DETAILED ACTION
In application filed on12/15/2023, Claims 1-31 are pending. The claim set submitted on 03/04/2024 is considered because this is the most recent claim set. Claims 1-31 are considered in the current 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 Objections
Claim 1 is objected to because of the following informalities:
Claim 1 recites “a capillary tube” in line 6 of the Claim. It appears that this limitation should be recited as “the capillary tube”.
Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 1 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims have been analyzed for eligibility in accordance with their broadest reasonable interpretation. All claims are directed to statutory categories, i.e., a method (Claim 1) (Step 1: YES).
Analysis:
Claim 1: Ineligible.
Step 1:
The claim recites a series of steps or acts, including “glycan analysis”. Thus, the claim is directed to a process, which is one of the statutory categories of invention (Step 1: YES).
Step 2A, Prong 1:
Claim 1 recites “analyzing the separated and detected charged glycan fragments, whereby one or more structural characteristics of said plurality of glycan moieties are determined”. Therefore, the claim is directed towards an abstract idea, and more specifically to the abstract idea group of a math or mental process since claim 1 relates to using a math or mental process to perform the steps reciting the abstract ideas. (Step 2A, Prong 1: YES).
Step 2A, Prong Two:
This judicial exception is not integrated into a practical application. In particular, the claim recites ‘additional elements’ which are the steps performed before and after the recited abstract ideas. However, the steps before the abstract ideas are performed in order to gather data necessary to perform the determination step. Thus, these steps do not add a meaningful limitation since these steps are insignificant pre-solution activity.
Once the analyzing is done, , No further action takes place, much less a particular practical application. Also the steps of “providing…”; “allowing…”; “separating…”; “injecting…” and “separating and …” are recited at a high level of generality that it amounts to mere data gathering (insignificant extra-solution activity). See MPEP 2106.05(g).
Accordingly, these steps are ‘additional elements’ which do not integrate the abstract ideas into a practical application because they do not impose meaningful limits on practicing the abstract ideas (Step 2A, Prong Two: NO).
Step 2B:
Furthermore, the courts have found that limitations adding insignificant extrasolution activity to the judicial exception, such as mere data gathering in conjunction with a law of nature or abstract idea, are limitations found not to be enough to qualify as ‘significantly more’ when recited in a claim with a judicial exception (see the 2014 Interim Guidance on Patent Subject Matter Eligibility of the Federal Register dated December 16, 2014; and MPEP 2106.05(I)(A)). Note that mere data gathering is not significantly more than the abstract idea. See MPEP 2106.05(g).
Here, there are no additional elements which are significantly more than the abstract idea.
The steps of the steps of “providing…”; “allowing…”; “separating…”; “injecting…” and “separating and …”appears to be well-understood, routine, and conventional (WURC) in the field of CE-MS and glycomics as evidenced by Snyder et al. ("Capillary electrophoresis–mass spectrometry for direct structural identification of serum N-glycans." Journal of chromatography A 1523 (2017): 127-139.) in view of Szigeti et al. ("Rapid N-glycan release from glycoproteins using immobilized PNGase F microcolumns." Journal of Chromatography B 1032 (2016): 139-143).
Thus, the claims do not amount to significantly more (Step 2B: NO).
Therefore, Claim 1 is ineligible.
Moreover, Claims 2-31 will be rejected by virtue of dependency on Claim 1; . Also, each of the dependent claims do not solve the issues of claim 1.
Claims 2-31: Ineligible.
Step 2A, Prong One and Prong Two: Claims 2-31 further define the data gathering steps which appear to be generic and WURC.
Step 2B: The claims do not recite any elements which are significantly more.
It is noted that these steps are insignificant. The steps appear to be more data gathering and are well-understood, routine, and conventional (WURC)
Therefore, Claims 2-31 are ineligible.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-2, 5-11, 13, 15-19, 21-27 and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Snyder et al. ("Capillary electrophoresis–mass spectrometry for direct structural identification of serum N-glycans." Journal of chromatography A 1523 (2017): 127-139.) in view of Szigeti et al. ("Rapid N-glycan release from glycoproteins using immobilized PNGase F microcolumns." Journal of Chromatography B 1032 (2016): 139-143).
