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 1-6, 8-9, 12-13, and 17 are cancelled.
Claims 7, 10-11, and 14-16 are pending and under examination on the merits.
Priority
This application is a CON of 15/738,498 12/20/2017 PAT 11,567,065 which is a 371 of PCT/US2016/039313 06/24/2016 which claims benefit of 62/183,997 06/24/2015.
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e)or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has notcomplied with one or more conditions for receiving the benefit of an earlier filing dateunder 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an inventionwhich is also disclosed in the prior application (the parent or original nonprovisionalapplication or provisional application). The disclosure of the invention in the parentapplication and in the later-filed application must be sufficient to comply with therequirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112,except for the best mode requirement. See Transco Products, Inc. v. PerformanceContracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
Claims 7, 10-11, and 14 are present in the original disclosure of theprovisional application and have the priority date of 06/24/2015 (finding support in US Provisional Application No. 62/183,997).
Claims 15-16 have the priority date of 06/24/2016 (finding support in US Patent Application No 15/738,498, but not in US Provisional Application No. 62/183,997 which, while mentioning the method in the context of CMV and depicting differences over 1 standard deviation as significant, does not even mention administration of a composition suitable for treating a suspected virulent).
IDS
The information disclosure statement (IDS) filed 06/10/2024 has been considered.
Specification
35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, requires the specification to be written in “full, clear, concise, and exact terms.” The specification is replete with terms which are not clear, concise and exact. The specification should be revised carefully in order to comply with 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112. Examples of some unclear, inexact or verbose terms used in the specification are referring to references as.” (refs)“ see [0047].
The disclosure is objected to because of the following informalities: the specification is complete with grammatical inaccuracies.
Appropriate correction is required.
Sequence compliance
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821 (a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR
1.821 through 1.825 for the reason(s) set forth on the attached Notice To Comply With Requirements For Patent Applications Containing Nucleotide Sequence And/Or Amino Acid Sequence Disclosures. A copy of the "Sequence Listing" in computer readable form has not been submitted as required by 37 C.F.R. 1.821 (e). Applicant is required to comply with the corrections for the sequence listing as per above as part of a complete response to this official action. Said sequence listing must comply with ST.26 sequence guidelines (see the Applicability section (f) of 87 Fed. Reg. 30806). Applicant is requested to return a copy of the attached Notice to Comply with the response.
The disclosure is objected to because of the following informalities: The specification at paragraph 0059 discloses amino acid sequences that must be identified by a sequence identifier. Appropriate correction is required.
Applicant's assistance in identifying any other instances where the specification states nucleotide/amino acid sequences within the sequence rules, is respectfully requested.
Claim Objections
Claims 7, 14, and 16 are objected to for reasons iterated below.
Claim 7 is objected to because of the following informalities: the limitation "the frequency" in line 1 should be amended to recite “a frequency”.
Claim 7 is objected to because of the following informalities: the limitation "the subtracting" in line 13 should be amended to recite “subtraction of fluorescence intensity”.
Claim 7 is being objected to because abbreviations such as; “PBMC” should be spelled out at the first encounter in the claims.
Claim 7 is objected to because of the following informalities: the recitation of “a well” in line 6 from which the recitation of “the wells” in line 8 derives antecedent basis in singular whereas the latter recitation is plural. This should be made to be consistent throughout claim 7 and in the dependent claims for consistency which promotes clarity. Additionally “Calcium” as recited in line 12 should not be capitalized as the claim is a single sentence (see MPEP §608.01(m)).
Claim 7 is objected to because of the following informalities: recitations of “peptide-MHC” in lines 8-9, 14, and 16 and switches to reciting “pMHC” in lines 11 and 15. This should be made to be consistent throughout claim 7 and in the dependent claims for consistency which promotes clarity.
Claim 7 is objected to for failure to comply with standard US drafting practice. Each claim is to take the form of a single sentence (see MPEP §608.01(m)). Claim 7 is drafted as two distinct sentences.
Claim 14 is objected to because of the following informalities: the recitation of “…wherein an efficiency is reduced…indicates a compromised immune system” is grammatically inaccurate.
Claim 16 is objected to because abbreviations such as; “CMV” should be spelled out at the first encounter in the claims.
Appropriate correction is required.
Claim Interpretation
A preamble is generally not accorded any patentable weight where it merely recites the
purpose of a process or the intended use of a structure, and where the body of the claim does not depend on the preamble for completeness but, instead, the process steps or structural limitations are able to stand alone. See In re Hirao, 535 F.2d 67, 190 USPQ 15 (CCPA 1976) and Kropa v. Robie, 187 F.2d 150, 152, 88 USPQ 478, 481 (CCPA 1951).
The preamble of claim 7 does not breathe life and meaning into the claim and is therefore not deemed to lend patentable weight to the method. The claim body, comprising the active steps and reagents required for the claimed method are what is being examined for a determination of patentability.
Where claim 14 is being interpreted such that the recitation of “…wherein an efficiency is reduced…indicates a compromised immune system” is understood and examined as reciting/reading “…wherein an efficiency that is reduced…indicates a compromised immune system.”
The claims are being interpreted as requiring steps and elements allowing for measurement of intracellular calcium signaling.
Recitations of terms such as pMHC, peptide-MHC, etc (noting that many terms are synonymously, though inconsistently used throughout the instant disclosure) are interpreted to encompass an antigen that binds MHC type I of the T cell (see for example, paragraphs 0011, 0014, 0016-0017, 0021).
Claim Rejections - 35 USC § 112
35 USC § 112(a)
Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 7, 10-11, and 14-16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
The purpose of the written description requirement is to ensure that the inventor had possession, at the time the invention was made, of the specific subject matter claimed. To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B. V. v. Dianwnd Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116.
The Application claims broad genera of capture antibodies and capturing protein without disclosure of a conserved structure/representative number of species to adequately describe said genus. The Application discloses 1 example (1 set of 6 CDRs with varied framework region; the commercially available TS2/4 antibody (see for example, paragraphs 0065, 0067, 0077, and 0118) of a capturing antibody that performs in the method as claimed and does not provide evidence of other antibodies or variants of the single set of 6 CDRs that would predictably function to bind as claimed. The Application discloses 1 example (Poly-l-lysine (see for example, paragraph 0077) of a capturing protein that performs in the method as claimed and does not provide evidence of other proteins that would predictably function as claimed. Therefore, in view of this disclosure, Applicant is claiming broad genera of capture antibodies and capturing protein without a representative number of species of said genera. The specification does not provide adequate written description for the broad genera of species claimed, because in the absence of empirical determination, one skilled in the art would be unable to immediately envision, recognize, or distinguish at least most of the members comprised within the genera claimed.
