DETAILED ACTION
The amendment and RCE filed on 01/27/2026 has been entered and fully considered. Claims 1-15, 17 and 23 are pending, of which claims 1-8, 14, 14 and 23 are amended, and claim 24 is newly added.
Response to Amendment
In response to amendment, the examiner maintains rejection over the prior art established in the previous Office 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 .
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 1-7, 10-15, 17 and 23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hongo et al. (WO 2018/136553) (Hongo) in view of Miller et al. (WO 2018/023113) (Miller).
Regarding claim 1, Hongo teaches method for quantifying a monoclonal (M-) protein (par [0049]) in a sample of a subject suffering from, or having suffered from, plasma cell dyscrasia (multiple myeloma) (par [0050][0234]), the method comprising the steps of:
subjecting a body sample of a subject to serum protein electrophoresis (SPE) in an agarose gel, to separate proteins in said body sample into different protein fractions (par [0234][0235]);
drying said gel to provide a dried gel (par [0235]);
excising from said dried gel a gel lane part corresponding to an M-protein band of a separated protein fraction comprising, or suspected of comprising, a M-protein (par [0235]);
performing an enzymatic digestion on proteins or on a protein extract thereof in order to provide a peptide mixture comprising or suspected of comprising M-protein peptides (par [0213]);
subjecting said peptide mixture to mass spectrometry (MS) to determine a quantity of said at least one M-protein peptide, thereby quantifying said M-protein-specific in said sample by MS (par [0219]).
Hongo teaches a sample of a subject suffering from, or having suffered from, plasma cell dyscrasia (multiple myeloma) (par [0050]).
Hongo explicitly teaches performing tryptic digestion followed by mass spectrometric analysis to quantify antibody proteins (par [0213] [0219]), where the anti-PD-L1 antibody is digested and quantified by LC-MS to determine the amount of antibody present in a biological sample, including serum. Hongo further teaches that therapeutic monoclonal antibodies must be distinguished from endogenous immunoglobulins such as M-proteins during clinical monitoring in multiple myeloma patients (par [0232]-[0237]). M-protein is also a monoclonal antibody.
Hongo teaches that “A variety of mass spectrometry systems capable of high mass accuracy, high sensitivity, and high resolution are known in the art and can be employed in the methods of the invention” (par [0219]). Here, Hongo fairly suggests to one of ordinary skill in the art that a M-protein contained a dried gel as disclosed in this invention can be analyzed by a variety of mass spectrometry known in the art.
Hongo expressly teaches agarose gel-based SPE for detection and characterization of M-proteins in serum samples (see Hongo par [0235]). Hongo further teaches that mass spectrometry systems “can be employed in the methods of the invention” for analysis of antibody-derived peptides (Hongo par [0219]). The Examiner notes that paragraph [0219] is not limited to reagent validation, but broadly teaches MS as an analytical modality usable within Hongo’s disclosed antibody detection framework.
A reference need not explicitly exemplify every combination of disclosed techniques in order to render the combination obvious. See In re Keller, 642 F.2d 413 (CCPA 1981). Hongo teaches both (i) electrophoretic separation of serum immunoglobulins in agarose gels and (ii) MS-based peptide quantification of antibodies from biological samples. One of ordinary skill in the art would have understood these teachings to be combinable.
While Hongo teaches “analyzing the dried gel of step (k)” (par [0235]), and performing an enzymatic digestion on proteins or on a protein extract thereof in order to provide a peptide digest comprising at least one M-protein peptide (par [0213]), Hongo dos not specifically teach performing an enzymatic digestion on proteins present in said gel part (in-gel digestion). A person skilled in the art would have appreciated that performing an enzymatic digestion on proteins present in said gel part would help the peptides off the gel. For example, Miller teaches
drying said gel to provide a dried gel (page 49, line 15-16)
excising from said dried gel a gel part comprising, or suspected of comprising, a protein (page 49, line 16-17);
performing an enzymatic digestion on proteins present in said gel part would help the peptides off the gel (page 49, lines 16-22); and
subjecting said peptide digest comprising said at least one protein peptide to mass spectrometry (MS) to determine a quantity of said at least one protein peptide, thereby quantifying said protein in said sample by MS (page 50, lines 2-14).
