Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 103
2. 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. This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
4. Claims 1-4, 6-8, 11-12, 28, and 37-40 are rejected under 35 U.S.C. 103 as being unpatentable over Parkhurst et al (Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 expression, Clinical Cancer Research, 23, 10, 2491-2505, published 15 May 2017) in view of McGinnis et al (MULTI-Seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid tagged indices, BioRxiv 387241, doi: https://doi.org/10.1101/387241).
Regarding claim 1, Parkurst teaches a method of isolating mutation-reactive T cells that mediated recognition of neoepitopes via upregulation of CD137 (i.e., identifying an antigen capable of activating a T cell; pg. 2491 column 2 ¶ 2). Parkurst teaches a unique biological sample comprising dendritic cells (DCs, i.e., antigen presenting cells that inherently comprise a surface-bound MHC; pg. 2493 column 1 ¶ 2 and 3), a unique antigen (DCs were electroporated with IVT RNAs encoding antigens; pg. 2493 column 1 ¶ 1, FIG 1 and associated caption), and a plurality of T cells having different TCR sequences (pg. 2493 column 1 ¶ 5, and FIG 1A specifically demonstrates the plurality of different TCRs in that only a small portion were activated by co-incubation with the DCs presenting a unique antigen). Parkhurst teaches that each plurality of T cells is cocultured with a population of DCs expressing a single antigen (i.e., the distinct antigens of each biological sample are different from the distinct antigens of other biological samples; FIG 1A). Parkhurst teaches the sorting of activated T cells by the upregulation of CD137 (i.e., sorting an activated T cell based on the expression of an activation induced marker; FIG 1A and pg. 2493 column 1 ¶ 5). Parkhurst teaches sequencing the sorted T cells by single cell sequencing (pg. 2493 column 2 ¶ 2).
Parkhurst does not teach that the biological sample comprises a distinct hashtag oligonucleotide (HTO) that is conjugated to a molecule that incorporates into the cell membrane of T cells and/or binds a cell surface marker expressed by T cells, that the HTO of each unique biological sample is different than the distinct HTOs of other biological samples such that the distinct HTO of each unique biological sample is associated with the distinct antigen of that unique biological sample, or that the distinct HTO is identified by sequencing to identify the distinct antigen of the unique biological sample from which the HTO-labeled activated T cell was sorted.
However, McGinnis teaches a method wherein individual biological samples are labeled with a distinct HTO that is conjugated to a molecule that incorporates into a cell membrane (pg. 3 ¶ 3 and FIG 1), and that the distinct HTOs of each sample are different than the distinct HTOs of other samples (each sample was barcoded before pooling, and each barcode has a Hamming distance of >3 relative to all other utilized barcodes; pg. 6 ¶ 2, pg. 11 ¶ 2, and FIG 1). McGinnis teaches that barcodes are sample-specific (i.e., a distinct HTO is associated with the conditions of a distinct sample; FIG 2). McGinnis further teaches that the HTO labeling is stable and barcodes do not appreciably exchange after pooling and FACS sorting (pg. 14 ¶ 5 and FIG S1)
It would have been obvious to one having ordinary skill in the art to have modified the antigen-TCR pairing method taught by Parkhurst to incorporate the HTO labels taught by McGinnis to arrive at the instantly claimed invention with a reasonable expectation of success. One having ordinary skill in the art would have been motivated to make this modification because the method taught by McGinnis allows each sample to be uniquely labeled such that all samples can be pooled together before FACS sorting and sequencing because McGinnis teaches that pooling these samples substantially reduces cost and reagent usage (pg. 13 ¶ 3 and pg. 6 ¶ 2). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the sequencing of nucleic acids related to distinct experimental conditions. Further, McGinnis specifically teaches that MULTI-seq is universally applicable to all cells with accessible plasma membranes (i.e., the T cells of Parkhurst).
Regarding claim 2, Parkhurst teaches that the T cells are cocultured with DCs (i.e., antigen presenting cells having surface bound MHC; pg. 2493 column 1 ¶ 3, 4 and 5) and that tumor-infiltrating lymphocytes (i.e., T cells) are isolated from tumor biopsy fragments (i.e., isolated from a subject; pg. 2492 column 2 ¶ 3).
Regarding claim 3, Parkhurst teaches that the APCs are monocyte-derived dendritic cells (pg. 2492, column 2, ¶ 4).