The written description requirement for a claimed genus or genera may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. A “representative number of species” means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. Applicant has only fully disclosed 1 set of 6 CDRs (1 species) for a capture antibody and 1 capture protein for consideration. Thus, given the substantial antibody and protein structure variation within the genera as well as the high level of unpredictability in the art, the disclosure is not sufficiently representative of the entire genera claimed.
Furthermore, regarding the claimed genus of capture antibody, Applicant has not disclosed relevant, identifying characteristics of CDR region amino acid sequences that confer upon an antibody the ability to function as claimed because the instant specification does not provide structural antibody features that correlate with a functional ability to bind in a non-stimulatory manner in the method as claimed.
Absent a clear description of the at least minimal structural features correlating with a functional ability to bind as claimed which are shared by members of a genus commonly sharing this function, it is submitted that the skilled artisan could not immediately envision, recognize, or distinguish which heavy and light chain CDR amino acid sequences may be mutated/varied/interchanged such that the resultant heavy and light chain variable regions comprise six CDRs that confer the ability to function as claimed.
Furthermore, while the prior art teaches some understanding of the structural basis of antigen-antibody recognition, it is noted that the art is characterized by a high level of unpredictability, since the skilled artisan still cannot accurately and reliably predict the consequences of amino acid substitutions, insertions, and deletions in the antigen-binding domains. For example, Al Qaraghuli et al (2020, Nature Scientific Reports 10:13969), state that the six CDRs form a continuous surface to form the paratope that binds the epitope of the cognate antigen. This suggests that a change in the CDR sequence may result in a conformationally different paratope which may fail to bind target as claimed. Here, a mutation in the CDRs may result in a paratope unable to bind the T cell in a nonstimulatory manner as claimed. Rabia et al (2018, Biochemical Engineering Journal 137:365-374) teach what effects mutations can have on an antibody's stability, solubility, binding affinity and binding specificity. Rabia et al report that an increase in antibody affinity can be associated with a decrease in stability (p. 366, col. 2 last paragraph; Fig. 2). Tiller et al (2017, J. Biol. Chem. (2017) 292(40) 16638–16652) and Tsuji et al (2022, J Virol 96:e00071-22) teach that mutations in the CDRs (especially HCDR3 are unpredictable and accompanied by tradeoffs in performance (for example increased affinity may lead to decreased specificity); see references in their entirety paying particular attention to the abstract of Tiller et al and the abstract and results section of Tsuji et al). The above cited references underscore the unpredictability of even a single mutation in the CDRs. Thus, the claims need to specify exact CDR sequences of the claimed capture antibody.
Accordingly, absent empirical determination, one skilled in the art would be unable to predict or envision which CDR sequences comprised within the genus comprising the claimed CDR sequences may be combined/mutated such that the resultant antibody possesses an antigen-binding site capable functioning as claimed. The general knowledge and level of skill in the art does not adequately supplement the omitted description, because specific, not general guidance is needed. Since the disclosure fails to describe relevant, identifying structural characteristics, in the form of fixed heavy and light chain CDR amino acid sequence combinations, that correlate with the ability to function as claimed, and because the one disclosed species detailed above is not sufficient to describe the claimed genus, it is submitted that the written description requirement of 35 U.S.C. 112(a) has not been met.
Applicant is directed to MPEP § 2163 for guidelines on compliance with the written description requirement. Here, applicant has not described a reasonable number of members of the genus of antibodies that would function in the method(s) as claimed, but rather has presented the public with an idea of how to perform an assay that might identify some peptides that fall within the scope of the claim. Of course, depending on what agents are used in the screening assay, it may well identify none. The Court of Appeals for the Federal Circuit addressed claims of this sort in great detail in University of Rochester v. G.D. Searle and Co. (69 USPQ 2nd 1886, CAFC 2004). In Rochester, the Federal Circuit upheld the district court's ruling that patent claims which recited administration of compounds not disclosed, but rather to be identified in a screening assay, were invalid on their face.
In Ariad, the court further noted that the written description plays a particularly important role in the biological arts, where patentees might otherwise be tempted to claim a genus of compounds by its function or result:
“The written description requirement also ensures that when a patent claims a genus by its function or result, the specification recites sufficient materials to accomplish that function—a problem that is particularly acute in the biological arts. 5 See Guidelines for Examination of Patent Applications Under the 35 U.S.C. 112, 1, “Written Description” Requirement, 66 Fed. Reg. 1099, 1105-1106 (Jan. 5, 2001). This situation arose not only in Eli Lilly but again in University of Rochester v. G.D. Searle & Co., Inc., 358 F.3d 916 [69 USPQ2d 1886] (Fed. Cir. 2004). In Rochester, we held invalid claims directed to a method of selectively inhibiting the COX-2 enzyme by administering a non-steroidal compound that selectively inhibits the COX-2 enzyme. Id. at 918. We reasoned that because the specification did not describe any specific compound capable of performing the claimed method and the skilled artisan would not be able to identify any such compound based on the specification's function description, the specification did not provide an adequate written description of the claimed invention. Id. at 927-28. Such claims merely recite a description of the problem to be solved while claiming all solutions to it and, as in Eli Lilly and Ariad's claims, cover any compound later actually invented and determined to fall within the claim's functional boundaries—leaving it to the pharmaceutical industry to complete an unfinished invention.”
Ariad Pharmaceuticals., Inc. v. Eli Lilly & Co., 94 USPQ2d 1161, 1173 (Fed. Cir. 2010) (en banc). Emphasis added.
The Federal Circuit has clarified Written Description as it applies to antibodies in the recent decision Amgen v. Sanofi, 872 F.3d 1367 (Fed. Cir. 2017). The Federal Circuit explained in Amgen that when an antibody is claimed, 35 U.S.C. 112(a) (or pre-AIA first paragraph) requires adequate written description of the antibody itself. Amgen, 872 F.3d at 1378-79. The Amgen court expressly stated that the so-called “newly characterized antigen” test, which had been based on an example in USPTO-issued training materials and was noted in dicta in several earlier Federal Circuit decisions, should not be used in determining whether there is adequate written description under 35 U.S.C. 112(a) for a claim drawn to an antibody. Citing its decision in Ariad Pharmaceuticals, Inc. v. Eli Lilly & Co., the court also stressed that the “newly characterized antigen” test could not stand because it contradicted the quid pro quo of the patent system whereby one must describe an invention in order to obtain a patent. Amgen, 872 F.3d at 1378-79, quoting Ariad, 598 F.3d 1336, 1345 (Fed. Cir. 2010). In view of the Amgen decision, adequate written description of an antigen alone is not considered adequate written description of a claimed antibody to that antigen, even when preparation of such an antibody is routine and conventional. Id.