Regarding Claim 1, Snyder teaches a method of glycan analysis (See Abstract…Through direct coupling of capillary electrophoresis (CE) to mass spectrometry (MS) with a sheathless interface, we have identified 77 potential N-glycan structures derived from human serum), the method comprising the steps of:
providing an open tube capillary electrophoresis instrument (referred to as a CESI 8000 Instrument [Section 2.4; Page 128]) whose output (referred to as nanospray source [Section 2.4; Page 128]) provides an electrospray input (referred to as the provided adapter kit Section 2.4; Page 128]; See Section 2.4… Electrospray was initiated by applying 1.2–1.6 kV for 5–30 s) for a mass spectrometer (referred to as an LTQ Orbitrap mass spectrometer [Section 2.4; Page 128]), a glycan release agent solution (referred to as 0.5 μL of PNGase F in phosphate buffer [Section 2.2]); a capillary tube (referred to as capillary/separation capillary [Section 2.4]) of the open tube capillary electrophoresis instrument (referred to as a CESI 8000 Instrument [Section 2.4; Page 128]), and a sample comprising a glycoprotein in an aqueous medium (See Section 2.2…samples were suspended in 10 µL phosphate buffer (pH 7.5))
introducing the sample into an inlet of a capillary tube (referred to as capillary/separation capillary [Section 2.4]; under BRI, the capillary has an inlet) of the open tube capillary electrophoresis instrument (referred to as a CESI 8000 Instrument [Section 2.4; Page 128]) (See Section 2.4…Hydrostatic injections at 1–5 psi for 5–30 s were used to introduce analytes to the capillary before a separation voltage of 24 or 30 kV was applied), whereby the glycoprotein contacts the glycan release agent solution (See Section 2.2…N-Glycans were enzymatically cleaved from standard glycoproteins (200 µg) and human serum (5 µL) with PNGase F)
(c) allowing the glycan release agent to release one or more glycan moieties from the glycoprotein without modification of glycan structure or composition (See Section 2.2… N-Glycans were enzymatically cleaved from standard glycoproteins; Under BRI, Snyder does not disclose “with modification of glycan structure or composition” );
(d) separating the released glycan moieties (See Page 130…Methylamidated, APTS-labeled N-glycans were introduced into the Orbitrap mass spectrometer via electrospray ionization after being electrophoretically separated) within the capillary tube (See Page 130… bare fused silica capillary) using the open tube capillary electrophoresis instrument (See Fig. 5… the capillary electrophoresis system) based on charge and hydrodynamic volume of the released glycan moieties to form a plurality of separated glycan moieties (See Fig. 5… separate APTS-labeled glycans) within the capillary tube (See Fig. 5…APTS-labeled glycans are separated by charge-to-size ratio in the order of ascending hydrodynamic volume);
(e) injecting the separated glycan moieties (See Page 130…Methylamidated, APTS-labeled N-glycans were introduced into the Orbitrap mass spectrometer via electrospray ionization after being electrophoretically separated) from an outlet of the capillary tube into the mass spectrometer (See Section 2.4…The capillary was interfaced with the nanospray source of an LTQ Orbitrap mass spectrometer (Thermo Fisher) through the provided adapter kit,), whereby the separated glycan moieties are ionized and fragmented to form a plurality of charged glycan fragments (See Page 130… Methylamidated, APTS-labeled N-glycans were introduced into the Orbitrap mass spectrometer via electrospray ionization after being electrophoretically separated in a bare fused silica capillary.);
(f) separating and detecting the charged glycan fragments based on mass-to-charge ratio using the mass spectrometer (See Page 130… For MS analysis, the primary charge state for most APTS-labeled N-glycans was z = −3 (charge of APTS), but N-glycans with total masses <2100 Da, including the mass of APTS, also exhibited z = −2 because these ions picked up a proton from the BGE (pH 2.8).); and
(g) analyzing the separated and detected charged glycan fragments, whereby one or more structural characteristics of said plurality of glycan moieties are determined (See Page 130…Mass spectra were collected in negative ion mode due to the negatively charged APTS label used to give the neutralized Nglycans a charge for electrophoretic separation. This mode proved to be beneficial for structural identification because negative mode MS produces less complicated spectra than positive mode [34–36,57]…To confirm peak assignments, peak order and relative abundances were compared for all N-glycans identified in electropherograms from both microchip and capillary separations. In all cases, assignments of non-bisected and bisected glycans from microchip electrophoresis were in good agreement with the CE-MS experiments).
Snyder does not teach “a glycan release agent solution disposed within a capillary tube”.
In the analogous art of N-glycosylation profiling of glycoprotein biotherapeutics, Szigeti teaches that “a glycan release agent solution (See Page 140; Section 2.2…After washing the microcolumns, 1.0 µL of GST PNGase F (16 IUB mU/mL) enzyme was mixed with 1 mL of 20 mM Tris-HCl buffer (pH 7.3) and spirated/dispensed for 3 h using 0.06 mL min−1 flow rate at 4 ◦C for compete binding) disposed within (See Section 2.2…”Immobilization of GST tagged PNGase F”) a capillary tube (referred to as microcolumns [Page 141]) (See Page 141…However, as Fig. 1 revealed, with the use of PNGase F functionalized microcolumns, efficient N-deglycosylation was obtained in approximately 10 min and negligible differences were observed in peak areas, peak area percentages and migration time values (see numerical comparison in Supplementary Tables 1–3)).
