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 .
Status of the Claims
Claims 1, and 21-36 are pending in the application.
Claims 27-30 are withdrawn.
Claims 1, 21-26, and 31-36 are the subject of this office action.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 13 March 2026 has been entered.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 13 October 2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Browser-executable language is found on at least Pg. 19 of the instant specification.
Claim Rejections - 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.
Claims 1, 21-26, and 31-36 are 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.
Claims 1, 32, and 35 all recite an amino acid sequence which may be SEQ ID NO: 1 (embodiment (a)), but also requires “wherein a mutant cysteine residue is positioned in the alpha-1 domain at amino acid residue 84 or 85 and a mutant cysteine residue is positioned in the alpha-2 domain at amino acid residue 139”. This is indefinite because it is not clear how the amino acid sequence could meet both recited requirements when SEQ ID NO: 1 does not contain the recited cysteine mutations. Additionally, the recitation of cysteine mutations at specific positions in an amino acid sequence is indefinite if that amino acid sequence is not explicitly defined (i.e. embodiment (b) encompasses an amino acid sequence having at least 83% sequence identity to SEQ ID NO: 1, wherein different variants could have different lengths and different amino acids at positions 84, 85, and 139, such that which amino acids are specifically cysteine mutated is not clear in this embodiment). Clarification is required.
Dependent claims 21-26, 31, 33-34, and 36 are rejected as indefinite because they depend from an indefinite claim and fail to remedy its deficiencies.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1, 21-26, and 31-36 are rejected under 35 U.S.C. 103 as being unpatentable over Vigneault et al (US 2017/0268056 A1; previously cited) in view of Moritz et al (US 2020/008726 A1).
Regarding claims 1, 26, 32, and 36 Vigneault teaches:
A method for detection of one or more antigenic peptide responsive T cells in a sample and/or for determining the interaction between a TCR or antigenic peptide responsive T cell and a library of antigenic peptides (Abstract; Par. 5: the affinity-oligonucleotide conjugate can be used to acquire TCR pair sequences, clone abundance, and relative tetramer affinity. A tetramer-oligonucleotide conjugate can be used to simultaneously acquire TCR pair sequences that bind to the peptide of the tetramer, determine the affinity of binding of the TCR to a pMHC complex of the tetramer-oligonucleotide conjugate, and differentiate between TCRs with low binding affinity as compared to TCRs with a high binding affinity for a pMHC complex of the tetramer-oligonucleotide conjugate; Par. 34-35; Par. 47; Par. 59), comprising:
Providing detection molecules comprising at least one pMHC class I molecule and at least one detectable label, wherein the peptide of the pMHC class one molecule is an antigenic peptide (Par. 5; Par. 34-35; Par. 44-45: the affinity portion of the tetramer-oligonucleotide conjugate comprises a pMHC complex; Par. 9: the tetramer conjugate may comprise an oligonucleotide detectable label; Par. 173);
Contacting the detection molecules with a sample (Par. 35: incubating one or a plurality of T cells in the presence of one or a plurality of tetramer oligonucleotide conjugates);
Detecting binding of the detection molecules to one or more antigenic peptide responsive T cells, wherein each of the at least one antigenic peptide is represented by at least one detectable label which is a nucleic acid label (Par. 7: incubating cells in a mixture or solution with one or more affinity-oligonucleotide conjugates. The cells can be washed to remove unbound conjugate; Par. 5: the affinity oligonucleotide conjugate can be used to detect the sequence and abundance of TCRs which bind to a pMHC complex; Par. 59; Par. 196-197; Par. 173: an antigen identification sequence (AID) can be used to identify the one or more antigens to which the affinity-oligonucleotide conjugate specifically interacts);
Vigneault does not specifically teach the method wherein the detection molecule is a loadable detection molecule comprising at least one peptide-free MHC class I molecule which is contacted with at least one antigenic peptide to provide loaded detection molecules comprising at least one pMHC class I molecule wherein the pMHC class I molecule comprises a heavy chain comprising an alpha-1 domain and an alpha-2 domain connected by a disulfide bridge, said heavy chain comprising an amino acid sequence selected from SEQ ID NO: 1, an amino acid sequence having at least 83% sequence identity to SEQ ID NO: 1, and wherein a mutant cysteine residue is positioned in the alpha-1 domain at amino acid residue 84 or 85 and a mutant cysteine residue is positioned in the alpha-2 domain at amino acid residue 139.
