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 .
Claim Status
1. The amendment filed 03/26/2026 has been entered. Claims 1, 2, 4, 13, 14, and 57 – 61 remain pending and are under consideration. Claims 3, 56, and 62 – 65 have been canceled.
Election/Restrictions
2. Applicant’s election without traverse of Group I (claims 1 – 4, 13, and 14) in the reply filed on 10/16/2024 is acknowledged.
3. Claims 15, 16, 25 – 29, 31, 32, 35 – 37, 44 – 46, 48, and 50 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 10/16/2024.
Priority
4. This application is a National Phase Application of International Patent Application No. PCT/US2020/013095, filed January 10, 2020, which claims priority to U.S. Provisional Patent Application No. 62/790,898, filed on January 10, 2019, U.S. Provisional Patent Application No. 62/826,209, filed on April 8, 2019, and US. Provisional Patent Application No. 62/896,354, filed on September 5, 2019.
Withdrawn Specification Objection
5. The objection to the specification for improper trade name or marker usage is withdrawn in view of Applicant’s amendment to the specification.
Withdrawn Claim Rejections
6. The rejection of claims 3 and 62 – 65 are under 35 U.S.C. 112(b) is rendered moot in view of Applicant’s cancellation of these claims.
7. The rejection of claim 3 under 35 U.S.C. 103 is rendered moot in view of Applicant’s cancellation of the claim.
8. The rejection of claims 62 – 65 under 35 U.S.C. 103 is rendered moot in view of Applicant’s cancellation of these claims.
9. The rejection of claims 1, 2, and 4 under 35 U.S.C. 103 is withdrawn in view of Applicant’s amendment to claim 1.
10. The rejection of claims 13 and 14 under 35 U.S.C. 103 is withdrawn in view of Applicant’s amendment to claim 1.
11. The rejection of claim 56 under is rendered moot in view of Applicant’s cancellation of the claim.
12. The rejection of claims 57 and 59 under 35 U.S.C. 103 is withdrawn in view of Applicant’s amendment of claim 57 to now depend from claim 1 instead of canceled claim 56, and amendment of claim 59 to now depend from claim 58 instead of claim 56.
13. The rejection of claim 58 under 35 U.S.C. 103 is withdrawn in view of Applicant’s amendment to the claim.
14. The rejection of claims 60 and 61 under 35 U.S.C. 103 is withdrawn in view of Applicant’s amendment to claim 1.
Rejections Necessitated by Amendment
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
15. Claim(s) 1, 2, 4, and 57 are rejected under 35 U.S.C. 103 as being unpatentable over Wardell (Wardell, Seth. P203 SITC 32nd Annual Meeting, National Harbor, MD. Vol. 1. 2017; previously cited), hereinafter Wardell in view of Radvanyi (Radvanyi LG, et. al. Clin Cancer Res. 2012 Dec 15;18(24):6758-70; previously cited), hereinafter Radvanyi in view of Cooper (Cooper ZA, et. al. Oncoimmunology. 2013 Oct 1;2(10):e26615; previously cited), hereinafter Cooper in view of Faham (US-10155992-B2; Filed 03/04/2016; Published 12/18/2018; previously cited), hereinafter Faham.
Regarding step (i) of claim 1, Wardell teaches identifying TCR-CDR3 encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of a therapeutic population of TILs called Gen1 and Gen2 wherein the clonal diversity is approximately 7000 unique CDR3’s for Gen1 TILs and approximately 15000 unique CDR3’s in Gen2 TILs (Figure 5; middle col. para. 5). Wardell does not teach steps (ii) – (v).
Regarding “wherein identifying TCR CDR3-encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of the therapeutic population of TILs and/or the first population of PBMCs is performed by simultaneously measuring lymphocyte numbers and clonotype expression levels in a sample comprising the therapeutic population of TILs and/or the first population of PBMCs” of claim 1 and step (b) of claim 57, Wardell teaches RNA from infusion products was isolated and subjected to a multiplex PCR with VDJ specific primers and CDR3 sequences expressed within the TIL product were semi-quantitatively amplified and deep sequenced to determine the frequency and prevalence of unique TIL clones (middle col. para. 5; Figure 5). Wardell does not teach DNA sequencing or comparing the DNA and RNA sequencing results of step (a) and step (c) of claim 57.
Regarding claim 4, Wardell teaches isolating RNA from TILs, subjecting the RNA to multiplex PCR with VDJ specific primers, amplifying CDR3 sequences and sequencing by deep sequencing (middle col. para. 5).
Wardell does not teach steps (ii) – (v) or “wherein identifying TCR CDR3-encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of the therapeutic population of TILs and/or
the first population of PBMCs is performed by simultaneously measuring lymphocyte numbers and clonotype expression levels in a sample comprising the therapeutic population of TILs and/or the first population of PBMCs” of claim 1 or steps (a) and (b) of claim 2 or steps (a) and (c) of claim 57. However, Wardell teaches Gen2 produces highly pure TILs with a diversity of TCR receptors which when engaged initiate a robust secretion of IFNγ (Figure 2 and 4; right col. Conclusions). Wardell teaches Gen2 allows for the rapid generation of clinical scale doses of TILs for cancer patients in immediate need of a novel therapy option (right col. Conclusions).
Regarding step (ii) of claim 1, Radvanyi teaches identifying TCR CDR3 nucleic acid sequence clones of a therapeutic population of TILs (page 6761, right col. paragraph 2; Table S5). Radvanyi teaches identifying the TCR CDR3-encoding nucleic acid sequence clones of a first population of PBMCs isolated from a subject at one month after administration of the TILs (Table S5).