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 of Snyder to include “a glycan release agent solution disposed within a capillary tube”, as taught by Szigeti for the benefit of efficient N-glycan removal in 10 min from all major N-linked glycoprotein types including: (i) neutral (IgG), (ii) highly sialylated (fetuin), and (iii) high mannose (ribonuclease B) carbohydrate containing glycoprotein standards (Szigeti, Abstract),allowing for provision of automated sample preparation systems for glycosylation profiling of glycoprotein biotherapeutics (Szigeti, Abstract).
Regarding Claim 2, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder further teaches that the glycan release agent is PNGase F, and the released glycan moieties are N-glycans (See Section 2.2…N-Glycans were enzymatically cleaved from standard glycoproteins (200 µg) and human serum (5 µL) with PNGase F).
Regarding Claim 5, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder further teaches wherein the analyzing of step (g) results in complete structure elucidation of at least one glycan moiety (See Page 130…Mass spectra were collected in negative ion mode due to the negatively charged APTS label used to give the neutralized Nglycans a charge for electrophoretic separation. This mode proved to be beneficial for structural identification because negative mode MS produces less complicated spectra than positive mode [34–36,57]…To confirm peak assignments, peak order and relative abundances were compared for all N-glycans identified in electropherograms from both microchip and capillary separations. In all cases, assignments of non-bisected and bisected glycans from microchip electrophoresis were in good agreement with the CE-MS experiments, thereby teaching “the analyzing of step (g) results in complete structure elucidation of at least one glycan moiety”).
Regarding Claim 6, the method of claim 5 is obvious over Snyder in view of Szigeti.
Snyder further teaches that the complete structure elucidation (See Page 130…This mode proved to be beneficial for structural identification) comprises identification of all monosaccharides of the glycan moiety (See Section 3.3…Criteria for structural assignment included: presence of a tri-mannosylcore, 0–3 fucosyl groups, and alternating GlcNAc and Gal monosaccharides…The emphasis here was to confirm the presence of specific monosaccharides and to obtain general structural information ) and glycan derivative moieties (See Table 4… Possible linkage isomers present for sialylated N-glycans from serum, thereby teaching “identification of glycosidic linkages of the glycan moiety”) and identification of glycosidic linkages of the glycan moiety (See Table 4… Possible linkage isomers present for sialylated N-glycans from serum, thereby teaching “identification of glycosidic linkages of the glycan moiety”; See Section 3.4…fragmentation is the primary mode of fragmentation for negative ion mode, instead of glycosidic fragmentation in positive mode, we observed losses of full monosaccharides corresponding to Y-type ions [58] at a normalized collision energy of 35).
Regarding Claim 7, the method of claim 5 is obvious over Snyder in view of Szigeti.
Snyder further teaches that the complete structure elucidation (See Page 130…This mode proved to be beneficial for structural identification) identifies an intact native structure of the glycan moiety (See Page 131….Section 3.2…This direct structural identification also allowed us to uncover N-glycans that may have been masked by species with similar mobilities; Section 3.3…Direct structural identification through CE-MS analysis helped us to identify new m/z values that correspond to potential N-glycan structures in serum).
Regarding Claim 8, the method of claim 6 is obvious over Snyder in view of Szigeti.
Snyder teaches that the structural elucidation (See Page 130…This mode proved to be beneficial for structural identification) comprises the identification of glycan moieties containing from 1 to about 20 sialic acid residues (See Section 3.4…and MS/MS analysis was performed on these analytes to correlate expected structural losses with proposed structures, e.g., one sialic acid per antenna of a biantennary N-glycan instead of two sialic acids stacked on a single antenna (see Fig. 2); See Table 2, Page 133…1 sialic acid…2+ sialic acid; See Section 3.3…For example, two disialylated, bifucosylated N-glycans).
Regarding Claim 9, the method of claim 6 is obvious over Snyder in view of Szigeti.
Snyder teaches that the structural elucidation (See Page 130…This mode proved to be beneficial for structural identification) comprises the identification of glycan moieties containing from 1 to about 10 fucose residues (See Section 3.3…These structures were then refined based on the presence of the tri-mannosyl core, 0–3 fucosyl groups, and standard GlcNAc and Gal ordering; See Section 3.3…For example, two disialylated, bifucosylated N-glycans).
Regarding Claim 10, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches wherein the analyzing of step (g) (See Page 130…Mass spectra were collected in negative ion mode due to the negatively charged APTS label used to give the neutralized Nglycans a charge for electrophoretic separation. This mode proved to be beneficial for structural identification because negative mode MS produces less complicated spectra than positive mode [34–36,57]…To confirm peak assignments, peak order and relative abundances were compared for all N-glycans identified in electropherograms from both microchip and capillary separations. In all cases, assignments of non-bisected and bisected glycans from microchip electrophoresis were in good agreement with the CE-MS experiments) comprises using output of peak areas and intensities (See Section 3.1…To confirm peak assignments, peak order and relative abundances were compared for all N-glycans identified in electropherograms from both microchip and capillary separations;See Section 3.3… calculated through electrophoretic mobility standards for APTS-labeled N-glycans [39], correspond to N-glycan peaks from serum samples that do not have assigned structures, and the relative peak areas between the capillary and microchip separations are in good agreement) from the mass spectrometer(referred to as an LTQ Orbitrap mass spectrometer [Section 2.4; Page 128]).