Vigneault does teach that the method may be used for multiplexed detection of multiple targets, implying the use of a plurality pMHC affinity agents which comprise multiple different species of antigenic peptides (i.e. a library of antigenic peptides which can be used in the methods described for determining the interaction between a TCR and a library of antigenic peptides) (Par. 60: the methods and compositions disclosed herein can be used for multiplexed TCR affinity measurement by sequencing; Par. 106: a tetramer ID sequence corresponds to a tetramer batch and allows multiplexing of different target, such as peptide-MHC targets in a single experiment; Par. 59, 201).
Regarding claims 1, 26, 32, and 36, Moritz teaches:
A method for detection of one or more antigenic peptide responsive T cells in a sample and/or for determining the interaction between a TCR or antigenic peptide responsive T cell and a library of antigenic peptides (Par. 66, 69 , 75, 97-98, 102);
Providing a loadable detection molecule comprising at least one peptide-free MHC-I molecule and a label (Par. 53: the present invention involves the use of disulfide-stabilized, initially empty, MHC molecules that can be loaded by simply adding suitable peptide before the use thereof. pMHCs generated using this disulfide-modified MHC molecule are representative of the non-modified wt variant, and are suitable for screening; Par. 66, 69, 92);
Providing at least one antigenic peptide and/or a library of antigenic peptides and contacting the loadable detection molecules with the at least one antigenic peptide to provide loaded detection molecules comprising pMHC class I complexes; contacting the loaded detection molecules with the sample, and detecting binding of the TCR or antigenic peptide responsive T cell with the library of loaded detection molecules (Par. 53, 66, 69: the stabilized MHC molecule is contacted with a multitude of peptide ligands, in order to form pMHC complexes; Par. 74: the pMHC complexes are screened for TCR binding; Par. 198-208);
Wherein the peptide-free MHC-I molecule comprises a heavy chain comprising an alpha-1 domain and an alpha-2 domain connected by a disulfide bridge (Par. 28: a stabilized MHC molecule encompasses at least one artificially introduced covalent disulfide bridge between two amino acids. For example, mutating the amino acids at positivs 84 and 139 into cysteines);
Said heavy chain comprising an amino acid sequence selected from SEQ ID NO: 1 or an amino acid sequence having at least 83% sequence identity to SEQ ID NO: 1, wherein a mutant cysteine residue is positioned in the alpha-1 domain at amino acid residue 84 or 85 and a mutant cysteine residue is positioned in the alpha-2 domain at amino acid residue 139 (Par. 28; Par. 170: production of empty Y84C/A139C HLA-A*02:01 (SEQ ID NO: 323) complexes). See the sequence alignment provided below which shows Moritz SEQ ID NO: 323 which is identical to instant SEQ ID NO: 2 (wherein instant SEQ ID NO: 2 is the same as instant SEQ ID NO: 1 except that it comprises the claimed cysteine mutations).