Regarding step (iii) of claim 1, Radvanyi teaches calculating the frequency of each dominant clonotype by determining the percentage of each specific CDR3 sequence found within the clones picked and sequenced and that clonotypes were analyzed in the TIL infusion product and in PBMC isolated from patients (page 6761, right col. paragraph 2; Table S5). Radvanyi teaches unique TCR CDR3 clones in Table S5 at one month after infusion of TILs.
Regarding step (iv) of claim 1, Radvanyi teaches the frequency of unique TCR CDR3 sequence clones at one month after infusion of TILs identified from the TIL infusion product and in PBMC isolated from patients in Table S5. However, Radvanyi does not teach sorting the data from highest frequency to lowest frequency.
Regarding step (v) of claim 1, Radvanyi teaches the frequency of unique TCR CDR3 sequence clones at one month after infusion of TILs identified from the PBMC isolated from patients in Table S5. Radvanyi teaches ten unique TCR CDR3 sequence clones from multiple patients and the unique clones from patient #2150/2153 include VB11-2 (frequency = 2.5%) and VB24-1 (frequency = 55.6%) where this patient showed tumor regression at one month after receiving TIL therapy, thereby identifying the clinically effective population of TILs (Table S5; Figure 1; page 6763, left col. paragraph 3).
Regarding DNA sequencing and comparing the DNA and RNA sequencing results of claim 1 and step (a) of claim 57, Radvanyi teaches synthesizing TCR Vβ-specific cDNA and adding end adapters for PCR amplification and sequencing the CDR3 region from TIL or patients’ PBMC after adoptive transfer (page 6761, right col. para. 2; Table S5; page 6764, right col. para. 3). Radvanyi does not teach step (c) of claim 57.
Regarding claim 2, Radvanyi teaches collection of blood samples before TIL infusion (page 6761, left col. paragraph 1). However, Radvanyi does not teach identifying the TCR CDR3 sequence clones or frequency or diversity.
Radvanyi does not teach sorting the data from highest frequency to lowest frequency (step (iv) of claim 1) or “simultaneously measuring lymphocyte numbers and clonotype expression levels” of claim 1 or identifying the TCR CDR3 sequence clones or frequency or diversity (claim 2) of a second population of PBMCs isolated prior to administration of therapeutic TILs or step (c) of claim 57. However, Radvanyi teaches the use of TILs for treating metastatic melanoma and one patient administered TILs was treated with a BRAF inhibitor (Abstract; page 6762, right col. paragraph 1). Radvanyi teaches the TILs induced a high rate of objective tumor regression in melanoma patients and that this response can be long lasting (page 6768, right col. paragraph 2). Radvanyi teaches most of the TILs had specific antitumor IFNγ responses (page 6764, left col. para. 2). Radvanyi teaches future efforts will focus on developing strategies to generate more effective T cells and exploring future TIL clinical trials in combination with new FDA-approved agents for melanoma (page 6768, right col. paragraph 2). Radvanyi teaches sequencing of cDNA to determine frequency (page 6761, right col. paragraph 2). Radvanyi teaches metastatic melanoma is an aggressive form of cancer highly resistant to traditional forms of therapy (page 6758, left col.). One would have been motivated to combine the teachings of Wardell and Radvanyi because both teach TILs secrete IFNγ and are for treating cancer.
Regarding sorting data of step (iv) of claim 1 and claim 2, Cooper teaches determining the clonality of TILs from melanomas by sequencing the CDR3 region before treatment with a BRAF inhibitor (BRAFi) and 10 – 14 days after BRAFi administration (page e26615-2, left col. paragraph 2). Cooper teaches determining the TIL clonality, which is a term to quantify the diversity of clones and frequency of any given clone (page e26615-2, left col. paragraph 3; Figure 2A). Cooper teaches sorting the dominant clones by frequency (page e26615-2, right col. paragraph 1). Cooper teaches the software used for determining clonality scores define clonality by an equation that considers unique sequences (page e26615-6, right col. paragraph 1). Cooper teaches a significant increase in clonality upon BRAFi administration was observed in 7 out of 8 patients (page e26615-2, left col. paragraph 3; Figure 2A). Cooper teaches 80% of clones from BRAFi treatment were shown to be new clones when compared to clones from pre-treatment (page e26615-2, right col. paragraph 2). Cooper teaches the presence of new clones post-treatment suggests influx of T cells within the neoplastic lesions of melanoma patients treated with BRAFi (page e26615-2, right col. paragraph 2). Cooper teaches there was a striking difference in the relationship between the maximal response to therapy and the presence of new dominant clones suggesting that the response to BRAFi may rely on pre-existing TILs rather than on new clones, however the specificity of this clonal response requires further investigation (page e 26615-4, left col. paragraph 2). Cooper teaches the characterization of TIL populations pre- and post-treatment may provide insights into the propensity of patients to respond to this form of immunotherapy (page e26615-5, left col. paragraph 2). Cooper does not teach “simultaneously measuring lymphocyte numbers and clonotype expression levels” of claim 1 or step (c) of claim 57. One would have been motivated to combine the teachings of Wardell, Radvanyi, and Cooper in a method to develop an effective TIL treatment for melanoma patients because Cooper teaches the characterization of TIL populations pre- and post-treatment may provide insights into the propensity of patients to respond to this form of immunotherapy.