Applicant is further directed to In re Alonso (545 F.3d 1015 (Fed. Cir. 2008), which involved claims that were directed to methods of using antibodies wherein the court found that the claims lacked adequate written description for the recited genus of antibodies recited in the methods. (C) See p. 8, 3rd paragraph, where Applicant argues that the claims recite all essential features of the invention. Therefore, products used in methods are rightfully subject to the written description requirement.
While generically the structure of antibodies is known, the structure of the presently recited antibodies can vary substantially within the above given claimed recitations. As noted in Amgen, knowledge that an antibody binds to a particular epitope on an antigen tells one nothing at all about the structure of the antibody, wherein “instead of analogizing the antibody-antigen relationship to a ‘key in a lock,’ it [is] more apt to analogize it to a lock and ‘a ring with a million keys on it.” (Internal citations omitted). The relevant antibody art confirms this quandary, indicating that “knowledge of an epitope or antigen used to generate a monoclonal antibody is insufficient for making the original antibody available, even if suitable in vitro test systems for screening are used.” See p. 8, lines 3-5 of WO 2009/033743 A1. Therefore, those of skill in the art would not accept that the inventor had been in possession of the full genus of antibodies in the present claims.
Goel et al (2004, J. Immunol. 173: 7358-7367) teach that three mAbs that bind to the same short (12-mer) peptide, exhibit diverse V gene usage, indicating their independent germline origin. Said reference further teaches that two of these mAbs recognize the same set of amino acid residues defining the epitope (alternate amino acid residues spread over the entire sequence), however, the relative contribution of each set of residues in the peptide showed significant variation. The reference notes that all of the mAbs do not show any kind of V gene restriction among themselves, implying variable paratope structure, despite that two of these mAbs bind to the peptide through a common set of residues (see entire reference).
Khan et al (2014, J. Immunol. 192: 5398-5405) teach that two structurally diverse germline mAbs recognizing overlapping epitopes of the same short peptide do so in different topologies, the antibodies possessing entirely different CDR sequences. Said reference teaches that unrelated mAbs structurally adjust to recognize an antigen, indicating that the primary B cell response is composed of BCRs having a high degree of structural adaptability. Said reference also teaches that the common epitope(s) also adopt distinct conformations when bound to different mAbs, with the higher degree of structural plasticity inherent to the mAbs. Said reference further teaches “[i]t has been shown that both the framework region and the CDRs have a considerable amount of inherent conformational plasticity...Therefore, it is not surprising that distinct germline Abs recognize the same epitope by rearranging the CDR conformations. This may well have implications of Ag specificity beyond the naive BCR repertoire, because Kaji et al (as cited by Khan et al)....have shown in a recent report that the B cell memory can contain both germline-encoded and somatically mutated BCRs,” (see entire reference of Khan et al).
Poosarla et al (2017, Biotechn. Bioeng. 114(6): 1331 -1342) teach substantial diversity in designed mAbs (sharing less than 75% sequence similarity to all existing natural antibody sequences) that bind to the same 12-mer peptide, binding to different epitopes on the same peptide. Said reference further teaches “most B-cell epitopes... in nature consist of residues from different regions of the sequence and are discontinuous...de novo antibody designs against discontinuous epitopes present additional challenges...." (see entire reference.)
Janeway et al (Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; 2001. The generation of diversity in immunoglobulins. Available from: https://www.ncbi.nlm.nih.gov/books/NBK27140/) teach that, “[v]irtually any substance can elicit an antibody response. Furthermore, the response even to a simple antigen bearing a single antigenic determinant is diverse, comprising many different antibody molecules each with a unique affinity, or binding strength, for the antigen and a subtly different specificity,” (see for example, paragraph 1 of page 1/12).
Although screening techniques can be used to isolate CDR variant antibodies that possess the ability to function as claimed, Applicant is reminded that the written description requirement of 35 U.S.C. 112 is severable from the enablement provision. As stated in Vas-Cath Inc. v. Mahurkar (CA FC) 19 USPQ2d 1111, 935 F2d 1555, “The purpose of the 'written description' requirement is broader than to merely explain how to 'make and use'; the applicant must also convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed.”
Therefore, the antibodies, as claimed are only disclosed by function/insufficient structure, without a representative number of species or unifying, conserved structure clearly enabling one skilled in the art to readily envisage the members of the genus claimed which would function as claimed in the claimed method(s).
Furthermore, Proteintech (The importance of epitope selection in experimental design, Proteintech, obtained from: https://www.ptglab.com/news/blog/the-importance-of-epitope-selection-in-experimental-design/?srsltid=AfmBOophB0oOURPWVt8-Ev696rJUsE1_yPXsMEFvA57ECk6diMWAmt6D; accessed 02/10/2026) teaches that, when designing an experiment that uses antibodies, one often overlooked parameter is the exact binding site of your antibody on the protein of interest, also known as the epitope. An antibody’s primary role is to bind to a specific protein (also known as the antigen or immunogen) which in turn allows for the detection, neutralization, or modification of the protein’s activity. Carefully choosing your antibodies based on epitope binding site can greatly influence experimental outcomes, therapeutic strategies, and diagnostic accuracy (see for example, paragraph 1 of page 1-13). Additionally, Proteintech teaches that an epitope which functions in one assay method may fail in another) see for example, pages 1/13-2/13). The artisan is effectively invited to screen for epitopes which function in the assay method as claimed due to the absence of description which enables the artisan to readily envisage which members of the recited genus of epitopes would function as claimed.