PNG
media_image1.png
572
722
media_image1.png
Greyscale
Moritz teaches that the cys-mutant peptide-free MHC class I molecule disclosed is preferable over pre-loaded pMHC class I molecules and previously disclosed unloaded preptide-free MHC class I molecules of the prior art (Par. 42: the modification of amino acids in the above-described amino acid regions of MHC I and at the respectively indicated positions, and thus the introduction of covalent bonds between amino acids at positions which are not naturally connected by covalent bonds allows the generation of modified MHCI molecules that are properly folded, bind peptides with high affinity, and are recognized by TCR molecules with high specificity and selectivity; Par. 49-50: current methods for the large scale generation of pMHC libraries suffer from stability problems. With the present technology, the inventors gain multiple advantages over the wt molecule or other existing exchange technologies: the empty monomer can be produced in bulk way ahead of the desired experiment, and pMHC generation is not restricted by any other method aside from procuring desired peptides and quick peptide loading reaction. The peptide free MHC class I molecules can be stored for at least a year with no degradation or impaired peptide receptiveness detected. The inventors have also successfully stored the resulting pMHC complexes for at least two weeks without loss of signal. In addition to all these advantages achieved by introducing the modification, the pMHC complexes generated with the disclosed methods are substantially representative of wt complexes with respect to TCR ligand binding).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method an detection molecules of Vigneaul to comprise the peptide-free MHC class I molecules which can be contacted with different antigenic peptides to provide a plurality of loaded detection molecules comprising at least one pMHC class I molecules, as taught by Moritz. One would be motivated to make this modification because Moritz teaches that the production of stable peptide-free MHC class I molecules is advantageous in allowing for easier and more efficient production of different pMHC complexes loaded with different antigenic peptides, as discussed above, especially in multiplexed assays such as the assays disclosed by Vigneault which would require the use of pMHC affinity agents with multiple different species of antigenic peptides. One of ordinary skill in the art would have a reasonable expectation of success in making this modification because both Vigneault and Moritz disclose MHC class I detection molecules which may be used to comprise pMHC complexes for detection of TCR binding and affinity.
Regarding the recitation in the preamble of claim 36 “for determining the interaction between a T cell receptor (TCR) or antigenic peptide responsive T cell and a library of antigenic peptides”, the normal purpose of a claim preamble is to recite the purpose or intended use of the claimed invention. Such statements merely define the context in which the invention operates and usually will not limit the scope of the claim or distinguish it over the prior art (MPEP 2111.02). During claim examination proceedings, claims are given their broadest reasonable interpretation consistent with the specification (MPEP 211. In re Hyatt, 211 F.3d 1367, 1372 (Fed. Cir. 2000)). If the claim preamble when read in the context of the entire claim, recites limitations of the claim, or, if the claim preamble is ‘necessary to give life, meaning, and vitality’ to the claim, then the claim preamble should be construed as if in the balance of the claim (MPEP 2111.02; Pitney Bowles Inc. v. Hewlett Packard Co., 182 F.3d 1298, 1305 (Fed. Cir. 1999)).
However, when the body of the claim fully and intrinsically sets forth the complete invention, including all of its limitation, and the preamble offers no distinct definition of any of the claimed invention’s limitations, but rather merely state, for example, the purpose or intended use of the invention, then the preamble is of no significance to the claim construction because it cannot be said to constitute or explain a claim limitation (MPEP 2111.02 II; Pitney Bowles Inc. v. Hewlett Packard Co., 182 F.3d 1298, 1305 (Fed. Cir. 1999)).
In the instant case, the statement in the preamble merely express the purpose of the claimed method and fail to clearly result in a manipulative difference. The statements in the preamble do not provide antecedent basis for terms in the body of the claim and are not essential to understand the limitations or terms in the body of the claim. For these reasons, the preamble may be reasonably interpreted simply as referring to the intended use of the recited method.
Additionally (for the sake of compact prosecution), the teachings Vigneault in view of Moritz are understood to read on a method “for determining the interaction between a T cell receptor (TCR) or antigenic peptide responsive T cell and a library of antigenic peptides” insofar as Vigneault teaches the recited method steps and teaches that the disclosed invention can be used to investigate the specificity and affinity of a particular TCRs for particular antigenic peptides (Par. 5).