Regarding “simultaneously measuring lymphocyte numbers and clonotype expression levels” of claim 1 and step (c) of claim 57, Faham teaches a method of simultaneously measuring lymphocyte numbers and clonotype expression levels in a sample (col. 5, lines 44 – 61; col. 22, lines 24 – 46; col. 23, lines 18 – 20; col. 128, lines 59 – 67; col. 129, lines 1 – 4). Faham teaches the method of simultaneously measuring lymphocyte numbers and clonotype expression levels in a sample of T cells comprises sequencing spatially isolated individual molecules derived from genomic DNA of the cells of the sample, such spatially isolated individual molecules comprising a number of clonotypes corresponding to a number of lymphocytes in the sample (“(a)” of claim 57) and sequencing spatially isolated individual molecules derived from RNA of said cells, such spatially isolated individual molecules comprising numbers of clonotypes corresponding to expression levels thereof in the lymphocytes of the sample (“(b)” of claim 57) and determining clonotype expression levels in lymphocytes of the sample by comparing for each clonotype the number determined from isolated individual molecules derived from genomic DNA of said cells and the number determined from isolated individual molecules derived from RNA of said cells (“(c)” of claim 57) (col. 5, lines 44 – 61; col. 22, lines 24 - 46).
Faham teaches clonotypes may be used to count lymphocytes; therefore, by measuring clonotypes derived from genomic DNA and the same clonotypes derived from RNA, cell-based expression of clonotypes may be determined (col. 22, lines 24 – 29). Faham teaches there is a need to improve methods of aiding prognosis of disease for which the immune system plays a central role (col. 2, lines 18 – 21). Faham teaches methods that would identify which of the many cells in a given individual are involved with disease processes would be of great value to human health (col. 2, lines 25 – 38). Faham teaches it would be advantageous if there were available assays for assessing clonotype profiles of individuals that were more sensitive and comprehensive than current techniques and that were generally applicable without the need of manufacturing individualized reagents (col. 4, lines 40 – 45). Faham teaches the method provides sequence-based methods for measuring with much greater sensitivity clonotypes correlated with disease or health conditions and is applicable to any patient without the need for manufacturing patient-specific reagents (col. 5, lines 62 – 67). Faham teaches next generation sequencing technologies to evaluate the levels of TCR rearrangements in a population of lymphocytes where sequencing can obtain 1 million or more reads from a sample at a reasonable cost and where a clonotype present at a frequency of 1/1,000,000 or lower can still be detected in a specific manner (col. 7, lines 17 – 23). Faham teaches the method for sequencing the CDR3 (col. 10, lines 42 – 47; col. 25, lines 19 – 24).
It would have been obvious prior to the effective filing date of the invention as claimed for the person of ordinary skill in the art to combine the teachings of Wardell regarding a therapeutic population of TILs having greater than 3000 unique CDR3s with the teachings of Radvanyi regarding identifying a clinically effective population of TILs with the teachings of Cooper regarding identifying clonal diversity of TILs before and after treatment with the teachings of Faham regarding a method of simultaneously measuring lymphocyte numbers and clonotype expression levels to arrive at the claimed method for identifying a clinically effective population of tumor infiltrating lymphocytes (TILs) in a therapeutic population of TILs administered to a subject, the method comprising: (i) identifying T cell receptor (TCR) complementarity determining region 3 (CDR3)encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of the therapeutic population of TILs, wherein the clonal diversity of the therapeutic population of TILs comprises between about 3000 and about 115000 unique TCR CDR3 sequences; (ii) identifying TCR CDR3-encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of a first population of peripheral blood mononuclear cells (PBMCs ), wherein the first population of PBMCs is isolated from the subject at least 14-days after the therapeutic population of step (i) is administered to said subject; (iii) for each unique TCR CDR3-encoding nucleic acid sequence clone identified in step (ii), determining a frequency of such unique TCR CDR3 clone in each of the therapeutic population of TILs and the first population of PBMCs; (iv) sorting the unique TCR CDR3-encoding nucleic acid sequence clones identified in step (ii) from highest frequency to lowest frequency for each of the therapeutic population of TILs and the first population of PBMCs; and, (v) selecting ten highest frequency unique TCR CDR3-encoding nucleic acid sequence clones from the first population of PBMCs sorted in step (iv), wherein the TILs expressing such clones in the therapeutic population of TILs constitute a clinically effective population of TILs, thereby identifying the clinically effective population of TILs; and wherein identifying TCR CDR3-encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of the therapeutic population of TILs and/or the first population of PBMCs is performed by simultaneously measuring lymphocyte numbers and clonotype expression levels in a sample comprising the therapeutic population of TILs and/or the first population of PBMCs. One would have been motivated to combine the teachings of Wardell, Radvanyi, Cooper, and Faham in a method to develop an effective TIL treatment for melanoma patients as Wardell teaches Gen2 produces highly pure TILs with a diversity of TCR receptors which when engaged initiate a robust secretion of IFNγ and Radvanyi teaches metastatic melanoma is an aggressive form of cancer highly resistant to traditional forms of therapy and Cooper teaches the characterization of TIL populations pre- and post-treatment may provide insights into the propensity of patients to respond to this form of immunotherapy and Faham teaches it would be advantageous if there were available assays for assessing clonotype profiles of individuals that were more sensitive and comprehensive than current techniques and that were generally applicable without the need of manufacturing individualized reagents. One would have a reasonable expectation of success in combining the teachings as Radvanyi teaches the TILs induced a high rate of objective tumor regression in melanoma patients and that this response can be long lasting and Radvanyi teaches most of the TILs had specific antitumor IFNγ responses and Radvanyi teaches identification of a clinically effective TIL population with high frequency of a specific clone and Faham teaches the method provides sequence-based methods for measuring with much greater sensitivity clonotypes correlated with disease or health conditions and is applicable to any patient without the need for manufacturing patient-specific reagents.