Regarding claims 4 and 6, Parkhurst teaches that the sorting is fluorescence activated cell sorting of activated T cell based on the expression of CD137 (i.e., the AIM; pg. 2493, column 1, ¶ 5) and that the presence of the CD137 surface marker was determined based on a fluorescently labeled antibody (pg. 2492, column 2, ¶ 2).
Regarding claims 7, 8 and 40, Parkhurst teaches that after sorting T cells are expanded, the dominant TCR α/β chains are identified and cloning into a retroviral vector to transduce open-repertoire peripheral blood lymphocytes (PBLs), and that these transduce PBLs were determined to mediate specific peptide recognition (i.e., multimer analysis; FIG 2 and pg. 2498, columns 1 and 2, ¶ 1). Parkhurst additionally teaches the %CD137 expression of the expanded (i.e., post-sorting) population of T cells in response to coincubation with DCs carrying relevant peptide antigens (i.e., measures the protein expression levels of CD137; FIG 2).
Regarding claim 11, Parkhurst teaches that the AIM is CD137/4-1BB (pg. 2491, column 2, ¶ 2).
Regarding claim 12, Parkhurst teaches that the TCR α and TCR β chains were identified by deep sequencing (pg. 2497, column 1, ¶ 1), and provides the dominant CDR3 peptide sequences as determined by sequencing (FIGs 1-5).
Regarding claim 28, Parkhurst teaches determining the presence of mutation-reactive T cells in patients treated with adoptive cell therapy (i.e., analyzing a T cell mediated immune response of a patient to an immunotherapy; pg. 2500, columns 1 and 2).
Regarding claims 37 and 39, Parkhurst teaches that the DCs presenting peptides and the T cells are cocultured in 50/50 media before T cell activation was measured (i.e., the unique biological sample comprises media that supports T cell activation; pg. 2493, column 1, ¶ 4 and 5).
Regarding claim 38, Parkhurst teaches the single cell sequencing of enriched T cells (i.e., T cells that comprise TCRs that specifically bind to the unique antigen) to identify the TCR α and TCR β chain sequences (pg. 2493 column 2 ¶ 2).
5. Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Parkhurst et al (Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 expression, Clinical Cancer Research, 23, 10, 2491-2505, published 15 May 2017) in view of McGinnis et al (MULTI-Seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid tagged indices, BioRxiv 387241, doi: https://doi.org/10.1101/387241) as applied to claim 1 above, and further in view of Levine et al (Global manufacturing of Car T Cell Therapy, Methods and Clinical Development, 4, 92-101, published 04 March 2017).
Regarding claim 9, the method of claim 1 is discussed fully above and incorporated here. Parkhurst teaches that DCs are generated from leukaphereses samples (i.e., PBMCs; pg. 2492, column 2, ¶ 4).
Parkhurst does not teach that the T cells used in their experiments were derived from these leukaphereses samples.
However, Levine teaches that T cells are harvested from leukaphereses samples (pg. 92, column 2, ¶ 1).
It would have been obvious to one having ordinary skill in the art to have simply substituted the T cells derived from tumor infiltrating lymphocytes taught by Parkhurst with T cells isolated from leukaphereses samples (i.e., PBMCs) as taught by Levine, to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this substitution in order to both the DCs and the T cells needed for the experiment from the same sample, in order to reduce processing steps and costs. In addition, the ordinary artisan would have recognized that the known techniques in the cited references could have been substituted with predictable results, because the known techniques of the cited references predictably result in the isolation of T cells and APCs from leukaphereses samples.
6. Claims 1 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Parkhurst et al (Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 expression, Clinical Cancer Research, 23, 10, 2491-2505, published 15 May 2017) in view of Stoeckius et al (Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics, Genome Biology, 19, 224, published 19 December 2018).
Regarding claim 1, Parkurst teaches a method of isolating mutation-reactive T cells that mediated recognition of neoepitopes via upregulation of CD137 (i.e., identifying an antigen capable of activating a T cell; pg. 2491 column 2 ¶ 2). Parkurst teaches a unique biological sample comprising dendritic cells (DCs, i.e., antigen presenting cells that inherently comprise a surface-bound MHC; pg. 2493 column 1 ¶ 2 and 3), a unique antigen (DCs were electroporated with IVT RNAs encoding antigens; pg. 2493 column 1 ¶ 1, FIG 1 and associated caption), and a plurality of T cells having different TCR sequences (pg. 2493 column 1 ¶ 5, and FIG 1A specifically demonstrates the plurality of different TCRs in that only a small portion were activated by co-incubation with the DCs presenting a unique antigen). Parkhurst teaches that each plurality of T cells is cocultured with a population of DCs expressing a single antigen (i.e., the distinct antigens of each biological sample are different from the distinct antigens of other biological samples; FIG 1A). Parkhurst teaches the sorting of activated T cells by the upregulation of CD137 (i.e., sorting an activated T cell based on the expression of an activation induced marker; FIG 1A and pg. 2493 column 1 ¶ 5). Parkhurst teaches sequencing the sorted T cells by single cell sequencing (pg. 2493 column 2 ¶ 2).
