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 .
Claim Status
Claims 1-87, 89, 93-95, and 99 are cancelled. Claims 88, 90-92, 96-98, 100, and 103-113 as filed on 21 November 2025 are pending and under examination.
Rejections Withdrawn
Rejections of claims under 35 U.S.C. 103 over Welch, Grys, Kölbl, and Sun; & Welch, Grys, Kölbl, Sun, and Astashchanka are withdrawn with applicant amendment of claims.
Applicant amendment of claims required a new search and new grounds for rejection.
The rejection of claims 107 and 110 are maintained and are after the New Rejections.
Applicant Arguments
Applicant arguments to previous rejections are still relevant to current rejections but are not related to a current rejection. These arguments are responded to before the new grounds for rejection.
Applicant argues art does not teach all the elements required by the claims 88 and 100.
Applicant argues unexpected results. Applicant points to Example 2 which states use of StcE improves mass spectrometry analysis.
Response to Arguments
Applicant's arguments filed 11/21/2025 have been fully considered but they are not persuasive.
New Rejections have been made as necessitated by applicant amendment to the claims.
Other elements have been added which are only recitations of biological activity inherent to the active method steps of the claims.
Applicant’s arguments with respect to elements added to the claims with amendments and to Grys in relation to Welch and have been considered but are moot because the new ground of rejection does not rely on any teaching or matter specifically challenged in the argument.
The art rejection on the record has use of StcE in a method of sample preparation for mass spectrometry making the active step in the method step in the claims known in the art.
New Rejections – Necessitated by Applicant Amendment to Claims
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.
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.
Claims 88, 90-92, 96, 98, 100, 108-109, and 111-113 are rejected under 35 U.S.C. 103 as being unpatentable over Chen et. al. Amino Acids. 44: (1381-1389) (2013) (PTO-892) and Morelle et. al. Proteomics. 6: 3993-4015. (2006) (PTO-892), as evidenced by Welch (US 7704718 B2) (IDS).
Regarding claims 88, 90-92, 98, 100 and 107-110, Chen teaches applying C1 esterase inhibitor to a native gel where in-gel digestion will occur followed by analysis and identification of peptides (abstract). Chen further teaches the use of mass spectrometry to identify deglycosylation for functional study (Abstract and Figure 1). Chen teaches the application of their method includes separation and purification of proteins to be analyzed in native state by mass spectrometry to study sequence and modification (page 1382 in col 1 in par 3). SEQ ID NO: 1 is StcE as evidenced by Welch.
Chen teaches these functional changes are of importance because they impact protein function and protein-protein interactions (page 1382 in col 1 in par 4).
The cleavage of the sites of claims and elected by applicant is an inherent property of StcE as shown in applicant’s Figure 2 ([0013]). By placing StcE of the claims in a sample Chen is teaching the required steps for this biological activity to occur.
Regarding claim 96, the protein taught by Chen is an acellular proteinaceous sample (Figure 1).
Chen further teaches the method is cost intensive (page 1382 in col 2 in par 2).
Chen does not teach the method comprising identifying the amino acids that are glycosylated at the mucin-specific glycan-peptide cleavage motif.
This deficiency is filled by Morelle.
Morelle teaches the use of mass spectrometry in identifying amino acid specific glycosylation in biological samples for use in proteomic work. Morelle teaches the role of glycosylation in folding, solubility, aggregation, and propensity to degrade by protease activity by the presence or absence of glycosylation (abstract, Figure 1, and page 3994 in col 1 in lines 6-11 and par 1).
It would have been obvious at the time the application was filed to combine the method of Chen comprising gel based processing of proteins for use in mass spectrometry for further analysis with the method of measuring glycosylation at protease sites using mass spectrometry by Morelle. One of skill in the art would have been motivated by Chen’s teaching that glycosylation impacts protein to protein interactions and the teachings of Morelle that protease activity changes with glycosylation. Chen teaches one with skill in the art a method of sample preparation for analyzing protein modifications via mass spectrometry while Morelle teaches additional analysis by mass spectrometry. One of skill in the art would further be motivated by the cost noted by Chen as additional applications would justify the cost of preparing the samples. There would have been a reasonable expectation of success as Chen teaches the preparation of samples for use in mass spectrometry and Morelle teaches mass spectrometry both testing for post translational modifications.
Claims 88, 97, 100, 103-104, and 108-109 are rejected under 35 U.S.C. 103 as being unpatentable over Chen et. al. Amino Acids. 44: (1381-1389) (2013) (PTO-892), Morelle et. al. Proteomics. 6: 3993-4015. (2006) (PTO-892), Kölbl et. al. Frontiers in Oncology. 5(219):1-5. (2015) (Of Record), and Sun et. al. Molecular & Cellular Proteomics. 6(1): 141-149. (2007) (Of Record), as evidenced by Welch (US 7704718 B2) (IDS).