16. Claim(s) 13 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Wardell (Wardell, Seth. P203 SITC 32nd Annual Meeting, National Harbor, MD. Vol. 1. 2017; previously cited), hereinafter Wardell in view of Radvanyi (Radvanyi LG, et. al. Clin Cancer Res. 2012 Dec 15;18(24):6758-70; previously cited), hereinafter Radvanyi in view of Cooper (Cooper ZA, et. al. Oncoimmunology. 2013 Oct 1;2(10):e26615; previously cited), hereinafter Cooper in view of Faham (US-10155992-B2; Filed 03/04/2016; Published 12/18/2018; previously cited), hereinafter Faham as applied to claims 1, 2, 4, and 57 above, and further in view of Kuang (Kuang M, et. al. Sci Rep. 2017 Aug 10;7(1):7762; previously cited), hereinafter Kuang which is cited on the IDS filed 10/21/2021 as evidenced by Bolotin (Bolotin, D., et. al. Nat Methods 10, 813–814 (2013); previously cited), hereinafter Bolotin.
Wardell, Radvanyi, Cooper, and Faham make obvious the limitations of claim 1 as set forth above. Wardell, Radvanyi, Cooper, Faham do not teach mRNA clones of claims 13 and 14. However, Cooper teaches T-cell clonality can be studied by observing changes in the variable V, D, J region of the CDR3-coding sequence within tumor biopsies (page e26615-3, right col. paragraph 2). Cooper teaches changes in clonality may be suggestive of an antigen-specific response (page e26615-4, left col. paragraph 2).
Regarding claims 13 and 14, Radvanyi teaches isolation of total RNA from TILs and patients’ PBMCs, cDNA synthesis from total RNA, and sequencing of the CDR3 region (“RNA sequencing” of claim 13) (page 6761, right col. paragraph 2). Radvanyi teaches detection of the clones that were identified from total RNA of TCR CDR3 clones at 1 month, 5, 7, 11 – 13 and 22 months (claim 14) in Table S5. Radvanyi does not teach mRNA clones are identified by RNA sequencing.
Kuang teaches sequencing of the TCRβ CDR3 regions of TILs from the total RNA extracted from tumor biopsies using a modified ARM-PCR procedure (page 7, paragraph 2 – 3). Kuang teaches the raw sequencing data and MiTCR was used to assign rearranged mRNA sequences to their germline V, D, and J counterparts (page 7, paragraph 4). MiTCR is a software for rapid, robust and comprehensive analysis of raw sequencing reads containing TCR sequences and for assembling clonotypes where the CDR3 is covered by a sequencing read as evidenced by Bolotin (page 1, left col. paragraph 2; Figure 1). Kuang teaches additional software to analyze diversity and frequency (page 7, paragraph 4, 8; page 2, paragraph 5). Kuang teaches CDR3 shapes the spectrum of TCR diversity and TCR repertoire sequencing can be used to assess the immune responses of cancer patients (page 2, paragraph 2). Kuang teaches TCRβ sequencing to investigate TILs to determine the potential clinical values of variations in the TCR repertoire (page 2, paragraph 3). Kuang teaches TILs may undergo a selective antigen-driven clonal expansion (page 5, last paragraph).
It would have been obvious prior to the effective filing date of the invention as claimed for the person of ordinary skill in the art to combine the teachings of Wardell regarding a therapeutic population of TILs having greater than 3000 unique CDR3s with the teachings of Radvanyi regarding identifying a clinically effective population of TILs with the teachings of Cooper regarding identifying clonal diversity of TILs before and after treatment with the teachings of Faham regarding a method of simultaneously measuring lymphocyte numbers and clonotype expression levels with the teachings of Kuang regarding RNA sequencing to assign rearranged mRNA sequences to their germline V, D, and J counterparts, and analyze diversity and frequency to arrive at the claimed method where unique TCR CDR3-encoding nucleic acid clones are mRNA clones identified by RNA sequencing. One would have been motivated to combine the teachings of Wardell, Radvanyi, Cooper, Faham and Kurang in a method to develop an effective TIL treatment for melanoma patients as Radvanyi teaches metastatic melanoma is an aggressive form of cancer highly resistant to traditional forms of therapy and Cooper teaches T-cell clonality can be studied by observing changes in the CDR3-coding sequence within tumor biopsies and Kuang teaches TCRβ sequencing to investigate TILs to determine the potential clinical values of variations in the TCR repertoire. One would have a reasonable expectation of success in combining the teachings as Wardell teaches Gen2 allows for the rapid generation of clinical scale doses of TILs for cancer patients in immediate need of a novel therapy option and Radvanyi teaches identification of a clinically effective TIL population by RNA sequencing.
17. Claim(s) 60 and 61 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wardell (Wardell, Seth. P203 SITC 32nd Annual Meeting, National Harbor, MD. Vol. 1. 2017; previously cited), hereinafter Wardell in view of Radvanyi (Radvanyi LG, et. al. Clin Cancer Res. 2012 Dec 15;18(24):6758-70; previously cited), hereinafter Radvanyi in view of Cooper (Cooper ZA, et. al. Oncoimmunology. 2013 Oct 1;2(10):e26615; previously cited), hereinafter Cooper in view of Faham (US-10155992-B2; Filed 03/04/2016; Published 12/18/2018; previously cited), hereinafter Faham as applied to claims 1, 2, 4, and 57 above, and further in view of Dziubianau (Dziubianau, M., et al. American journal of transplantation 13.11 (2013): 2842-2854; previously cited), hereinafter Dziubianau.
Wardell, Radvanyi, Cooper, and Faham make obvious the limitations of claim 1 as set forth above.
Regarding “RNA sequencing” of claims 60 and 61, Radvanyi teaches isolation of RNA and sequencing to determine frequency (page 6761, right col. paragraph 2). Radvanyi does not teach “DNA sequencing” of claims 60 and 61 or “is compared” of claim 61.