Regarding Claim 11, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches wherein, in step (d), isomers of glycan moieties are separated (See Page 130…Methylamidated, APTS-labeled N-glycans were introduced into the Orbitrap mass spectrometer via electrospray ionization after being electrophoretically separated) within the open tube capillary electrophoresis instrument (See Fig. 5… the capillary electrophoresis system) in a single run (See Section 2.4…CE-ESI-MS, thereby teaching “single run”).
Regarding Claim 13, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that the method enables identification and quantification of intact (See Page 131….Section 3.2…This direct structural identification also allowed us to uncover N-glycans that may have been masked by species with similar mobilities; Section 3.3…Direct structural identification through CE-MS analysis helped us to identify new m/z values that correspond to potential N-glycan structures in serum) and native glycan moieties (See Section 3.3…Masses found in spectra of methylamidated N-glycans from serum that did not correspond to a previously identified N-glycan were compiled, and five lists of possible native masses corresponding to neutral through tetra-sialylated species were generated).
Regarding Claim 15, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that the method does not comprise use of any other endoglycosidase or exoglycosidase (See Section 2.1…only peptide-N-glycosidase F (PNGase F) is used).
Regarding Claim 16, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that dried samples were reconstituted in 20–50 µL 1:10 BGE:water prior to analysis, depending on initial sample amount. Hydrostatic injections at 1–5 psi for 5–30 s were used to introduce analytes to the capillary before a separation voltage of 24 or 30 kV was applied (See Section 2.4.CE-ESI-MS). Further, Szigeti teaches that labeled glycans from the three types of glycoprotein samples were analyzed by CGE-LIF (Section 3…Results and discussion).
The combination of Snyder and Szigeti does not that glycans from at least 10, at least 20, at least 30, at least 40, or at least 50 different glycoproteins are released, separated, fragmented, and analyzed in a single run.
However, one having ordinary skill in the art at the time the invention was made would recognize that the at least 10, at least 20, at least 30, at least 40, or at least 50 different glycoproteins being released, separated, fragmented, and analyzed in a single run as nothing more than the duplication of parts (plurality of constrictions) for a multiple effect towards simultaneous processing of glycoprotein samples and could seek the benefits of automation, to speed up glycoprotein sample processing for multiple glycoproteins samples. Please see In re Harza, 274 F.2d 669, 671, 124 USPQ 378, 380 (CCPA 1960) and MPEP 2144.04(VI)(B) for further details.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to include that glycans from at least 10, at least 20, at least 30, at least 40, or at least 50 different glycoproteins are released, separated, fragmented, and analyzed in a single run for the benefit of obtaining direct structural information about Nglycans present in serum, we used CE-MS to identify 77 potential N-glycan structures present in serum and to differentiate several co-migrating species (Snyder, Introduction).
Regarding Claim 17, the method of claim 1 is obvious over Snyder in view of Szigeti.
The combination of Snyder and Szigeti does not expressly teach that the sample has a volume of less than 1 µL.
However, MPEP § 2144.05, Part II, Subpart B holds that a particular parameter that is recognized as a result effective variable (“a variable that achieves a recognized result”) would be one, but not the only motivation for a person of ordinary skill in the art to experiment to reach another workable product or process. In the operation of method of using CE-ESI–MS, the selection of optimal experimental conditions including injection volume of the sample affects detection sensitivity and separation resolution. Thus, the c the sample having a volume of less than 1 µL is a result effective variable.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use or operate CE-ESI–MS, where the sample has a volume of less than 1 µL, for the benefit of of obtaining direct structural information about Nglycans present in serum, we used CE-MS to identify 77 potential N-glycan structures present in serum and to differentiate several co-migrating species (Snyder, Introduction).
Regarding Claim 18, the method of claim 16 is obvious over Snyder in view of Szigeti.
The combination of Snyder and Szigeti does not expressly teach that the sample has a volume of less than 1 nL.
However, MPEP § 2144.05, Part II, Subpart B holds that a particular parameter that is recognized as a result effective variable (“a variable that achieves a recognized result”) would be one, but not the only motivation for a person of ordinary skill in the art to experiment to reach another workable product or process. In the operation of method of using CE-ESI–MS, the selection of optimal experimental conditions including injection volume of the sample affects detection sensitivity and separation resolution. Thus, the sample having a volume of less than 1 nL is a result effective variable.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use or operate CE-ESI–MS, where the sample has a volume of less than 1 nL, for the benefit of of obtaining direct structural information about Nglycans present in serum, we used CE-MS to identify 77 potential N-glycan structures present in serum and to differentiate several co-migrating species (Snyder, Introduction).