With regard to the claimed genus of capture protein, Listov et al (Opportunities and challenges in design and optimization of protein function. Nat Rev Mol Cell Biol 25, 639–653 (2024)) teach that the primary amino acid sequence determines downstream structure (protein folding), which then determines function (presenting both the inverse folding problem and the inverse function problem (see for example, Figure 1 and its caption; see also Mishra et al (Inaccurate secondary structure predictions often indicate protein fold switching. Protein Sci. 2019 Aug;28(8):1487-1493. doi: 10.1002/pro.3664. Epub 2019 Jun 17)). Expanding on these problems in proteomics, Reardon (Nature 635, 246-248 (2024)) explains that the goal of designing a protein with known and predictable function, binding partners, size, location, and other traits is, for the moment, a dream. Reardon teaches that further challenges in protein design include predicting how a protein, even if it binds to target, will function upon said binding. Reardon teaches that the primary structure (amino acid sequence) of a protein is critical to function, noting that even proteins of similar shape do not execute the same functions, while those with different shapes may carry out the same tasks. Reardon goes on to teach that it is not always apparent which parts of the primary sequence are important; a seemingly useless amino-acid chain on the side of an enzyme, for instance, might affect how tightly a protein can bind to other molecules or its ability to flip between conformational states. Moreover, Reardon explains that when researchers attempt to solve the structure of a protein experimentally, they often end up seeing only the most stable conformation, which is not necessarily the form the protein takes when it is active (see for example, pages 246-247 of Reardon).
Therefore, claims 7, 10-11, and 14-16 are deemed to fail to meet the written description requirement, as presently drafted.
Enablement
Claims 7, 10-11, and 14-16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method to determine the frequency and functional activity of antigen-specific CD8 T cells from human PBMC through an assay based on measurement of T cell intracellular Ca2+ signaling induced in response to antigen recognition by T cell receptor comprising immobilized, freshly isolated CD8 T cells from human PBMC labeled with Ca2+ sensitive fluorophore, does not reasonably provide enablement for the claimed embodiment of the method to determine the frequency and functional activity of antigen-specific CD8 T cells from human PBMC through an assay based on measurement of T cell intracellular Ca2+ signaling induced in response to antigen recognition by T cell receptor wherein the immobilized CD8+ T cells and the pMHC are unlabeled or the embodiment where the immobilized T cell is unlabeled and fluorescently labeled peptide-MHC proteins assembled on nanoparticles or any other peptide-MHC oligomers are used to detect antigen-specific T cells and/or to induce Ca2+ signaling in the responding T cells. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to practice the invention commensurate in scope with these claims.
MPEP 2164.01(a) states that in order to determine compliance with the enablement requirement, the Federal Circuit developed a framework of factors in In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988), referred to as the Wands factors to assess whether any necessary experimentation required by the specification is “reasonable” or is “undue.”
These factors include but are not limited to: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
The breadth of the claims
Claims 7, 10-11, and 14-16 are broadly directed to a method to determine the frequency and functional activity of antigen-specific CD8 T cells through an assay which measures calcium-dependent fluorescence intensity which informs a downstream calculated fraction of responding T cells with the specify of interest. The specification discloses a method in which the rate of calcium signaling as measured by the claimed assay, using immobilized T cells labeled with a calcium-sensitive fluorescent probe which may be subsequently used to inform downstream determinations of T cell frequency and functional activity which are used to form conclusions regarding immunocompetency and treatment.
The nature of the invention
Claims 7, 10-11, and 14-16 are broadly directed to a method to determine the frequency and functional activity of antigen-specific CD8 T cells through an assay which measures calcium-dependent fluorescence intensity which informs a downstream calculated fraction of responding T cells with the specificity of interest. The claims are directed to biological subject matter which is understood to be complex and often unpredictable.
The state of the prior art
A search of the prior art supports that, while measuring of calcium signaling is understood to require a calcium sensitive probe, such as a fluorophore, it was not obvious in the prior art to measure intracellular calcium signaling where the T cell was not labeled with a calcium-sensitive fluorophore other calcium-sensitive probe/fluorophore (see for example, Christo et al (Sci Rep 5, 7760 (Jan. 2015). https://doi.org/10.1038/srep07760) and Hanani, M ( (2015). Re: How can I measure changes in cellular Ca2+ concentration?. Retrieved from: https://www.researchgate.net/post/How_can_I_measure_changes_in_cellular_Ca2_concentration/5603c5a75dbbbd765e8b4588/citation/download).
The level of one of ordinary skill
As the claims are directed to determination of antigen-specific CD8 T cell frequency and functional activity, the artisan is presumed to be highly skilled, tending to have an advanced degree (such as a Ph.D. or an M.D.).
The level of predictability in the art
The art supports that measurement of intracellular calcium is understood to be accomplished using a calcium-sensitive probe, such as a fluorophore. A search of the prior art failed to reveal known methods for measuring intracellular calcium Ca2+ sensitive fluorophore signaling/oscillation/fluctuation without the use of a calcium-sensitive probe for the cell of interest, let alone methods for such measurement which would appear to be predictably compatible with the claimed methods (see supra).
(F) The amount of direction provided by the inventor
Applicant discloses methods for measuring intracellular calcium signaling in immobilized CD8 T cells where the T cells are labeled with the Ca2+-sensitive fluorophore (see for example, paragraphs 0016, 0047 and 0119 of the instant specification). No other examples are provided in the instant disclosure. The specification alleges that “[t]he binding of fluorescently labeled cognate pMHC to unlabeled T cells will identify both responding and non-responding T cells specific for the same peptide-MHC ligands; and calculating a fraction of responding T cells with the specificity of interest,” but provides no further explanation, guidance or working examples related thereto (see for example, paragraph 0018 of the instant specification). No guidance is provided relating to an embodiment with no assay component labeled with a Ca2+-sensitive fluorophore.
The existence of working examples
Applicant discloses 1 working example (see supra and instant Figures 1-9 as well as paragraph 0075 of the instant specification).
The quantity of experimentation needed to make or use the invention based on the content of the disclosure
The case is directed to biological subject matter, which is by nature complex. There is
only one working example provided (which is notably not commensurate with the breadth of what is claimed) and the state of the art fails to step in to provide enablement where the instant disclosure is lacking. The artisan would be forced into burdensome experimentation so as to effectively invent what applicant only suggests may be possible.
Thus, in light of the state of the prior art and the complexity of the subject matter claimed, the method is not deemed to be enabled where the instant disclosure and prior art fail to provide enablement for the method where the immobilized CD8+ T cells are not labeled with a Ca2+ fluorophore. Therefore claim 7 is rejected and its dependent claims (10-11 and 14-16) are included in this rejection because they incorporated (via dependency) and fail to remedy the above noted deficiency.