Regarding “DNA sequencing” of claims 60 and 61 and “is compared” of claim 61, Dziubianau teaches a method comprising isolating genomic DNA and RNA simultaneously followed by next generation sequencing (NGS) of T cells from PBMCs and allograft-infiltrating lymphocytes (page 2843, left col. 3 – 4 and right col. paragraph 4 – 8). Dziubianau teaches clonotype analyses were routinely performed on mRNA level but specific TCRs can be identified only on genomic DNA (gDNA) and not mRNA level (page 2845, right col. last paragraph; page 2852, left col. paragraph 4). Dziubianau teaches it was proposed that clonotypes possessing different TCR affinity/avidity might differentially regulate TCR-coding mRNA (page 2845, right col. last paragraph). Dziubianau teaches comparing the repertoires of T cells using both gDNA and mRNA in Figure 4A. Dziubianau teaches although the majority of dominant and subdominant clones identified by sequencing gDNA were also found on mRNA level, the relative proportions of individual clones differed greatly with many clones showing a difference of up to a factor of about 10-fold (page 2845, right col. last paragraph). Dziubianau teaches NGS allows analysis of extremely rare T cell clones (Figure 3; page 2845, right col. paragraph 2). Dziubianau teaches the clonotype characterization performed on cDNA level is biased as compared to the analysis performed on gDNA (page 2852, left col. paragraph 4). Dziubianau teaches the method is fast and can provide new insights into the regulation of anti-tumor immunity and contribute to design of adoptive immunotherapy and vaccination studies (page 2852, right col. last paragraph; page 2856, left col. paragraph 1).
It would have been obvious prior to the effective filing date of the invention as claimed for the person of ordinary skill in the art to combine the teachings of Wardell regarding a therapeutic population of TILs having greater than 3000 unique CDR3s with the teachings of Radvanyi regarding identifying a clinically effective population of TILs with the teachings of Cooper regarding identifying clonal diversity of TILs before and after treatment with the teachings of Faham regarding a method of simultaneously measuring lymphocyte numbers and clonotype expression levels with the teachings of Dziubianau regarding a method of comparing the repertoires of T cells using both gDNA and mRNA to arrive at the claimed method where the frequency of unique TCR CDR3-encoding nucleic acid sequence clones identified in the therapeutic population of TILs and the frequency of unique TCR CD3-encoding nucleic acid sequence clones identified in the first population of PBMCs are determined by both DNA and RNA sequencing and the frequency of the unique clones in the first population of PBMCs as determined by RNA sequencing is compared to the frequency of unique clones in the first population of PBMCs as determined by DNA sequencing to determine a clinically effective population of TILs. One would have been motivated to combine the teachings of Wardell, Radvanyi, Cooper, Faham, and Dziubianau in a method to develop an effective TIL treatment for melanoma patients as Radvanyi teaches metastatic melanoma is an aggressive form of cancer highly resistant to traditional forms of therapy and Dziubianau teaches clonotype analyses were routinely performed on mRNA level but specific TCRs can be identified only on genomic DNA and not mRNA level and Dziubianau teaches NGS allows analysis of extremely rare T cell clones. One would have a reasonable expectation of success in combining the teachings as Dziubianau teaches the method can provide new insights into the regulation of anti-tumor immunity and contribute to design of adoptive immunotherapy.
18. Claim(s) 58 and 59 rejected under 35 U.S.C. 103 as being unpatentable over Wardell (Wardell, Seth. P203 SITC 32nd Annual Meeting, National Harbor, MD. Vol. 1. 2017; previously cited), hereinafter Wardell in view of Sarnaik (Sarnaik, Amod. Society for Immunotherapy of Cancer (2017); previously cited), hereinafter Sarnaik in view of Vignard (Vignard, Virginie, et al. The Journal of Immunology 175.7 (2005): 4797-4805; previously cited), hereinafter Vignard in view of Zhou (Zhou, Juhua, et al. Journal of immunotherapy 28.1 (2005): 53-62; previously cited), hereinafter Zhou in view of Faham (US-10155992-B2; Filed 03/04/2016; Published 12/18/2018; previously cited), hereinafter Faham.
Regarding step (i) and “22-day rapid expansion process” of claim 58, Wardell teaches determining the frequency and prevalence of unique TIL clones in Gen 2 TILs manufactured by a 22 day rapid expansion process (left col. paragraph 2; middle col. last paragraph and Figure; last bullet under Conclusions; Table 1; Figure 5). Regarding “wherein the clonal diversity of the therapeutic population of TILs comprises between about 3000 and about 115000 unique TCR CDR3 sequences”, Wardell teaches the number of unique CDR3 sequences in Gen1 TILs is approximately 7000 and the number of unique CDR3 sequences in Gen2 TILs is approximately 15000 in Figure 5. Wardell does not teach step (ii).
Regarding step (iii) and (iv), Wardell teaches in Figure 5 the average total number of unique CDR3 sequences present in Gen 2 TILs and the unique CDR3 sequences were indexed relative to frequency (“determining a frequency of such unique TCR CDR3 clone in” “the therapeutic population of TILs”). Ward does not teach “first population of PBMCs” of step (iv).
Wardell does not teach steps (ii) or (v) or “first population of PBMCs” of step (iv) or “simultaneously measuring lymphocyte numbers and clonotype expression levels” of claim 58 or “DNA sequencing of claim 59. However, Wardell teaches the Gen 2 TILs (LN-144) manufactured by the 22-day process time decreases the turnaround time to cancer patients in immediate need of a novel therapy option (Table 1; last bullet under Conclusions).