Regarding Claim 19, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that the sample is obtained from blood, plasma, a bodily fluid, a biopsy sample, a cell suspension, a subcellular fraction, or a cell culture, or an extract or fraction of any of the foregoing (See Abstract…human serum; Under BRI, human serum is obtained from blood).
Regarding Claim 21, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches wherein the sample (See Abstract…human serum; Under BRI, human serum is obtained from blood) is cell-free (See Abstract…under BRI, human serum does not have cells).
Regarding Claim 22, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches wherein the sample (See Abstract…human serum; Under BRI, human serum is obtained from blood) is not subjected to any purification, homogenization, chromatography, centrifugation, or fractionation prior to use in the method. (See Abstract…Snyder does not teach that human serum is subject to prior chromatography).
Regarding Claim 23, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches wherein the sample (See Abstract…human serum; Under BRI, human serum is obtained from blood) is subjected to purification, homogenization, chromatography, centrifugation, or fractionation prior to use in the method (See Abstract…under BRI, human serum is obtained from centrifugation from blood).
Regarding Claim 24, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that the separated glycan moieties (See Page 130…Methylamidated, APTS-labeled N-glycans were introduced into the Orbitrap mass spectrometer via electrospray ionization after being electrophoretically separated) are subjected to electrospray ionization when injected into the mass spectrometer in step (e) (See Page 130…Methylamidated, APTS-labeled N-glycans were introduced into the Orbitrap mass spectrometer via electrospray ionization after being electrophoretically separated).
Regarding Claim 25, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that the capillary electrophoresis/tandem mass spectrometry (CE/MS/MS) is used to perform steps (b) through (f) (See Abstract…Through direct coupling of capillary electrophoresis (CE) to mass spectrometry (MS) with a sheathless interface, we have identified 77 potential N-glycan structures derived from human serum).
Regarding Claim 26, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that wherein hydrodynamic pressure, electrospray, or electrokinetic injection is used to introduce the sample into the inlet of the capillary tube in step (b) (See Section. 2.4…Hydrostatic injections at 1–5 psi for 5–30 s were used to introduce analytes to the capillary before a separation voltage of 24 or 30 kV was applied; Under BRI, a hydrostatic injection will produce hydrodynamic pressure).
Regarding Claim 27, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that the method is capable of full structure elucidation of a glycan present in a sample (See Page 131….Section 3.2…This direct structural identification also allowed us to uncover N-glycans that may have been masked by species with similar mobilities; Section 3.3…Direct structural identification through CE-MS analysis helped us to identify new m/z values that correspond to potential N-glycan structures in serum) in amounts over a range of at least 4 orders of magnitude (See Abstract… we have identified 77 potential N-glycan structures derived from human serum).
Regarding Claim 30, the method of claim 29 is obvious over Snyder in view of Szigeti.
Snyder teaches that wherein the multiomic profiling (See Section 3.3…Criteria for structural assignment included: presence of a tri-mannosylcore, 0–3 fucosyl groups, and alternating GlcNAc and Gal monosaccharides…The emphasis here was to confirm the presence of specific monosaccharides and to obtain general structural information; Examiner further submits that glycan cleavage from proteins is a key sample preparation step within glycoproteomics) comprises glycomic profiling (See Section 3.3…Criteria for structural assignment included: presence of a tri-mannosylcore, 0–3 fucosyl groups, and alternating GlcNAc and Gal monosaccharides…The emphasis here was to confirm the presence of specific monosaccharides and to obtain general structural information, thereby teaching “glycomic profiling”) and one or more of proteomic, genomic, transcriptomic, and metabolomic profiling (See Section 3.3…Criteria for structural assignment included: presence of a tri-mannosylcore, 0–3 fucosyl groups, and alternating GlcNAc and Gal monosaccharides…The emphasis here was to confirm the presence of specific monosaccharides and to obtain general structural information; Examiner further submits that glycan cleavage from proteins using PNGase F is a key sample preparation step within proteomics as evidenced by Hosfield et al.).
Claims 3-4, 12 and 28-29 are rejected under 35 U.S.C. 103 as being unpatentable over Snyder et al. ("Capillary electrophoresis–mass spectrometry for direct structural identification of serum N-glycans." Journal of chromatography A 1523 (2017): 127-139.) in view of Szigeti et al. ("Rapid N-glycan release from glycoproteins using immobilized PNGase F microcolumns." Journal of Chromatography B 1032 (2016): 139-143) as applied to claim 1 above, and further in view of Mehta et al. (US20210208156A1).
Regarding Claim 3, the method of claim 1 is obvious over Snyder in view of Szigeti.
The combination of Snyder and Szigeti does not teach that the one or more glycans are released, separated, fragmented, and analyzed from glycoproteins of 1 to about 20 single cells present in the sample.
