially for progressive tumor or for bulky tumor which needs urgent treatments (p. 11010, and Figure 1).
Kato does not teach:
the method further comprises contacting non-cancer cells expressing an endogenous antigen in complex with the same exogenous MHC molecule in order to identify a second set of T cells (or TCR-expressing cells) reactive with the antigen, and that express a different TCR;
the genomic alteration of the cancer cell line and primary cancer cell have a correlation coefficient equal to or greater than 0.1;
preparing a pharmaceutical composition comprising the neoantigen-reactive T cell.
Cafri teaches an in vitro stimulation (IVS) method for identifying and isolating neoantigen-reactive T cells from a cancer patient, the method comprising:
Isolating normal and tumor cell samples from the cancer patient, conducting whole-exome and RNA sequencing in both samples to identify somatic mutations present in two metastatic tumors derived from the patient, wherein two endogenous neoantigens identified include SMAD5 and DDX1 mutations;
Isolating PBMCs from the patient and co-culturing them with autologous DCs loaded with RNA encoding the endogenous neoantigen (i.e., non-cancer cells presenting endogenous antigen with the patient’s MHC, wherein DCs do not naturally express the endogenous SMAD5 or DDX1 antigens expressed by the patient’s tumor cells);
Sorting the cells based on markers CD8, CD4, and T-cell activation marker 41BB to enrich for neoantigen-reactive T cells by FACS;
Expanding and screening the sorted cells for T cells reactive against specific neoantigens by co-culturing the enriched T cells with autologous DCs pulsed with each neoantigen (i.e., non-cancer cells presenting the neoantigen + patient’s MHC), and identifying T cells specifically reactive with the SMAD5 neoantigen;
Isolating a neoantigen-reactive T cell for single-cell RT-PCR to identify their T-cell receptor (TCR) Vβ and Vα sequences;
Genetically engineering autologous peripheral blood T cells to express the SMAD5-reactive TCR sequences; and
Determining that the genetically engineered T cell successfully recognizes the SMAD5 neoantigen that is HLA-restricted by the patient’s HLA molecule.
Cafri concludes that using IVS of memory T cells can lead to the identification and enrichment of neoantigen-reactive T cells (p. 2, col. 2 to p. 3, col. 1; Methods section).
Cafri teaches performing this method for the purpose of identifying and isolating tumor-reactive T cells from patient peripheral blood to they can be used to develop an effective personalized T cell-based cancer immunotherapy (abstract). Cafri teaches the prior art has already demonstrated that tumor-infiltrating lymphocytes (TILs) are enriched with neoantigen-specific T cells and that adoptive cell therapy using neoantigen-specific TIL can lead to durable tumor regression. Cafri teaches their method of isolating neoantigen-specific T cells from patient peripheral blood lymphocytes is a non-invasive approach for identifying and isolating neoantigen-reactive T cells or their T-cell receptors, and their approach detects and isolates T cells that target unique as well as shared somatic mutations in oncogenes (p. 2, col. 1). Cafri suggests using the identified neoantigen-reactive T cells or their TCRs for personalized treatment of cancer (Discussion).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to add step of identifying more neoantigen-reactive TCRs to antigen utilizing non-cancer cells presenting another antigen and same MHC molecule, and to identify different neoantigen-reactive TCRs. One would have been motivated to, and have a reasonable expectation of success to, given: (1) both Kato and Cafri teach isolating and identifying neoantigen-reactive TCRs from peripheral blood for the same purpose of producing neoantigen-reactive T cells or TCRs for personalized tumor therapy; (2) Cafri teaches this purpose can be accomplished by utilizing DCs (non-cancer cells) presenting neoantigen with a patient’s MHC; (3) Kato and Cafri demonstrate successfully producing neoantigen-reactive T cells and isolating TCR sequences utilizing either of their methods. It is well within the level of the ordinary skilled artisan to combine the two known methods of Kato and Cafri for the same purpose of producing neoantigen-reactive T cells and isolating TCR sequences, and with a reasonable expectation of success.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to identify the same mutation in the sequenced cancer cell line and sequenced patient tumor cells. One would have been motivated to, and have a reasonable expectation of success to, given: Kato and Cafri teach performing whole-exome sequencing on cancer cells or utilizing known sequence databases for a cancer cell line to identify somatic mutations that are neoantigen candidates for producing and isolating reactive TCRs for the same purpose of utilizing the TCRs in the adoptive T cell therapy of cancer. It is well within the level of the ordinary skilled artisan to identify the same neoantigen in a cancer cell line and patient tumor and to utilize the neoantigen in the assays taught by Kato and Cafri with a reasonable expectation of success.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to prepare a pharmaceutical composition comprising the neoantigen-reactive T cell identified by Kato and Cafri. One would have been motivated to, and have a reasonable expectation of success to, given: Kato and Cafri teach performing their assays for the same purpose to identify neoantigen-reactive T cells and TCRs for pharmaceutical use in treating cancer patients.
4. Claim(s) 104, 121 and 122 are rejected under 35 U.S.C. 103 as being unpatentable over Kato et al (Oncotarget, 2018, 9:11009-11019); in view of Qin et al (Journal of Surgical Research, 2019, 233:57-64).
Kato teaches a method as set forth above.
Kato does not teach killing the cancer cells chemically before activating the T cells.
Qin teaches chemically killed (mitoxantrone) cancer cells are still able to stimulate T cell activation (p. 60, col. 1; Figures 3 and 4).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to utilize chemically killed cancer cells in the method of Kato. One would have been motivated to, and have a reasonable expectation of success to, given Kato teaches utilizing cancer cells to stimulate reactive T cells and Qin teaches killed cancer cells still stimulate reactive T cells.
5. Conclusion: No claim is allowed.
6. Any inquiry concerning this communication or earlier communications from the examiner should be directed to LAURA B GODDARD whose telephone number is (571)272-8788. The examiner can normally be reached Mon-Fri, 7am-3:30pm.
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/Laura B Goddard/Primary Examiner, Art Unit 1642