Regarding step (ii), Sarnaik teaches administration of Gen 2 LN-144 TILs to patients with metastatic melanoma (cohort 2) (left col. Study Design). Sarnaik teaches plasma levels of HMBGI and IP-10 were measured at day 4 and 14 post LN-144 infusion in Figures 4 – 5 indicative of an immune-mediated mechanism of anti-tumor activity (“first population of PBMCs is isolated from a subject at least 14-days after the therapeutic population of step (i) is administered to said subject”). Sarnaik teaches in Figures 1 – 3 patient response to the TILs where Gen 2 LN-144 leads to clinical responses in patients and the disease control rate was 78% (right col. Conclusions). Sarnaik does not teach “identifying TCR CDR3-encoding nucleic acid sequence clones constituting TCR CD3 clonal diversity of a first population of peripheral blood mononuclear cells” or “simultaneously measuring lymphocyte numbers and clonotype expression levels” of claim 58. One would have been motivated to combine the teachings of Wardell regarding identifying clonal diversity of Gen 2 LN-144 and Sarnaik regarding immune-mediated mechanism of anti-tumor activity in patient samples at 14 days to identify the clonal diversity and frequency of unique TCR CDR3 clones and sort the unique clones by frequency to identify the ten highest frequency clones in patient PBMCs at 14 days after administration of Gen 2 LN-144 because Wardell teaches the Gen 2 TILs are a novel therapy option for cancer patients and Sarnaik teaches where Gen 2 LN-144 leads to clinical responses in patients and the disease control rate was 78%.
Regarding “identifying TCR CDR3-encoding nucleic acid sequence clones constituting TCR CD3 clonal diversity of a first population of peripheral blood mononuclear cells” of step (ii) and “first population of PBMCs” of step (iii) and “first population of PBMCs” of step (iv) and “DNA sequencing” of claim 59, Vignard teaches collecting PBMC samples at days 0, 7, 30, and 60 following infusion of cytotoxic T lymphocytes (CTL) to melanoma patients and determining the TCRVβ repertoire with DNA sequencing (claim 59) and clonotypic analysis including the frequency of the clonotypes in the PBMCs coupling Immunoscope analysis with clonotypic-specific PCR (page 4798, left col. paragraph 2 – 3 and right col. paragraph 1; page 4799, right col. paragraph 3 – 4; Table I – III; page 4800, left col. paragraph 3 and right col. paragraph 1; page 4804, right col. paragraph 3 – 4).
Regarding step (v), Vignard does not teach “ten highest frequency” clones but instead teaches the persistence in blood of infused clones in three patients for periods ranging from 1 to 2 months whereas in some patients CTL clones were undetectable (page 4803, left col. last paragraph and right col. paragraph 1; Table 3). Vignard teaches seven patients experienced a clinical response suggesting the transferred cells did initiate an antitumor response and in six of these patients, infused clones were not detected in the peripheral blood (page 4804, right col. paragraph 2 – 3). Vignard teaches adoptive therapy may help to recruit other Melan-A-specific T cell clonotypes (page 4804, right col. paragraph 2). Vignard teaches one patient (Mela01) experienced the best clinical response where the infused clone was not detected in the blood at any time (before or after adoptive therapy) indicating the presence of two dominant clonotypes posttransfer that were hardly detectable before treatment (page 4804, right col. paragraph 3). Vignard teaches in patient Mela01, the potential reasons for the new clonotypes could be due to selective amplification during the course of in vitro expansion or could be a new Melan-A-specific repertoire in PBMCs resulting from T cell therapy (page 4804, right col. paragraph 3). Vignard teaches qualitative and quantitative variations in the Melan-A-specific repertoire could be indicative of an antitumor response induced by immunotherapy treatment, the efficiency of which will depend on the extent of disease at the time of immunotherapy (page 4804, right col. paragraph 4). Vignard teaches the fate of the transferred T cells in the patient is a crucial question for the success of adoptive therapy (page 4803, left col. last paragraph). Vignard does not teach “simultaneously measuring lymphocyte numbers and clonotype expression levels” of claim 58. One would have been motivated to combine the teachings of Wardell, Sarnaik, and Vignard to identify therapeutic TILs because Vignard teaches one patient (Mela01) experienced the best clinical response where the infused clone was not detected in the blood at any time (before or after adoptive therapy) indicating the presence of two dominant clonotypes posttransfer that were hardly detectable before treatment.
Regarding “ten highest frequency” of step (v), Zhou teaches considerable heterogeneity was observed in a therapeutic population of TILs (TIL 2098) for treating metastatic melanoma where 37 distinct clonotypes were identified following the sequencing of 96 cDNA clones amplified from TIL 2098 (Abstract; page 55, right col. paragraph 2 – 3; Figure 2). Zhou teaches six dominant clonotypes were identified that represent at least 5% of the sequences amplified from TIL 2098 and eleven of the 37 clonotypes were present at a level of at least 1% in PBMC samples that were obtained 6 days following adoptive transfer whereas only five of the original TIL clonotypes were detected in a sample obtained 4 weeks following transfer (page 55, right col. paragraph 3; Figure 2). Zhou teaches patient 2098 showed a complete response to adoptive immunotherapy with TIL 2098 (page 55, right col. paragraph 2; page 61, left col. last paragraph). Zhou does not teach “simultaneously measuring lymphocyte numbers and clonotype expression levels” of claim 58. One would have been motivated to combine the teachings of Wardell, Sarnaik, Vignard, and Zhou to identify therapeutic TILs because Vignard teaches one patient (Mela01) experienced the best clinical response where the infused clone was not detected in the blood at any time (before or after adoptive therapy) indicating the presence of two dominant clonotypes posttransfer that were hardly detectable before treatment and Zhou teaches six dominant clonotypes were identified that represent at least 5% of the sequences amplified from TIL 2098 and eleven of the 37 clonotypes were present at a level of at least 1% in PBMC samples that were obtained 6 days following adoptive transfer whereas only five of the original TIL clonotypes were detected in a sample obtained 4 weeks following transfer.