In the analogous art of methods and compositions for glycan analysis of complex solutions, including proteins and cells in a biological sample, Mehta teaches that the one or more glycans are released, separated, fragmented, and analyzed from glycoproteins of 1 to about 20 single cells present in the sample (See Para 0029…FIG. 12A through FIG. 12D depict the results of experiments demonstrating N-glycan profiling of endothelial cell (EC) single cell layers through simplified MALDI MS workflows). (FIG. 12A) Before delipidation. (FIG. 12B) After delipidation. (FIG. 12C) Complex N-glycan profiles obtained from a single cell layer of EC).
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 of the combination of Snyder and Szigeti to include that the one or more glycans are released, separated, fragmented, and analyzed from glycoproteins of 1 to about 20 single cells present in the sample, as taught by Mehta for the benefit of demonstrating glycan analysis for single cells (Mehta, Para 0029), allowing for the use of protein and cell glycan analysis in the diagnosis and screening of disease states and disease progression (Mehta, Abstract).
Regarding Claim 4, the method of claim 3 is obvious over Snyder in view of Szigeti and further in view of Mehta.
The combination of Snyder and Szigeti does not teach one or more glycans are released, separated, fragmented, and analyzed from glycoproteins of a single cell.
In the analogous art of methods and compositions for glycan analysis of complex solutions, including proteins and cells in a biological sample, Mehta teaches that one or more glycans are released, separated, fragmented, and analyzed from glycoproteins of a single cell. (See Para 0029…FIG. 12A through FIG. 12D depict the results of experiments demonstrating N-glycan profiling of endothelial cell (EC) single cell layers through simplified MALDI MS workflows). (FIG. 12A) Before delipidation. (FIG. 12B) After delipidation. (FIG. 12C) Complex N-glycan profiles obtained from a single cell layer of EC).
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 of the combination of Snyder and Szigeti to include that one or more glycans are released, separated, fragmented, and analyzed from glycoproteins of a single cell., as taught by Mehta for the benefit of demonstrating glycan analysis for single cells (Mehta, Para 0029), allowing for the use of protein and cell glycan analysis in the diagnosis and screening of disease states and disease progression (Mehta, Abstract).
Regarding Claim 12, the method of claim 1 is obvious over Snyder in view of Szigeti.
The combination of Snyder and Szigeti does not teach that the sample comprises one or more single cells and the method preserves integrity of analyzed single cells.
In the analogous art of methods and compositions for glycan analysis of complex solutions, including proteins and cells in a biological sample, Mehta teaches that the sample comprises one or more single cells (See Para 0029…FIG. 12A through FIG. 12D depict the results of experiments demonstrating N-glycan profiling of endothelial cell (EC) single cell layers through simplified MALDI MS workflows). (FIG. 12A) Before delipidation. (FIG. 12B) After delipidation. (FIG. 12C) Complex N-glycan profiles obtained from a single cell layer of EC) and the method preserves integrity of analyzed single cells (See Para 0187… Maintaining cell integrity during capture and rinsing prior to PNGaseF treatment is achieved by fixation in formalin after antibody binding).
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 of the combination of Snyder and Szigeti to include that the sample comprises one or more single cells and the method preserves integrity of analyzed single cells, as taught by Mehta for the benefit of demonstrating glycan analysis for single cells (Mehta, Para 0029) and ensuring that the glycans from glycoprotein standards could be detected from 1 ng of antibody (Mehta, Para 0187), allowing for the use of protein and cell glycan analysis in the diagnosis and screening of disease states and disease progression (Mehta, Abstract).
Regarding Claim 28, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that the method (See Page 131….Section 3.2…This direct structural identification also allowed us to uncover N-glycans that may have been masked by species with similar mobilities; Section 3.3…Direct structural identification through CE-MS analysis helped us to identify new m/z values that correspond to potential N-glycan structures in serum) is used to aid in performing spatial glycomic profiling (See Section 3.3…Criteria for structural assignment included: presence of a tri-mannosylcore, 0–3 fucosyl groups, and alternating GlcNAc and Gal monosaccharides…The emphasis here was to confirm the presence of specific monosaccharides and to obtain general structural information).
The combination of Snyder and Szigeti does not teach that the profiling of single cells or non-cellular sub-nanogram samples.
In the analogous art of methods and compositions for glycan analysis of complex solutions, including proteins and cells in a biological sample, Mehta teaches that the profiling of single cells or non-cellular sub-nanogram samples (Under BRI, the claimed “or non-cellular sub-nanogram samples” is viewed as optional ) (See Para 0029…FIG. 12A through FIG. 12D depict the results of experiments demonstrating N-glycan profiling of endothelial cell (EC) single cell layers through simplified MALDI MS workflows). (FIG. 12A) Before delipidation. (FIG. 12B) After delipidation. (FIG. 12C) Complex N-glycan profiles obtained from a single cell layer of EC).