Claims 14-16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
MPEP 2164.01(a) states that in order to determine compliance with the enablement requirement, the Federal Circuit developed a framework of factors in In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988), referred to as the Wands factors to assess whether any necessary experimentation required by the specification is “reasonable” or is “undue.”
These factors include but are not limited to: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
The breadth of the claims
Claims 14-16 are broadly directed to a method to determine the frequency and functional activity of antigen-specific CD8 T cells through an assay which measures calcium-dependent fluorescence intensity which informs a downstream calculated fraction of responding T cells with the specify of interest. The specification discloses a method in which the rate of calcium signaling as measured by the claimed assay is used to inform downstream determinations of T cell frequency and functional activity which are used to form conclusions regarding immunocompetency and treatment.
The nature of the invention
Claims 14-16 are broadly directed to a method to determine the frequency and functional activity of antigen-specific CD8 T cells through an assay which measures calcium-dependent fluorescence intensity which informs a downstream calculated fraction of responding T cells with the specificity of interest. The claims are directed to biological subject matter which is understood to be complex and often unpredictable.
The state of the prior art
The state of the prior art supports that different assay methods in CD8 T cells often result in different measured binding kinetics, even when the same pMHC and TCR are used and that weaker antigens have different kinetics than stronger antigens (see for Edwards et al (Immunol Res. 2011 May;50(1):39-48. doi: 10.1007/s12026-011-8204-3) at for example, paragraph 3 of page 4)). Moreover, Carnahan et al (Pharmacotherapy. 2024;44:698–700; DOI: 10.1002/phar.4605) teach that underpowered studies that report significant findings are at an elevated risk of incorrectly identifying the sign and/or magnitude of a real effect. In a well-designed clinical trial meant to test the effect of an intervention, the target sample size is determined by specifying a minimum clinically important intervention effect that the investigators want to be able to detect and estimating the variability in or frequency of the outcome. This is usually based on prior knowledge or data. A decision is then made about what the achievable level of power to detect a particular magnitude of effect is, with conventions to ensure power of at least 80%–90%, leaving a 10%–20% chance that a true effect of that size will be missed. Small pilot studies are often underpowered. The effect estimates from these studies can have wide confidence or credible intervals, reflecting substantial uncertainty about true intervention effects, and variability in the outcome measures may be poorly estimated by small samples.3 Effects observed in these studies may be entirely due to chance, and effect estimates in the opposite direction of the true effect are more likely in small studies. Even statistically significant findings from small studies are more likely to be false positive findings due to random chance than those from larger studies when the same alpha is used. To make matters worse, if a study is underpowered to detect clinically meaningful effects, its use as a screening tool would be likely to exclude meaningful interventions from future study if effect size is not considered (see for example, pages 698-699).
The level of one of ordinary skill
As the claims are directed to determination of antigen-specific CD8 T cell frequency and functional activity, the artisan is presumed to be highly skilled, tending to have an advanced degree (such as a Ph.D. or an M.D.).
The level of predictability in the art
The art supports that different measures will result in different observed binding kinetics (which results in different Ca2+ fluorescence which indirectly represents measured frequency and functional activity of antigen-specific CD8 T cells. The art further supports that the strength of the pMHC plays a role in determining observed kinetics and supports that underpowered data are unpredictable for supporting a generalized conclusion, noting that the effect noted may be a false positive or an idiosyncratic response (see supra).
(F) The amount of direction provided by the inventor
Applicant does not disclose the claimed method that does not involve determination of a relative rate of calcium signaling fluctuation in response to pMHC. Applicant only discloses 1 example of the method (presumed to use the noted CMV epitopes from ThinkPeptide; see paragraph 00104 of the instant specification) where the rate calcium fluctuation/signaling of healthy/control T cells is compared to the rate of calcium fluctuation/signaling of T cells taken from a bone marrow transplant patient on the 152nd day after the transplant (both sets of T cells being CMV specific).
The existence of working examples
Applicant discloses 1 working example (see supra and instant Fig. 7).
The quantity of experimentation needed to make or use the invention based on the content of the disclosure
The case is directed to biological subject matter, which is by nature complex. There is only one working example provided (which is notably not commensurate with the breadth of what is claimed) and the state of the art fails to step in to provide enablement where the instant disclosure is lacking. Note that the data serving as proof of concept is woefully underpowered calling into question whether the effect observed is supported or indicates what Applicant believes may be true, but has not yet enabled. The artisan would be forced into burdensome experimentation so as to effectively invent what applicant only suggests may be possible.
Thus, in light of the contradictory findings in the prior art, the method is not deemed to be supported because even if the claims were to be amended to require determination of a relative Ca2+ signaling fluctuation rate, the data upon which the Application relies for proof of concept is so underpowered that a determination of enablement is precluded where the prior art fails to provide enablement for the method indicating a particular immune state, and treatment to be administered in the setting of CMV, or even the cutoff of +/->1 standard deviation of a control rate of Ca2+ fluorescence.
35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 7, 10-11, and 15 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 7 recites “peptide-MHC” in lines 8-9, and 14 and switches to reciting “pMHC” in line 11, “cognate pMHC” in line 15, and “peptide-MHC ligands” in line 16. This raises ambiguity as to whether these recitation refer to the same genus. The claims are being interpreted such that all of the enumerated recitations (alternative terms) are read and understood synonymously as is consistent with the specification in its apparent entirety (see the claim interpretation section supra). However, the lack of consistency unnecessarily creates confusion as to how each term is to be interpretated where artisans are likely arrive at conflicting understandings of what is claimed.
Claim 7, as noted in the claim objections section of this Office Action supra, is not drafted to recite a single sentence, but contains a period followed by a new sentence at “…oligomers. The binding of fluorescently labeled…,” which clouds the metes and bounds of the claim because it cannot be clearly determined whether the information presented after the period is part of the claim. Artisans are therefore left to argue as to what the full scope of the claim may be.
Claim 15 fails to recite a transition term (such as ‘and’ or ‘or’) which would clarify the connection of the steps of the claim so as to provide a clear and definite claim. Artisans are left to determine whether the administration step is connected by an ‘and’ or an ‘or’ such that the scope is indefinite.
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.