It would have been obvious prior to the effective filing date of the invention as claimed for the person of ordinary skill in the art to combine the teachings of Wardell regarding identifying clonal diversity of Gen 2 LN-144 with the teachings of Sarnaik regarding immune-mediated mechanism of anti-tumor activity in patient samples at 14 days with the teachings of Vignard regarding determining the TCRVβ repertoire and clonotypic analysis including the frequency of the clonotypes in the PBMCs coupling Immunoscope analysis with clonotypic-specific PCR with the teachings of Zhou regarding sorting dominant clonotypes of TILs by to arrive at the claimed method where Gen 2 LN-144 TILs are administered to a subject where the TILs have a diversity score of ~0.75 and ~15000 unique CDR3; the TCR CDR3 clonal diversity and frequency of each unique clone of PBMCs isolated 14 days after administration of Gen 2 LN-144 is identified; the unique TCR CDR3 clones from Gen 2 LN-144 and the PBMCs are sorted from highest frequency to lowest frequency; and the ten highest frequency unique clones from the PBMCs are selected to identify the clinically effective population of TILs. One would have been motivated to combine the teachings of Wardell, Sarnaik, Vignard, and Zhou to identify clinically effective TILs from LN-144 for treating melanoma as Wardell teaches the Gen 2 TILs are a novel therapy option for cancer patients and Sarnaik teaches where Gen 2 LN-144 leads to clinical responses in patients and the disease control rate was 78% and Vignard teaches the fate of the transferred T cells in the patient is a crucial question for the success of adoptive therapy. One would have a reasonable expectation of success in combining the teachings as Wardell teaches identifying clonal diversity and frequency by sequencing and both Vignard and Zhou teach identifying diversity and frequency of clones from PBMCs following adoptive cell transfer.
Regarding “simultaneously measuring lymphocyte numbers and clonotype expression levels” of claim 58, Faham teaches a method of simultaneously measuring lymphocyte numbers and clonotype expression levels in a sample (col. 5, lines 44 – 61; col. 22, lines 24 – 46; col. 23, lines 18 – 20; col. 128, lines 59 – 67; col. 129, lines 1 – 4). Faham teaches the method of simultaneously measuring lymphocyte numbers and clonotype expression levels in a sample of T cells comprises sequencing spatially isolated individual molecules derived from genomic DNA of the cells of the sample, such spatially isolated individual molecules comprising a number of clonotypes corresponding to a number of lymphocytes in the sample (“(a)” of claim 57) and sequencing spatially isolated individual molecules derived from RNA of said cells, such spatially isolated individual molecules comprising numbers of clonotypes corresponding to expression levels thereof in the lymphocytes of the sample (“(b)” of claim 57) and determining clonotype expression levels in lymphocytes of the sample by comparing for each clonotype the number determined from isolated individual molecules derived from genomic DNA of said cells and the number determined from isolated individual molecules derived from RNA of said cells (“(c)” of claim 57) (col. 5, lines 44 – 61; col. 22, lines 24 - 46).
Faham teaches clonotypes may be used to count lymphocytes; therefore, by measuring clonotypes derived from genomic DNA and the same clonotypes derived from RNA, cell-based expression of clonotypes may be determined (col. 22, lines 24 – 29). Faham teaches there is a need to improve methods of aiding prognosis of disease for which the immune system plays a central role (col. 2, lines 18 – 21). Faham teaches methods that would identify which of the many cells in a given individual are involved with disease processes would be of great value to human health (col. 2, lines 25 – 38). Faham teaches it would be advantageous if there were available assays for assessing clonotype profiles of individuals that were more sensitive and comprehensive than current techniques and that were generally applicable without the need of manufacturing individualized reagents (col. 4, lines 40 – 45). Faham teaches the method provides sequence-based methods for measuring with much greater sensitivity clonotypes correlated with disease or health conditions and is applicable to any patient without the need for manufacturing patient-specific reagents (col. 5, lines 62 – 67). Faham teaches next generation sequencing technologies to evaluate the levels of TCR rearrangements in a population of lymphocytes where sequencing can obtain 1 million or more reads from a sample at a reasonable cost and where a clonotype present at a frequency of 1/1,000,000 or lower can still be detected in a specific manner (col. 7, lines 17 – 23). Faham teaches the method for sequencing the CDR3 (col. 10, lines 42 – 47; col. 25, lines 19 – 24).