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 of the combination of Snyder and Szigeti to include the profiling of single cells or non-cellular sub-nanogram samples, as taught by Mehta for the benefit of demonstrating glycan analysis for single cells (Mehta, Para 0029) and ensuring that the glycans from glycoprotein standards could be detected from 1 ng of antibody (Mehta,Para 0187), allowing for the use of protein and cell glycan analysis in the diagnosis and screening of disease states and disease progression (Mehta, Abstract).
Regarding Claim 29, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder teaches that the method (See Page 131….Section 3.2…This direct structural identification also allowed us to uncover N-glycans that may have been masked by species with similar mobilities; Section 3.3…Direct structural identification through CE-MS analysis helped us to identify new m/z values that correspond to potential N-glycan structures in serum) is used to aid in performing spatial multiomics profiling (See Section 3.3…Criteria for structural assignment included: presence of a tri-mannosylcore, 0–3 fucosyl groups, and alternating GlcNAc and Gal monosaccharides…The emphasis here was to confirm the presence of specific monosaccharides and to obtain general structural information; Examiner further submits that glycan cleavage from proteins using PNGase F is a key sample preparation step within proteomics as evidenced by Hosfield et al. ).
The combination of Snyder and Szigeti does not teach that the profiling of single cells or non-cellular sub-nanogram samples.
In the analogous art of methods and compositions for glycan analysis of complex solutions, including proteins and cells in a biological sample, Mehta teaches that the profiling of single cells or non-cellular sub-nanogram samples (Under BRI, the claimed “or non-cellular sub-nanogram samples” is viewed as optional ) (See Para 0029…FIG. 12A through FIG. 12D depict the results of experiments demonstrating N-glycan profiling of endothelial cell (EC) single cell layers through simplified MALDI MS workflows). (FIG. 12A) Before delipidation. (FIG. 12B) After delipidation. (FIG. 12C) Complex N-glycan profiles obtained from a single cell layer of EC).
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 of the combination of Snyder and Szigeti to include the profiling of single cells or non-cellular sub-nanogram samples, as taught by Mehta for the benefit of demonstrating glycan analysis for single cells (Mehta, Para 0029) and ensuring that the glycans from glycoprotein standards could be detected from 1 ng of antibody (Mehta,Para 0187), allowing for the use of protein and cell glycan analysis in the diagnosis and screening of disease states and disease progression (Mehta, Abstract).
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Snyder et al. ("Capillary electrophoresis–mass spectrometry for direct structural identification of serum N-glycans." Journal of chromatography A 1523 (2017): 127-139.) in view of Szigeti et al. ("Rapid N-glycan release from glycoproteins using immobilized PNGase F microcolumns." Journal of Chromatography B 1032 (2016): 139-143) as applied to claim 1 above, and further in view of Biacchi et al. ("Glycoform separation and characterization of cetuximab variants by middle-up off-line capillary zone electrophoresis-UV/electrospray ionization-MS." Analytical chemistry 87.12 (2015): 6240-6250.).
Regarding Claim 14, the method of claim 1 is obvious over Snyder in view of Szigeti.
The combination of Snyder and Szigeti teaches that the method does not comprise labeling or derivatizing any glycan moiety.
In the analogous art of glycoform separation and characterization of cetuximab variants by middle-up off-line capillary zone electrophoresis-uv/electrospray ionization-ms, Biacchi teaches that the method does not comprise labeling or derivatizing any glycan moiety (See Abstract…glycoforms were detected and separated in three different peaks following the presence of N-glycolyl neuraminic acid residues in some glycan structures; The disclosed method does not disclose “labeling or derivatizing any glycan moiety”.
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 of the combination of Snyder and Szigeti to include that the method does not comprise labeling or derivatizing any glycan moiety, as taught by Biacchi for the benefit of performing off-line CZE-ESI-MS using CZE-UV/fraction collection technology to perform CZE separation, followed by ESI-MS infusion of the different fractions using the capillary electrophoresis-electrospray ionization (CESI) interface as the nanoESI infusion platform (Biacchi, Abstract), allowing for the benefit of demonstrating the potential of CZE technology to perform separation of mAbs especially when they carry sialic acid carbohydrates(Biacchi, Abstract).
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Snyder et al. ("Capillary electrophoresis–mass spectrometry for direct structural identification of serum N-glycans." Journal of chromatography A 1523 (2017): 127-139.) in view of Szigeti et al. ("Rapid N-glycan release from glycoproteins using immobilized PNGase F microcolumns." Journal of Chromatography B 1032 (2016): 139-143) as applied to claim 19 above, and further in view of Naylor et al. (US5800692A).
Regarding Claim 20, the method of claim 19 is obvious over Snyder in view of Szigeti.
Snyder teaches that the blood, plasma, bodily fluid, biopsy sample, cell suspension, subcellular fraction, cell culture, or extract or fraction thereof (See Abstract…human serum; Under BRI, human serum is obtained from blood).
The combination of Syder and Szigeti does not teach that the blood, plasma, bodily fluid, biopsy sample, cell suspension, subcellular fraction, cell culture, or extract or fraction thereof was obtained from a source previously contacted with a chemical or biological therapeutic agent.