Regarding claims 21-24 and 34, Vigneault in view of Moritz teaches the method and detection molecules of claims 1 and 32, wherein the loadable detection molecules comprise peptide-free MHC class I molecules. Vigneault further teaches the loadable detection molecule comprises four MHC class I molecules attached to a connector molecule via non-covalent interactions between the connector molecule and an affinity tag on the peptide-free MHC class I molecule; Vigneault specifically teaches an embodiment wherein the loadable detection molecules comprise four MHC class I molecules attached to streptavidin via non-covalent interactions between streptavidin and a biotin tag on each MHC class I molecule (Fig. 10A-10B: shows four biotinylated MHC class I molecules linked to a streptavidin core; the affinity-oligonucleotide conjugate may be a tetramer-oligonucleotide conjugate comprising four MHC class I molecules; Par. 45; Par. 157: tetramer may refer to a complex comprising four subunits bound to a single molecule of streptavidin, wherein a subunit can be an MHC molecule; Par. 189: exemplary multimerization comprises a biotinylated subunit bound to a multivalent binding partner such as streptavidin).
Regarding claim 25, Vigneault further teaches the at least one detectable label is attached to the connector molecule (see, e.g. Figs. 10A-10B and 18 which show an oligonucleotide label attached to a streptavidin connector molecule).
Regarding claims 31 and 33, Vigneault further teaches the method and loadable detection molecule wherein the at least one detectable label is a nucleic acid label comprising a 5’ first primer region (forward), a barcode region, a 3’ second primer region (reverse), and a unique molecular identifier (UMI) region of random nucleotide bases, wherein the barcode region is a unique barcode serving as an identification tag for the detection molecule (Par. 9, 12; Par. 197: the oligonucleotide coupled to the affinity portion of the affinity- oligonucleotide conjugate can comprise both an Antigen ID (AID) sequence and an antigen molecular barcode (AMB). An oligonucleotide can comprise an AID sequence, a fusion sequence, a primer site, an AMB sequence, a constant sequence, or any combination thereof; Par. 201: an oligonucleotide antigen barcode (Antigen ID, AID sequence) can allow for indtification of an affinity-oligonucleotide complex comprising the oligonucleotide antigen barcode. An oligonucleotide antigen barcode can be used to identify an affinity portion from a plurality of different affinity portions that binds to different target analytes; Par. 202: the AID can be a unique sequence that is barcoded to an affinity portion to which it is coupled such that a signal containing the AID sequence or compliment thereof can be used to identify an affinity portion of a plurality of different affinity portions that interact with different target analytes; Par. 203: the AID sequence can be barcoded to the peptide of a pMHC complex; Par. 205-207: the antigen molecular barcode sequence (AMB) can allow for identification of a molecule of an affinity-oligonucleotide complex comprising the AMB. An AMB can be a unique barcode sequence and can comprise randomly assembled nucleotide bases. An AMB sequence can enable the counting of the number of oligonucleotide molecules of an affinity-oligonucleotide conjugate; Par. 212-213).
Regarding claim 35, Vigneault further teaches that a plurality (i.e. at least two) of the loadable detection molecules as described in claim 32 may be provided in a composition (Par. 60: the methods and compositions disclosed herein can be used for multiplexed TCR affinity measurement by sequencing; Par. 106: a tetramer ID sequence corresponds to a tetramer batch and allows multiplexing of different target, such as peptide-MHC targets in a single experiment; Par. 59; Par. 201).
Response to Arguments
Applicant’s arguments filed 13 March 2026 have been fully considered.
The previous 103 rejection is withdrawn in view of the amendment which has removed SEQ ID NO: 11 from the instant claims. New grounds of 103 rejection which address the amended claims are presented above.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELLIS LUSI whose telephone number is (571)270-0694. The examiner can normally be reached M-Th 8am-6pm ET.
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, Bao-Thuy Nguyen can be reached at (571) 272-0824. 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.
/ELLIS FOLLETT LUSI/Examiner, Art Unit 1677
/BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 April 9, 2026
Prosecution Insights