Regarding claim 88, Chen teaches applying C1 esterase inhibitor to a native gel where in-gel digestion will occur followed by analysis and identification of peptides (abstract). Chen further teaches the use of mass spectrometry to identify deglycosylation for functional study (Abstract and Figure 1). Chen teaches the application of their method includes separation and purification of proteins to be analyzed in native state by mass spectrometry to study sequence and modification (page 1382 in col 1 in par 3). SEQ ID NO: 1 is StcE as evidenced by Welch.
Chen teaches these functional changes are of importance because they impact protein function and protein-protein interactions (page 1382 in col 1 in par 4).
The cleavage of the sites of claims and elected by applicant is an inherent property of StcE as shown in applicant’s Figure 2 ([0013]). By placing StcE of the claims in a sample Chen is teaching the required steps for this biological activity to occur.
Chen further teaches the method is cost intensive (page 1382 in col 2 in par 2).
Chen teaches the method comprising testing human samples for use in diagnosing disease (abstract and col 26 in lines 18-20). Chen does not teach a method of detecting a condition by comparing aberrant glycosylation in cancer to a healthy donor. Chen does not teach the method comprising identifying the amino acids that are glycosylated at the mucin-specific glycan-peptide cleavage motif.
These deficiencies are filled by Morelle, Kölbl, and Sun.
Morelle teaches the use of mass spectrometry in identifying amino acid specific glycosylation in biological samples for use in proteomic work. Morelle teaches the role of glycosylation in folding, solubility, aggregation, and propensity to degrade by protease activity by the presence or absence of glycosylation (abstract, Figure 1, and page 3994 in col 1 in lines 6-11 and par 1).
Sun teaches the capturing of glycoproteins that comprises proteolysis and mass spectrometry analysis of the released glycopeptides (Figure 1). The proteolysis de-glycosylation was done using PNGase F (page 144 in lines 1-7). Sun teaches determining the amino acid sequences of a portion of the glycopeptides (Table 1).
Sun teaches glycoproteins used as therapeutic targets and for use in cancer prognosis, diagnosis, and monitoring of cancers including breast cancer (page 141 in col 2 in lines 4-8).
Kölbl teaches glycosylation has a correlation to the formation of remote metastasis and that aberrant glycosylation plays a role in metastasis formation. Kölbl teaches that Mucin-1 and Galectin are key players in glycosylation and specifically teaches the role of aberrant glycosylation in metastasis of breast cancer including a role in brain metastasis (Abstract).
It would have been obvious at the time the application was filed to combine the method of Chen comprising gel based processing of proteins for use in mass spectrometry for further analysis with the method of measuring glycosylation at protease sites using mass spectrometry by Morelle for use in purified glycoproteins for use in cancer patients. One of skill in the art would have been motivated by the teachings of Chen that show an expensive, but productive method of preparing samples for mass spectrometry that can identify post translational modifications. Morelle and Sun teach mass spectrometry as a method of measuring glycosylation and characterizing proteins. Sun and Kölbl both teach the importance of glycosylation in cancer patients providing further applications of the expensive method of Chen. There would have been a reasonable expectation of success as Chen and Morelle teach analysis of post translational modifications of proteins using mass spectrometry.
Claims 100 and 103-106 are rejected under 35 U.S.C. 103 as being unpatentable over Chen et. al. Amino Acids. 44: (1381-1389) (2013) (PTO-892), Morelle et. al. Proteomics. 6: 3993-4015. (2006) (PTO-892), Kölbl et. al. Frontiers in Oncology. 5(219):1-5. (2015) (Of Record), Sun et. al. Molecular & Cellular Proteomics. 6(1): 141-149. (2007) (Of Record), and Astashchanka et. al. Breast Cancer Research and Treatment. 173: 289-299. (2019) (Of Record), as evidenced by Welch (US 7704718 B2) (IDS),
The teachings of Chen from the previous 103 rejections are incorporated here in full.
Chen does not teach a method of detecting a condition by comparing aberrant glycosylation in cancer to a healthy donor. Chen does not teach determining the amino acid sequence of at least a portion of the generated glycopeptides and identifying one or more of the glycopeptide glycosites. Chen does not teach the administration of a mucin-domain directed therapy for the cancer wherein it is an inhibitor of a mucin-domain.
These deficiencies are filled by Morelle, Kölbl, Sun, and Astashchanka.
The teachings of Morelle, Kölbl, and Sun from previous 103 rejections are incorporated here in full.
Astashchanka teaches MUC2 is expressed in breast cancer but not expressed in normal breast tissue. Astashchanka teaches the use of the MUC2 inhibitor shMUC2 and the result of decreased proliferation of breast cancer cells with the treatment. Astashchanka teaches MUC2 as an important guide in treatment of breast cancer (abstract).
It would have been obvious to one of ordinary skill in the art to combine the method of detection of Chen in view of Kölbl, Sun, and Morelle with the use of MUC2 inhibition in the treatment of breast cancer taught by Astashchanka. Chen in view of Kölbl, Sun, and Morelle teaches a method of detecting aberrant and normal glycosylation in a sample. Kölbl and Sun teach towards using the glycosylation in cancer samples to determine prognosis and to phenotype the tumor microenvironment.