Parkhurst does not teach that the biological sample comprises a distinct hashtag oligonucleotide (HTO) that is conjugated to a molecule that incorporates into the cell membrane of T cells and/or binds a cell surface marker expressed by T cells, that the HTO of each unique biological sample is different than the distinct HTOs of other biological samples such that the distinct HTO of each unique biological sample is associated with the distinct antigen of that unique biological sample, or that the distinct HTO is identified by sequencing to identify the distinct antigen of the unique biological sample from which the HTO-labeled activated T cell was sorted.
However, Stoeckius teaches a barcode oligonucleotide (i.e., an HTO) conjugated to an antibody that binds to a surface marker expressed by T cells (pg. 2, column 1, ¶ 3 and FIG 1) and that these barcodes are specifically associated with experimental conditions (abstract, pg. 2 column 1 ¶ 2, and FIG 1), and performing single cell sequencing on cells samples to determine the barcode of those cell samples wherein determining the barcode identifies the experimental condition of that sample (i.e., identifies the unique antigen associated with that cell sample; pg. 4, column 1, ¶ 2 and FIG 1).
It would have been obvious to one having ordinary skill in the art to have modified the antigen-TCR pairing method taught by Parkhurst to incorporate the HTO labels taught by Stoeckius to arrive at the instantly claimed invention with a reasonable expectation of success. One having ordinary skill in the art would have been motivated to make this modification because the method taught by Stoeckius allows each sample to be uniquely labeled such that all samples can be pooled together before FACS sorting and sequencing because Stoeckius teaches that pooling these samples substantially reduces cost and reagent usage (pg. 7 column 2 ¶ 3). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the sequencing of nucleic acids related to distinct experimental conditions. Further, Stoeckius specifically teaches that cell hashing is easily applied to virtually any human sample (i.e., the T cells of Parkhurst).
Regarding claim 10, Stoeckius teaches that the molecule that binds a cell surface marker expressed by T cells is an antibody (pg. 2, column 1, ¶ 3 and FIG 1).
7. Claims 13 and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Parkhurst et al (Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 expression, Clinical Cancer Research, 23, 10, 2491-2505, published 15 May 2017) in view of McGinnis et al (MULTI-Seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid tagged indices, BioRxiv 387241, doi: https://doi.org/10.1101/387241) as applied to claim 12 above, and further in view of Dijik et al (International Patent Application No. WO2018132739, published 19 July 2018).
Regarding claim 13, the method of claim 12 is discussed fully above and incorporated here. Neither Parkhurst nor McGinnis teach utilizing the TCR α and/or TCR β chain variable sequence in making a therapeutic. It is noted that TCR α and/or TCR β chain sequences, as determined by Parkhurst in claim 12 above, are inherently TCR α chain variable region sequences and/or TCR β chain variable regions sequences.
However, Dijik teaches utilizing the TCR α and/or TCR β variable chain sequences in treating cancer in a subject (i.e., as a therapeutic; claim 135).
It would have been obvious to one having ordinary skill in the art to have modified the method taught by Parkhurst in view of McGinnis to further use the identified TCR α and/or TCR β variable chain sequences in making a therapeutic to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Parkhurst specifically teaches that tumor infiltrating lymphocytes have therapeutic value in recognizing tumor-specific antigens (pg. 2491, column 2, ¶ 1 and pg. 2499, column 2, ¶ 4). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited methods could have been combined with predictable results, because the known techniques in the cited methods predictably result in the identification of therapeutically relevant TCR sequences.
Regarding claim 34, Dijik teaches that the CDR3 sequence of the TCR α chain is utilized in making a therapeutic (claim 135).
Response to Arguments
8. Any rejection not reiterated was overcome by applicant’s amendments to the claims. New rejections are set forth to address the amended claims.
9. 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.
Conclusion
10. No claims are allowed.
11. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-F 0730 - 1700.
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/BRIAN ELLIS YOUNG/ Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
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