It would have been obvious prior to the effective filing date of the invention as claimed for the person of ordinary skill in the art to combine the teachings of Wardell regarding identifying clonal diversity of Gen 2 LN-144 with the teachings of Sarnaik regarding immune-mediated mechanism of anti-tumor activity in patient samples at 14 days with the teachings of Vignard regarding determining the TCRVβ repertoire and clonotypic analysis including the frequency of the clonotypes in the PBMCs coupling Immunoscope analysis with clonotypic-specific PCR with the teachings of Zhou regarding sorting dominant clonotypes of TILs by with the teachings of Faham regarding a method of simultaneously measuring lymphocyte numbers and clonotype expression levels to arrive at the claimed method for identifying a clinically effective population of tumor infiltrating lymphocytes (TILs) in a therapeutic population of TILs administered to a subject, the method comprising: (i) identifying T cell receptor (TCR) complementarity determining region 3 (CDR3)encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of the therapeutic population of TILs, wherein the clonal diversity of the therapeutic population of TILs comprises between about 3000 and about 115000 unique TCR CDR3 sequences; (ii) identifying TCR CDR3-encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of a first population of peripheral blood mononuclear cells (PBMCs ), wherein the first population of PBMCs is isolated from a subject at least 14-days after the therapeutic population of step (i) is administered to said subject; (iii) for each unique TCR CDR3-encoding nucleic acid sequence clone identified in step (ii), determining a frequency of such unique TCR CDR3 clone in each of the therapeutic population of TILs and the first population of PBMCs; (iv) sorting the unique TCR CDR3-encoding nucleic acid sequence clones identified in step (ii) from highest frequency to lowest frequency for each of the therapeutic population of TILs and the first population of PBMCs; and, (v) selecting ten highest frequency unique TCR CDR3-encoding nucleic acid sequence clones from the first population of PBMCs sorted in step (iv), wherein the TILs expressing such clones in the therapeutic population of TILs constitute a clinically effective population of TILs, thereby identifying the clinically effective population of TILs, wherein the therapeutic population of TILs is obtained by a 22-day rapid expansion process; and wherein identifying TCR CDR3-encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of the therapeutic population of TILs and/or the first population of PBMCs is performed by simultaneously measuring lymphocyte numbers and clonotype expression levels in a sample comprising the therapeutic population of TILs and/or the first population of PBMCs. One would have been motivated to combine the teachings of Wardell, Sarnaik, Vignard, Zhou, and Faham to identify clinically effective TILs from LN-144 for treating melanoma as Wardell teaches the Gen 2 TILs are a novel therapy option for cancer patients and Vignard teaches the fate of the transferred T cells in the patient is a crucial question for the success of adoptive therapy. One would have a reasonable expectation of success in combining the teachings as Wardell teaches identifying clonal diversity and frequency by sequencing and both Vignard and Zhou teach identifying diversity and frequency of clones from PBMCs following adoptive cell transfer and Sarnaik teaches Gen 2 LN-144 leads to clinical responses in patients and the disease control rate was 78%.
Applicant’s Arguments/ Response to Arguments
19. Applicant Argues: On page 8, paragraph 5, Applicant asserts that the cited references merely teach individual steps of the claimed method without any motivation or reasonable expectation of success in combining the steps to identify a clinically effective population of TILs as claimed. .
Response to Arguments: Applicant's arguments filed 03/26/2026 have been fully considered but they are not persuasive. Wardell teaches identifying TCR-CDR3 encoding nucleic acid sequence clones constituting TCR CDR3 clonal diversity of a therapeutic population of TILs called Gen1 and Gen2 wherein the clonal diversity is approximately 7000 unique CDR3’s for Gen1 TILs and approximately 15000 unique CDR3’s in Gen2 TILs (Figure 5; middle col. para. 5; previously cited). Wardell does not teach administering the TILs to a subject. Radvanyi teaches identifying the TCR CDR3-encoding nucleic acid sequence clones of a first population of PBMCs isolated from a subject at one month after administration of the TILs (Table S5; previously cited). Radvanyi teaches calculating the frequency of each dominant clonotype by determining the percentage of each specific CDR3 sequence found within the clones picked and sequenced and that clonotypes were analyzed in the TIL infusion product and in PBMC isolated from patients (page 6761, right col. paragraph 2; Table S5; previously cited). Radvanyi teaches the use of TILs for treating metastatic melanoma and one patient administered TILs was treated with a BRAF inhibitor (Abstract; page 6762, right col. paragraph 1; previously cited). Radvanyi teaches the TILs induced a high rate of objective tumor regression in melanoma patients and that this response can be long lasting (page 6768, right col. paragraph 2; previously cited). Radvanyi teaches most of the TILs had specific antitumor IFNγ responses (page 6764, left col. para. 2; previously cited). Radvanyi teaches future efforts will focus on developing strategies to generate more effective T cells and exploring future TIL clinical trials in combination with new FDA-approved agents for melanoma (page 6768, right col. paragraph 2; previously cited). Cooper teaches determining the clonality of TILs from melanomas by sequencing the CDR3 region before treatment with a BRAF inhibitor (BRAFi) and 10 – 14 days after BRAFi administration (page e26615-2, left col. paragraph 2; previously cited). Cooper teaches sorting the dominant clones by frequency (page e26615-2, right col. paragraph 1; previously cited). Cooper teaches the software used for determining clonality scores define clonality by an equation that considers unique sequences (page e26615-6, right col. paragraph 1; previously cited). Cooper teaches there was a striking difference in the relationship between the maximal response to therapy and the presence of new dominant clones suggesting that the response to BRAFi may rely on pre-existing TILs rather than on new clones, however the specificity of this clonal response requires further investigation (page e 26615-4, left col. paragraph 2; previously cited). Cooper teaches the characterization of TIL populations pre- and post-treatment may provide insights into the propensity of patients to respond to this form of immunotherapy (page e26615-5, left col. paragraph 2; previously cited). One would have been motivated to combine the teachings of Wardell, Radvanyi, and Cooper in a method to develop an effective TIL treatment for melanoma patients because Cooper teaches the characterization of TIL populations pre- and post-treatment may provide insights into the propensity of patients to respond to this form of immunotherapy.
Conclusion
No claims allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ZANNA M BEHARRY whose telephone number is (571)270-0411. The examiner can normally be reached Monday - Friday 8:45 am - 5:45 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Peter Paras can be reached at (571)272-4517. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Z.M.B./Examiner, Art Unit 1632
/PETER PARAS JR/Supervisory Patent Examiner, Art Unit 1632
Prosecution Insights