Kölbl teaches that changes to glycosylation are associated with metastasis including in breast cancer metastasis into the brain. Astashchanka teaches the use of the MUC2 inhibitor was effective against breast cancer cell lines. One of ordinary skill in the art would have been motivated as Kölbl and Sun are teaching towards a role of mucin-domains in disease treatment and Astashchanka teaches its application. There would have been a reasonable expectation of success as shown by the teaching in Kölbl and Astashchanka in it the role of glycosylation in cancer.
Rejection Maintained – Amended as Necessitated by Applicant Amendment to Claims
Claims 107 and 110 are rejected under 35 U.S.C. 103 as being unpatentable over Jonckheere et. al. Biochimie. 95(6): 1077-1086 (2013) (Of Record), Xiao et. al. PNAS. 113(37): 10304-10309. (2016) (Of Record), Grys et. al. Journal of Bacteriology. 188(13):4646-4653 (2006) (Of Record), and Welch (US 7704718 B2) (IDS).
Jonckheere teaches mucins are gel-forming components of viscous mucus that protect the epithelia (page 1077 in col 1 in par 2 in lines 1-2). Jonckheere teaches recent study of mucin domains and their biological activities are an important target in the development of new therapies. Jonckheere further teaches a method of determining the amino acid sequence of membrane-bound mucins finding conserved sequences (Figure 3). Jonckheere teaches 3D modeling of the EGF-like domains (Figure 4) and that Muc4 interacts with the receptor ErbB2 (page 1080 in col 2 in par 2). Jonckheere then teaches the use of sequencing mucins to produce 3D models that would identify potential receptors that bind the mucin-domains.
Jonckheere does not teach contacting a cellular sample with a mucin-specific protease. Jonckheere does not teach StcE or SEQ ID NO: 1, or the cleavage motifs.
These deficiencies are filled by Xiao, Grys, and Welch.
Xiao teaches the use of sialidase to remove glycoproteins to inhibit binding of cancer cells to sialic acid-binding Ig-like lectin (Siglec) receptors in cancer immunotherapy (Abstract and Figures 1 and 4-5). Xiao thus teaches a method of removing glycoproteins from a cell with a protease to stop the binding of a known receptor to that cell. Xiao teaches a simple method of treating cells of interest with sialidase, confirming removal of sialic acid in a cancer cell line by immunostaining, then showing loss of receptor binding (Figures 4-5).
Grys teaches the use of StcE as a mucinase that plays a dual role in infection as a mucinase and an anti-inflammatory agent (Abstract). Grys further teaches different glycosylation in cancer cell lines and the need to characterize StcE and other proteases for their sequences, their interactions with glycosylation and their unique activities (page 4652 in col 1 in par 4 in lines 7 to col 2). Grys teaches StcE is a stable enzyme with high proteolytic activity (Abstract).
The teachings of Welch from all previous art rejections are incorporated here in full.
Welch teaches contacting a sample of human serum and the analysis showing cleavage by applicant’s elected species StcE (Figures 4-6 and description of figure bottom of col 2). Welch teaches StcE digestion as shown by the rejection of claim 88. Applicant shows that StcE recognized the sequence S/T*-X-S/T in applicant’s Figure 2 ([0013]). The method of Welch would inherently teach the biological activity of the claim.
Welch teaches contacting a sample of human serum and the analysis showing cleavage by applicant’s elected species StcE (Figures 4-6 and description of figure bottom of col 2). Welch teaches the analysis of peptide products using mass spectrometry and further teaches their identification (col 4 in lines 52-62, col 13 in lines 6-18, and col 30 in lines 50-61). Welch teaches the identification of MUC7 and gp-340/DBMT1 (col 30 in lines 50-61).
Welch teaches the StcE of instant SEQ ID NO: 1 in SEQ ID NO: 2 and 19.
Welch teaches the StcE of instant SEQ ID NO: 1 in SEQ ID NO: 2 and 19. Welch teaches the method comprising testing human samples for use in diagnosing disease (abstract and col 26 in lines 18-20).
It would have been obvious to one of ordinary skill in the art to combine the mapping and sequencing of Jonckheere with the method of Xiao or produce a method of testing candidate binding receptors by de-mucinating cells as taught by Xiao. Jonckheere teaches a number of mucins with suspected interaction with receptors that would have clinical implications. One of ordinary skill in the art would have been motivated to use the method of Xiao to confirm the suspected receptor binding of the sequences identified by Jonckheere for therapeutic uses. There would have been a reasonable expectation of success as Jonckheere teaches a short list with in silico data supporting their role as receptor binding and Xiao teaches a straightforward method for testing the binding.
It would have been further obvious to expand the method of Jonckheere in view of Xiao to use differing proteases including the elected species of StcE as taught by Grys and Welch. One of ordinary skill in the art would have been motivated to as Grys teaches StcE as a very effective protease that targets mucins. There would have been a reasonable expectation of success as StcE has been shown to be a very effective protease for use in human samples.
Conclusion
No claims allowable.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/F.E./Examiner, Art Unit 1643
/Meera Natarajan/Primary Examiner, Art Unit 1643