It would have been obvious to one of ordinary skill in the art to performing an enzymatic digestion on proteins present in said gel part, in order to help the peptide off the gel.
The claims do not require any particular electrophoretic denaturation state, pore size, or gel chemistry beyond “agarose gel.” Substituting one known gel matrix for another, where both are routinely used to separate proteins prior to downstream analysis, constitutes a matter of routine optimization and design choice, not patentable distinction. See In re Aller, 220 F.2d 454 (CCPA 1955); MPEP § 2144.05.
Physically isolating a region of interest from a gel for further analysis is an inherent and routine laboratory practice once a band of interest is identified. The claims do not require any particular cutting tool or template structure beyond excision itself. Miller explicitly teaches excision of gel portions for downstream digestion and MS, and Hongo provides the motivation and context for identifying the relevant M-protein region.
Regarding claim 2, Hongo teaches a method for quantifying a M-protein (par [0049]) in a sample of a subject suffering from, or having suffered from, plasma cell dyscrasia (multiple myeloma) (par [0050]), the method comprising
subjecting an extract of a dried serum protein electrophoresis (SPE) agarose gel (par [0235]) comprising a serum protein digest including M-protein peptides from the sample of the subject ([0213]) to mass spectrometry (MS) to determine a quantity of at least one M-protein-specific peptide in said exact, thereby quantifying said M-protein in said sample (par (0219]).
Regarding claim 3, Hongo teaches that wherein the step of subjecting said peptide mixture to mass spectrometry (MS) to determine a quantity of at least one M-protein-specific peptide therein coincides with or is preceded by identification of at least one subject specific M-protein-specific peptide, and wherein the identification of at least one M-protein-specific peptide comprises the steps of:
(i) providing a body sample of said subject comprising a plasma cell producing the M-protein, determining the amino acid sequence of the M-protein produced by said plasma cell, and identifying an M-protein-specific peptide sequence that is predicted to be generated by said enzymatic digestion of said M-protein (par [0094]);
(ii) providing the amino acid sequence of the M-protein produced by said subject,
and identifying M-protein-specific peptide sequence that is predicted to be
generated by said enzymatic digestion of said M-protein (par [0094]); or,
(iii) subjecting said peptide mixture to MS, determining the amino acid sequence of a multitude of peptides in said peptide mixture by de novo peptide sequencing, and identifying an M-protein-specific peptide sequence from the sequences determined (par [0094]),
wherein said method further comprises the step of subjecting said peptide mixture to M-protein-specific peptide targeted MS, to thereby quantify the identified M-protein-specific peptide in said peptide digest mixture (par [0094]).
Regarding claim 4, Hongo teaches that wherein said method further comprises the steps of preparing a stable isotope labelled (SIL) variant of said identified M-protein-specific peptide as a labeled reference peptide (par [0222]); and
adding said labeled reference peptide to said peptide mixture after said step of enzymatic digestion (par [0222]);
wherein the quantity of M-protein-specific peptide in said peptide mixture is determined by comparing an MS signal of said identified M-protein-specific peptide to an MS signal of said labeled reference peptide, thereby quantifying said M-protein in said sample (par [0222]).
Regarding claim 5, Hongo teaches that wherein the subject is a patient undergoing treatment for plasma cell dyscrasia (multiple myeloma) (par [0050]).
Regarding claim 6, Hongo teaches that wherein the subject is in remission of plasma cell dyscrasia, and suffering from or at risk of suffering from plasma cell dyscrasia (multiple myeloma) (par [0050]). MRD is one kind of plasma cell dyscrasia. Thus, it would have been obvious to one of ordinary skill in the art apply Hongo’s method to MRD patient.