Claim(s) 7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Su et al (J Immunol 1993; 151:658-667; citation 13 under the Non-Patent Literature heading of the 06/10/2024 IDS) in view of Steenblock et al (Mol Ther. 2008 Apr;16(4):765-72. doi: 10.1038/mt.2008.11. Epub 2008 Mar 4), ThermoFisher (Isolation of Untouched Human T cells from Peripheral blood Mononuclear Cells (PBMC), ThermoFisher Scientific, obtained from: https://www.thermofisher.com/us/en/home/references/protocols/proteins-expression-isolation-and-analysis/cell-separation-methods/human-cell-separation-protocols/isolation-of-untouched-human-t-cells-.html#pro1 (available as of May 2008)(see google screen capture as further the screen capture from Google search further evidencing the date of availability (obtained from: https://www.google.com/search?q=protocol+for+isolation+of+T+cell+from+patient+pbmc+sample+for+personalized+medicine&safe=active&sca_esv=db2351f46a6aa745&source=lnt&tbs=cdr%3A1%2Ccd_min%3A%2Ccd_max%3A2008&tbm=; accessed 02/26/2026), and Tay et al (Nature, Vol 466, 8 July 2010; doi:10.1038/nature09145).
A preamble is generally not accorded any patentable weight where it merely recites the
purpose of a process or the intended use of a structure, and where the body of the
claim does not depend on the preamble for completeness but, instead, the process
steps or structural limitations are able to stand alone. See In re Hirao, 535 F.2d 67, 190
USPQ 15 (CCPA 1976) and Kropa v. Robie, 187 F.2d 150, 152, 88 USPQ 478, 481
(CCPA 1951).
In this case, the body of the claim does not depend on the preamble for completeness
and the preamble is not given patentable weight.
Su et al teach a method comprising using an increase of cellular calcium ion as a measure of T-cell activation wherein peptide-dependent activation, recognized by MHC I (implicitly taught to be expressed by CD8+ T cells), of CD8+ T cell lymphocyte depends upon cell to cell contact (see for example, the abstract and paragraph 1 of column 1 of page pages 658 and Fig. 8 at and 664, respectively). Su et al teach that TCR molecules on a CD8+ T cell do not interact with peptide-MHC-I complexes on the same cell and only cells CD8+ that are in contact to one another display an increase in Ca level in the presence of the cognate peptide (see for example, paragraph 1 of column 1 at page 659). This suggests that the immobilized T cells were a monolayer upon the surface.
In particular Su et al teach labeling T cells with Ca2+ sensitive fluorophore (see for example, paragraph 3 of column 1 at page 660) adhering cells on a glass coverslip (which is held to make obvious immobilization on a glass well bottom as the chemical/mechanical process of the required adherence/immobilization is the same and would function predictably on any substantially flat surface comprised of glass) and measuring the level of fluorescence in all individual T cells to collect baseline measurements of Ca2+ with laser cytometry (see for example, paragraph 2 at column 2 at page 660). Su et al teach adding a single or multiple peptide epitopes such as for example Ov-8 peptide, that is recognized in association with MHC I by anti-OVA (antigen-specific) CD8 T cells, and measuring the level of fluorescence in every individual T cell by taking a second image of the T-cell monolayer on the glass coverslip (see for example, page 660 at paragraph 2 at column 2). An increase in calcium is seen in 4G3 CD8+ T cells which are in contract with each other, as for example by gentle centrifugation (see for example, Figs 8-9 at pages 664-665), as compared to baseline (shown in for example, Fig 8 at page 664) which reads on identifying an increase in intracellular Ca2+ level and fluorescence intensity for every individual T cell after subtracting fluorescence intensity for every individual T cell measured before the addition of the stimulatory pMHC from which a fraction of responding and non-responding cells (presumably responding/antigen-specific cells show an increase in Ca2+ and non-responding/antigen-non-specific cells will not show an appreciable increase in Ca2+ relative to baseline) may be identified/quantified/analyzed for functional activity. Su et al further teach measuring changes in number of individual T cells with increased intracellular fluorescence as a function of time to provide the kinetic curve of the TCR-mediated Ca2+ signaling (see for example, figure 664 at Fig. 8 from which it can be seen that all individual T cells that were closely packed by gentle centrifugation show increase fluorescence as a function of time as compared to baseline (i.e. cells that were not incubated with the peptide)).
Su et al do not teach that the T cells are immobilized on a glass bottom of a well using a capture peptide or capture antibody.
However, Steenblock et al teach that efficient T-cell stimulation and proliferation in response to specific antigens is a goal of immunotherapy against infectious disease and cancer (see for example, sentence 1 of paragraph 1 of column 1 at page 765). Steenblock et al further teach an assay where aAPC–T-cell binding was visualized by immobilizing B3Z cells (a T-cell line) to poly-L-lysine-coated cover slips, which were washed three times and blocked, and then incubated with a 5 mg/ml solution of targeted microparticle aAPCs containing encapsulated Rhodamine B and surface bound anti-CD3 and anti-CD28 for 1 hour at 4 °C (see for example, Fig 2 and its caption at page 766 and the fluorescence microscopy section of column 2 of page 771) . Here, Poly-L-lysine would represent the claimed capture protein.
Su et al and Steenblock et al do not explicitly teach taking the T cells from a PBMC sample.
However, it is noted that Applicant used commercially available T cells from PBMC indicating that such isolation and use in commonly known in the art (see for example, paragraph 00102 of the instant specification). Therefore, this limitation is considered to be admitted prior art by Applicant. However, even if Applicant were to argue the admission of said prior art, this limitation would still be deemed obvious because ThermoFisher teaches a protocol for isolation of T cells from PBMC and sells kits and products therefore (see the reference in its entirety).
Su et al, Steenblock et al, and Thermofisher et al do not explicitly teach calculation of a fraction of responding cells.