In the analogous art of the preseparation processor for use in capillary electrophoresis, Naylor teaches that that the blood, plasma, bodily fluid, biopsy sample, cell suspension, subcellular fraction, cell culture, or extract or fraction thereof was obtained from a source previously contacted with a chemical or biological therapeutic agent (See Col. 22, lines 34-40… A capillary electrophoresis system and processor apparatus similar to that used in Example 4 and 5 was used in this experiment to analyze the drug metabolites excreted in patient urine after the administration of the neuroleptic drug Haloperidol).
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 of the combination of Snyder and Szigeti to include that the blood, plasma, bodily fluid, biopsy sample, cell suspension, subcellular fraction, cell culture, or extract or fraction thereof was obtained from a source previously contacted with a chemical or biological therapeutic agent, as taught by Naylor for the benefit of processing of urine samples using a preseparation processor containing membrane-based sample processing material (Naylor, Col. 22, lines 30-34), allowing the provision of method useful for clinical diagnostics because it permits more rapid and accurate analyses of extremely small quantities of drug metabolites, peptides, and proteins from biological or physiological fluids such as urine, feces, serum, blood, plasma, cerebral spinal fluid, nasal drainage, aqueous humor, various biopsies, tissue homogenates, cultured cells, and/or extracts thereof (Naylor).
Claim 31 is rejected under 35 U.S.C. 103 as being unpatentable over Snyder et al. ("Capillary electrophoresis–mass spectrometry for direct structural identification of serum N-glycans." Journal of chromatography A 1523 (2017): 127-139.) in view of Szigeti et al. ("Rapid N-glycan release from glycoproteins using immobilized PNGase F microcolumns." Journal of Chromatography B 1032 (2016): 139-143) as applied to claim 1 above, and further in view of Snyder et al. (Snyder et al. "Complementary glycomic analyses of sera derived from colorectal cancer patients by MALDI-TOF-MS and microchip electrophoresis." Analytical chemistry 88.19 (2016): 9597-9605.; hereinafter Snyder2016).
Regarding Claim 31, the method of claim 1 is obvious over Snyder in view of Szigeti.
Snyder further teaches that the method (See Page 131….Section 3.2…This direct structural identification also allowed us to uncover N-glycans that may have been masked by species with similar mobilities; Section 3.3…Direct structural identification through CE-MS analysis helped us to identify new m/z values that correspond to potential N-glycan structures in serum) is used to aid in diagnosis and/or treatment of a disease or medical condition (See Introduction…Additionally, glycomic profiling has proved to be a powerful tool for differentiating among healthy individuals and patients with different types of cancer by multiple methods, thereby teaching “diagnosis and/or treatment of a disease or medical condition”, thereby teaching “aid in diagnosis and/or treatment of a disease or medical condition”).
The combination of Snyder and Szigeti does not explicitly teach that the sample is obtained from a subject suspected of having the disease or medical condition.
In the analogous art of complementary glycomic analyses of sera derived from colorectal cancer patients by maldi-tof-ms and microchip electrophoresis, Christa2016 teaches that the sample is obtained from a subject suspected of having the disease or medical condition (See Results and Discussion; See Page 9599…MALDI-TOF-MS was performed on control (N = 20) and colorectal serum samples from patients diagnosed with colorectal cancer after a first treatment cycle (“C1 samples”, N = 26) and a third treatment cycle (“C3 samples”, N = 16)).
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 of the combination of Snyder and Szigeti to that the sample is obtained from a subject suspected of having the disease or medical condition, as taught by Snyder2016 for the benefit of disclosing that Fucosyl isomer analysis further indicated the presence of colorectal cancer-specific biomarkers in the serum glycome (Snyder2016, See Page 9504), allowing for using several different cancer-specific biomarkers obtained from one sample to be used to unambiguously identify both disease and state at very high rates of sensitivity and specificity. With the inherent complexity of glycosylation, coupled with the need for in-depth glycomic analyses, multimethodological and complementary analytical workflows are needed to more accurately diagnose specific cancers in their earlier stages (Snyder2016, See Page 9604).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Hosfield et al. ("Recombinant PNGase F for Glycoprotein Analysis." Promega Notes. https://www. promega. com/resources/pubhub/recombinant-pngase-f-for-glycoprotein-analysis-article/(accessed Oct 10, 2023). There is no corresponding record for this reference (2013)”) teaches that PNGase F is an endoglycosidase that specifically removes N-linked glycans from glycoproteins. It is used extensively in workflows for characterizing N-linked glycan structures on therapeutic proteins and for identifying N-linked glycosylation sites in proteomic studies (See Abstract).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OYELEYE ALEXANDER ALABI whose telephone number is (571)272-1678. The examiner can normally be reached on M-F 7:30am-5:30pm.
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/OYELEYE ALEXANDER ALABI/ Examiner, Art Unit 1797
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