Regarding claim 7, Hongo teaches that wherein excision of said gel lane part from said dried gel is performed by using a patient-specific gel cutting template in order to ensure that an M-protein band that is present but invisible by normal SPE staining is correctly excised (par [0235]).
Regarding claim 10, Hongo teaches that wherein said plasma cell dyscrasia is selected from the group consisting of leukemia or lymphoma of B-cell non-Hodgkin type with plasma cell component; multiple myeloma (MM); plasmacytoma; lymphoplasmacytic lymphoma; AL amyloidosis; monoclonal gammopathy of undetermined significance (MGUS); smoldering multiple myeloma (SMM); macroglobulinemia; Waldenstrom disease; plasmacytoma; acute lymphoblastic leukemia (ALL); chronic lymphocytic leukemia (CLL); prolymphocytic leukemia (PLL); T-lymphoblastic lymphoma (TLL); acute myeloblastic leukaemia (AML); B-cell lymphoma, and cryoglobulinemia (par [0050]).
Regarding claim 11, Hongo teaches that wherein the subject has been treated with, or is undergoing treatment with, a therapeutic monoclonal antibody (par [0175]). Hongo does not specifically teach that wherein said therapeutic monoclonal antibody is daratumumab, nivolumab, elotuzumab, denosumab, blinatumomab or ipilimumab. However, it would have been obvious to one of ordinary skill in the art apply Hongo’s method to patients treated with the antibodies as recited in the claim.
Regarding claim 12, Hongo teaches that wherein said MS is high-resolution MS (par [0219]).
Regarding claim 13, Hongo teaches that wherein said enzymatic digestion is performed by using a protease (par [0213]).
Regarding claim 14, Hongo fairly suggests a method for typing a subject in plasma cell dyscrasia remission as having plasma cell dyscrasia minimal residual disease (MRD) comprising performing the method of claim 1 on a body sample of said subject, wherein said subject is typed as having plasma cell dyscrasia MRD if M-protein is detected in said body sample (For a patient to be classified as having a complete response (CR) by IMWG criteria, the serum and urine must be negative for M-protein as determined by IFE and SPE) (par [0234]).
Regarding claim 15, Hongo fairly suggests a method for monitoring a subject having plasma cell dyscrasia MRD, said method comprising performing a method of quantifying according to claim 1 on at least two longitudinal body samples that have been retrieved at different time points that are spaced apart by an interval of at least one or more days (par [0207]).
Regarding claim 17, Hongo fairly suggests a method of treating a subject suffering from plasma cell dyscrasia or having plasma cell dyscrasia MRD, comprising the step of:
performing the method of claim 1 in order to determine that M-proteins are present in said subject (par [0234]); and
administering to said subject a therapeutically effective amount of a standard-of-care therapeutic agent against plasma cell dyscrasia comprising a therapeutic monoclonal antibody or a small molecule inhibitor (par [0234]).
Regarding claim 23, Hongo teaches that wherein the M-protein peptides are patient specific M-protein peptides (par [0232]).
Patient specific M-protein is an abnormal antibody produced by a single clone of plasma cells, making it unique to an individual. These proteins are used to monitor diseases like multiple myeloma because they are produced in large amounts and can be tracked with high sensitivity to assess treatment response and detect relapses.
Hongo teaches analyzing M protein from a sample of a multiple myeloma patient (par [0050] [0232]). Therefore, Hongo teaches that wherein the M-protein peptides are patient specific M-protein peptides (par [0050][0232]).
Claim(s) 8-9 and 24 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hongo in view of Miller as applied to claims 1-7, 10-15, 17 and 20-21 above, and further in view of Trotter et al. (WO 2015/085172) (Trotter).
Regarding claim 8, Hongo teaches that samples are collected minutes, hours, days after administration drug (par [0207]).