It is noted that said fraction is generically recited with no particular steps for arriving at the fraction being required. Tay et al teach such a calculation by teaching that the fraction of responding cells at each concentration of a substance of interest was calculated as the number of responding cells divided by the sum of responding and non-responding cells and by first subtracting the baseline level, and then dividing the differential expression levels with the fraction of active cells at each dose measured (see for example, the final sentence of the last paragraph on column 1 of page 272 and column 2 of page 272) where the fraction of responding cells is a discrete measure of single cell activation (see for example, column 2 of page 267).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of the combined references. The artisan would have been motivated to make and use the invention as claimed because Su et al teach a method for determining T cell activation (by rate of intracellular Ca2+ flux) in response to a pMHC I antigen (to be chosen for the desired application) relative to baseline where Steenblock et al teach that efficient T-cell stimulation and proliferation in response to specific antigens is a goal of immunotherapy against infectious disease and cancer and where Tay et al teach a calculated fraction of responding cells relative to baseline is a discrete measure of single cell activation. The artisan would have found it obvious to substitute a glass well plate for a coverslip to enable analysis of multiple samples and or/conditions/concentrations of pMHC simultaneously where the chemistry and mechanics of immobilization among substantially flat glass surfaces and generically recited CD8 T cells would have been predictable altered in to use a glass well. Additionally, the artisan would have found it obvious to use antigen-specific T cells isolated from PBMC from a patient as an art-known, relatively non-invasive means for obtaining a patient-specific sample for personalized medicine. The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Claim(s) 10-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Su et al Steenblock et al, ThermoFisher, and Tay et al as applied to claim 7 above, in further view of Maecker et al (Cytometry Part A Doi 10.1002/cyto.a, first published Aug. 2006, obtained from: https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.20333).
Regarding claims 10-11, the combined references make obvious the method of claim 7, but do not explicitly teach comparison of a pathogen-specific or tumor-specific CD8 T cell to a control or a control that is a T cell sample from a healthy patient/donor.
However, Maecker et al teach that any experiment may, and probably should, contain at least three types of controls: setup (or instrument) controls, specificity (or gating) controls, and biological comparison controls, where biological comparison controls are those that provide biologically relevant comparison conditions, for example, unstimulated samples or healthy donor samples (see for example, column 1 of page 1037), noting that comparison of a disease phenotype and a healthy control is an art-known comparison and control in biological science (see for example, column 1 of page 1042).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of the combined references. The artisan would have found it obvious to use a control that is a corresponding sample (of PBMC isolated T cells) from a healthy donor to serve as a biological control relative to the test sample for comparative analysis of a disease state relative to a healthy/normal state (as taught by Maecker et al). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-3 of U.S. Patent No. 11567065 B2 (reference A) in view of Tay et al (Nature, Vol 466, 8 July 2010; doi:10.1038/nature09145). Although the claims at issue are not identical, they are not patentably distinct from each other because the reference claims and instant claims are directed to methods with substantially the same active steps and reagents.
Reference A claims a method for detection of the frequency of T cells responding to a single or multiple antigenic peptide epitope(s), by fluorescent microscopy comprising:
(a) coating a glass surface with an agent capable of binding an antibody, wherein the agent comprises poly-L-lysine,
(b) immobilizing on the glass surface of (a) an antibody that binds to a receptor on the T-cell surface without interfering with Ca2+ flux, wherein the antibody comprises the TS2/4 monoclonal antibody specific for Lymphocyte Function Associated Antigen 1 (LFA-1), to form a T-cell capturing surface,
(c) adding cloned or polyclonal T cells or gamma/delta T cells labeled with Ca2+ sensitive fluorophore to the T-cell capturing surface of (b) to generate a continuous monolayer of the T cells on the glass surface,
(d) taking a first image of the T-cell monolayer to determine a level of background fluorescence in every individual cell,
(e) performing antigen stimulation of the T-cell monolayer comprising adding a single or multiple antigenic peptide epitope(s) or live target cells presenting potential antigenic peptide epitope(s) to the T-cell monolayer wherein the antigenic peptide epitopes are capable of binding to MHC proteins expressed on the T-cell surface to form a peptide-MHC complex,
(f) measuring the level of fluorescence in every individual T cell of the stimulated T-cell monolayer of (e), by taking a second image of the T-cell monolayer of (e), wherein an increase of intracellular fluorescence of individual cells indicates T cells responding to the single or multiple antigenic peptide epitopes (understood to allow for identification of antigen-specific T cells); and
g) quantifying the frequency of responses of individual T cells to a single or multiple antigenic peptide epitopes by subtracting intracellular fluorescence of the first image measured prior to addition of said single or multiple antigenic peptide(s) epitopes from that acquired after the second image following addition of said single or multiple antigenic peptide epitope(s), wherein the number of individual T cells that exhibit fluorescence greater than background fluorescence are quantified to calculate the number of responding cells per the number of added cloned or polyclonal T cells , wherein the T cells may be CD8+ T cells from PBMC, wherein the method further comprises measuring the kinetics (rate) of Ca2+ flux in the T cell (intracellular and presumptively within each individual cell in light of the language employed in the drafting of the claim) that form the monolayer on the surface by repeating step (f) over time to determine a kinetic curve (see for example, claims 1-3 of reference A).
Reference A does not claim calculating a fraction of responding cells. It is noted that said fraction is generically recited with no particular steps for arriving at the fraction being required. Tay et al teach that the fraction of responding cells at each concentration was calculated as the number of responding cells divided by the sum of responding and non-responding cells and by first subtracting the baseline level, and then dividing the differential expression levels with the fraction of active cells at each dose measured (see for example, the final sentence of the last paragraph on column 1 of page 272 and column 2 of page 272) where the fraction of responding cells is a discrete measure of single cell activation (see for example, column 2 of page 267).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosure of reference A and Tay et al. The artisan would have been motivated to make and use the invention as claimed because As part of determining obviousness, it is to be considered that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 may bar its patentability. When considering obviousness of a combination of known elements, the operative question is thus “whether the improvement is more than the predictable use of prior art elements according to their established functions,” (see MPEP 2141. I.)). Here, the active method steps are essentially the same where any deviations are small and predictable variations on the reference method. The reagents used are substantially the same. Where the same active steps and measurements are taken using substantially similar reagents, the method of reference A is deemed to make obvious the method of instant claim 7. The artisan would have found it obvious to calculate a fraction of responding cells because Tay et al teach a calculated fraction of responding cells relative to baseline is a discrete measure of single cell activation The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Claims 10-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-3 of U.S. Patent No. 11567065 B2 (reference A) in view of Tay et al as applied to claim 7 above, in further view of Tay et al (Nature, Vol 466, 8 July 2010; doi:10.1038/nature09145) and Maecker et al (Cytometry Part A Doi 10.1002/cyto.a, first published Aug. 2006, obtained from: https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.20333). Although the claims at issue are not identical, they are not patentably distinct from each other because the reference claims and instant claims are directed to methods with substantially the same active steps and reagents
Regarding claims 10-11, reference A makes obvious the method of claim 7, but does not explicitly teach comparison of a pathogen-specific or tumor-specific CD8 T cell to a control or a control that is a T cell sample from a healthy patient/donor.
However, Maecker et al teach that any experiment may, and probably should, contain at least three types of controls: setup (or instrument) controls, specificity (or gating) controls, and biological comparison controls, where biological comparison controls are those that provide biologically relevant comparison conditions, for example, unstimulated samples or healthy donor samples (see for example, column 1 of page 1037), noting that comparison of a disease phenotype and a healthy control is an art-known comparison and control in biological science (see for example, column 1 of page 1042).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of the combined references. The artisan would have found it obvious to use a control that is a corresponding sample (of PBMC isolated T cells) from a healthy donor to serve as a biological control relative to the test sample for comparative analysis of a disease state relative to a healthy/normal state (as taught by Maecker et al). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Claim 7 and 10-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 15-25 of U.S. Patent Application No. 19/058,712 (reference B) in view of Tay et al (Nature, Vol 466, 8 July 2010; doi:10.1038/nature09145). Although the claims at issue are not identical, they are not patentably distinct from each other because the reference claims and instant claims are directed to methods with substantially the same active steps and reagents.
This is a provisional nonstatutory double patenting rejection.
Reference B claims a method of evaluating a T cell response comprising: a) binding mammalian T cells labeled with a Ca2+ sensitive fluorophore to a glass surface using a capturing protein to form a monolayer; b) exposing the T cells obtained in a) with an antigen that is capable of binding to Major Histocompatibility Complex (MHC) proteins, wherein the MHC proteins bind to the T cells; c) measuring the intracellular fluorescence of the T cells obtained in step b) wherein an increase of intracellular fluorescence in individual cells indicates T cells have been activated by the antigen; d) characterizing the T cell response as one of a rapid sustained response, a delayed sustained response, an oscillating response, or a sporadic transient response e) comparing the T cell response to a control, wherein the T cells are bound to the surface via attachment to a capturing protein, wherein the capturing protein binds to a receptor on the surface of the T cell without interfering with Ca2+ flux and wherein the capturing protein comprises a TS2/4 monoclonal antibody specific for lymphocyte function-associated antigen 1. (see for example, claims 15-17 of reference B). Reference B further claims the method wherein measuring the intracellular fluorescence of T cells comprises herein measuring the intracellular fluorescence of T cells comprises: a) measuring an initial background fluorescence of the T cell labeled with a Ca2+ sensitive fluorophore prior to exposure to the antigen; b) measuring fluorescence of the T cell labeled with a Ca2+ sensitive fluorophore following exposure to the antigen; and c) subtracting the initial background fluorescence of the T cell labeled with a Ca2+ sensitive fluorophore from the fluorescence following exposure to the antigen (see for example, claim 18 of reference B), wherein the antigen is a pathogen-specific or tumor-specific antigen (see for example, claim 20 of reference B). Reference B further claims that said method may be applied to determining immune status which informs administration of a suitable treatment where this application of the method requires comparison of the measured T cell response to a control (see for example, claims 21-23 of reference B), wherein said control may be the responses or a predetermined quality thereof observed from the responses of T cells from healthy patients to antigen (see for example, claim 25 of reference B).
Reference B does not claim calculating a fraction of responding cells. It is noted that said fraction is generically recited with no particular steps for arriving at the fraction being required. Tay et al teach that the fraction of responding cells at each concentration was calculated as the number of responding cells divided by the sum of responding and non-responding cells and by first subtracting the baseline level, and then dividing the differential expression levels with the fraction of active cells at each dose measured (see for example, the final sentence of the last paragraph on column 1 of page 272 and column 2 of page 272) where the fraction of responding cells is a discrete measure of single cell activation (see for example, column 2 of page 267).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosure of reference A. The artisan would have been motivated to make and use the invention as claimed because As part of determining obviousness, it is to be considered that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 may bar its patentability. When considering obviousness of a combination of known elements, the operative question is thus “whether the improvement is more than the predictable use of prior art elements according to their established functions,” (see MPEP 2141. I.)). Here, the active method steps are essentially the same where any deviations are small and predictable variations on the reference method. The reagents used are substantially the same. Where the same active steps and measurements are taken using substantially similar reagents, the method of reference B is deemed to make obvious the method of instant claims 7 and 10-11. The artisan would have found it obvious to calculate a fraction of responding cells because Tay et al teach a calculated fraction of responding cells relative to baseline is a discrete measure of single cell activation. The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Arrol et al (Clinical and Experimental Immunology, 153: 86–95; doi:10.1111/j.1365-2249.2008.03677.x), US 20140120557 A1 (citation 5 under US Patent/PGPub on the06/10/2024 IDS), Diener et al (Acta Biomaterialia 8 (2012) 99-107; citation 6 under the Non-Patent Literature heading of the 06/10/2024 IDS), Huse et al (Immunity 27, 76-88, July 2007 Elsevier Inc; citation 9 under the Non-Patent Literature heading of the 06/10/2024 IDS), Christo et al (Immunology and Cell Biology (March 2015) 93, 694–704; doi:10.1038/icb.2015.34), Christo (Aust. J. Chem. 2012, 65, 45-49, http;//dx.doi.org/10.1071/CHl 1311), WO 2015017889 A1 (Citation 1 under Foreign Patent Documents on the 06/10/2024 IDS), US 20110123994 A1, US 20070178532 A1, and Wulfing et al (J Exp Med. 1997 May 19;185(10):1815-25. doi: 10.1084/jem.185.10.1815) are deemed relevant.
Additionally, Schmittnaegel et al (Cancer Immunol Res. 2015 Jul;3(7):764-76. doi: 10.1158/2326-6066.CIR-15-0037. Epub 2015 Feb 17) teach that, in particular, memory CD8+ T cells play a major role in host defense by rapid recognition and lysis of virus-infected cells. CMV infects much of the population, existing in a viral latency stage where viral reactivation is kept in check by the immune system, but in immunocompromised patients and neonates such viral reactivation has a substantial influence on the number and the distribution of various T-cell subsets, especially CD8+ T cells. CMV-specific CD8+ T cells are believed to play an essential role in the defense against CMV, and a correlation is observed between a higher percentage of CMV-specific CD8+ T cells and more effective control of the virus. CMV-specific CD8+ T cells were isolated from PBMC preparations (see for example, pages 764-765).
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/Ashley Gao/
Examiner, Art Unit 1678
/GREGORY S EMCH/Supervisory Patent Examiner, Art Unit 1678