Thus, Hongo teaches that the method further comprising the steps of:
providing a second peptide mixture from said subject comprising, or suspected of comprising an M-protein-specific peptide (par [0207]); wherein said second peptide mixture is obtained by performing the steps of:
(i) subjecting a second body sample of said subject to serum protein electrophoresis in an agarose gel to separate proteins comprised in said body sample into separated protein fractions (par [0235]);
(ii) drying said gel to provide a dried gel (par [0235]):
(iii) optionally archiving said dried gel (par [0235]);
(iv) excising from said dried gel a gel lane part corresponding to the M-protein band of the separated protein fraction comprising, or suspected of comprising, an M-protein (par [0235]);
(v) performing an enzymatic digestion on proteins present in said gel part or on a protein extract thereof in order to provide a peptide mixture comprising, or suspected of comprising, digested M-protein peptide (par [0213]).
Hongo does not specifically teach
labeling said first peptide mixture with a first tandem mass tag (TMT) label and labelling said second peptide mixture with a second TMT label; wherein said first TMT label and second TMT label are of different mass;
mixing said labelled first and labelled second peptide mixture; and
subjecting said mixed labelled first and labelled second peptide mixtures to liquid chromatography-mass spectrometry (LC-MS)
quantifying said M-protein in said second body sample as a relative quantity of said M-protein in said first body sample, whereby the M-protein in the first and second sample is quantified by one the bases of at least M-protein-specific peptide that is different in mass and has the same LC retention time between the first sample and the second sample.
However, Trotter teaches labeling different timed sample (24 and 72 hours) with tandem mass tag (TMT) and quantify the relative quantity of M-protein in the timed sample (par [00558]). It would have been obvious to one of ordinary skill in the art to
labeling said first peptide mixture with a first tandem mass tag (TMT) label and labelling said second peptide mixture with a second TMT label; wherein said first TMT label and second TMT label are of different mass;
mixing said labelled first and labelled second peptide mixture; and
subjecting said mixed labelled first and labelled second peptide mixtures to liquid chromatography-mass spectrometry (LC-MS)
quantifying said M-protein in said second body sample as a relative quantity of said M-protein in said first body sample, whereby the M-protein in the first and second sample is quantified by one the bases of at least M-protein-specific peptide that is different in mass and has the same LC retention time between the first sample and the second sample, in order to obtain the benefit of high sensitivity of TMT method.
Regarding claim 9, remission and relapse are the responses to the drug treatment. Thus, it would have been obvious to one of ordinary skill in the art to arrange the sample collection during the different drug responses, so that said first body sample of said subject is obtained while said subject is in remission, and wherein said second body sample of said subject is obtained while said subject is in relapse.
Regarding claim 24, Hongo teaches that wherein the patient-specific M-protein peptides are stable isotope labelled (par [0222]). Hongo-Trotter fairly suggest that wherein the patient-specific M-protein peptides are labelled with tandem mass tags (TMT) (Trotter, par [00558]).
Response to Arguments
Applicant's arguments filed 01/27/2026 have been fully considered but they are not persuasive.
1. Hongo teaches agarose SPE and MS as analytical tools applicable to the claimed workflow
As amended, claim 1 now explicitly recites serum protein electrophoresis (SPE) in an agarose gel, drying the gel, excising a gel lane part corresponding to an M-protein band, enzymatic digestion, and MS quantification of an M-protein-specific peptide.
Hongo expressly teaches agarose gel-based SPE and immunofixation for detection and characterization of M-proteins in serum samples (see Hongo par [0235]). Hongo further teaches that mass spectrometry systems “can be employed in the methods of the invention” for analysis of antibody-derived peptides (Hongo par [0219]). The Examiner notes that paragraph [0219] is not limited to reagent validation, but broadly teaches MS as an analytical modality usable within Hongo’s disclosed antibody detection framework.
Applicant’s argument that Hongo “compartmentalizes” MS to anti-PD-L1 detection and excludes M-protein analysis is not persuasive. A reference need not explicitly exemplify every combination of disclosed techniques in order to render the combination obvious. See In re Keller, 642 F.2d 413 (CCPA 1981). Hongo teaches both (i) electrophoretic separation of serum immunoglobulins in agarose gels and (ii) MS-based peptide quantification of antibodies from biological samples. One of ordinary skill in the art would have understood these teachings to be combinable.
2. Miller teaches in-gel digestion and MS of excised gel portions
Miller teaches drying a gel, excising gel portions, performing in-gel enzymatic digestion, and subjecting the resulting peptide mixture to LC-MS/MS for protein analysis (Miller, page 49 line 15 – page 50 line 14). Miller therefore supplies the well-established technique for recovering peptides from gel matrices for MS analysis.
Applicant’s contention that Miller is limited to SDS-PAGE and therefore irrelevant is not persuasive. The claims do not require any particular electrophoretic denaturation state, pore size, or gel chemistry beyond “agarose gel.” Substituting one known gel matrix for another, where both are routinely used to separate proteins prior to downstream analysis, constitutes a matter of routine optimization and design choice, not patentable distinction. See In re Aller, 220 F.2d 454 (CCPA 1955); MPEP § 2144.05.
3. Motivation to combine and reasonable expectation of success
Hongo is expressly concerned with accurate detection and quantification of monoclonal immunoglobulins in serum, particularly in the presence of therapeutic antibodies. Miller teaches a known and effective solution for improving analytical specificity and sensitivity by converting gel-resolved proteins into peptide analytes suitable for MS.
A person of ordinary skill in the art would have been motivated to apply Miller’s in-gel digestion and MS workflow to Hongo’s agarose SPE system to improve quantification accuracy and specificity, especially where immunochemical or densitometric approaches suffer from interference. The expectation of success would have been reasonable, as enzymatic digestion followed by MS was well known at the time of the invention as a robust approach for protein quantification.
Applicant’s assertions regarding alleged difficulties of digesting dried agarose gels are unsupported by evidence in the record and amount to attorney argument. Absent evidence of unexpected results commensurate with claim scope, such assertions are insufficient to rebut a prima facie case of obviousness.
4. Clinical context limitations
Applicant further argues that the amended claims are distinguished because they are now limited to a subject “suffering from, or having suffered from, plasma cell dyscrasia.” This argument is not persuasive.
Hongo expressly teaches that the disclosed methods are applicable to subjects suffering from plasma cell dyscrasia, including multiple myeloma. Specifically, Hongo par [0050] teaches that the biological sample may be obtained from a subject suffering from plasma cell dyscrasia, in which endogenous M-proteins are present and must be distinguished from therapeutic monoclonal antibodies administered during treatment.
Accordingly, the newly added limitation regarding the disease state of the subject is explicitly taught by Hongo and therefore does not distinguish the claimed method from the prior art.
Moreover, limiting the claims to a particular patient population or disease condition constitutes an intended use of the analytical method rather than a structural or procedural limitation on the method steps themselves. The underlying analytical workflow—electrophoretic separation, digestion, and mass spectrometric analysis—remains unchanged. Such limitations do not confer patentability where the method steps are otherwise taught or suggested by the prior art. See In re Schreiber, 128 F.3d 1473 (Fed. Cir. 1997).
Therefore, the recitation of a subject suffering from, or having suffered from, plasma cell dyscrasia does not overcome the prima facie case of obviousness established by Hongo in view of Miller.
5. Gel excision and “cutting templates”
Applicant argues that Hongo’s use of templates in immunofixation is not equivalent to excising a gel lane part. However, physically isolating a region of interest from a gel for further analysis is an inherent and routine laboratory practice once a band of interest is identified. The claims do not require any particular cutting tool or template structure beyond excision itself. Miller explicitly teaches excision of gel portions for downstream digestion and MS, and Hongo provides the motivation and context for identifying the relevant M-protein region.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to XIAOYUN R XU, Ph. D. whose telephone number is (571)270-5560. The examiner can normally be reached M-F 8am-5pm.
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/XIAOYUN R XU, Ph.D./ Primary Examiner, Art Unit 1797