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 .
FINAL ACTION
Amendment Entry
1. Applicant’s response to the Non-Final action dated 1/16/25 is acknowledged (reply filed 7/16/25). In the amendment filed therein claims 30-35, 37, 39-41, 43-44, 46, 49, 51-55, and 57-58 were modified. Claims 1-29, 36, 45, 48, 50, and 56 were canceled without prejudice or disclaimer. Claims 30-35, 37-44, 46-47, 49, 51-55, and 57-58 are pending.
2. Claims 50, 51, 54, 55, 57, and 58 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made with traverse in the reply filed on 12/11/23.
3. Currently claims 30-35, 37-44, 46-49, 52, and 53 are under consideration.
4. Rejections and/or objections of record not reiterated herein have been withdrawn.
Priority
5. This application claims priority, through a series of applications, to provisional application number 62/435,409- filed December 16, 2016.
Information Disclosure Statement
6. The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609 A(1) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the Examiner on form PTO-892 or Applicant on PTO-1449 cited the references they have not been considered.
7. The information disclosure statement filed 2/12/25 has been considered as to the merits before Final Action.
NEW GROUNDS OF REJECTIONS
Claim Rejections - 35 USC § 112
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.
8. Claims 30-35, 37-44, 46-49, 52, and 53 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 pre-AIA the applicant regards as the invention.
A. Claim 30 step a is vague and indefinite because it is not clear as to what “a same volume” will encompass. Does Applicant intend to mean that the first particle, second particle and biological sample are presented in the same sample or will the assay be conducted in two separate sample wherein the volumes that are the same?
The specification appears to teach a sample volume of 10µl but it is not clear if this involves a single sample or two sample assays. See sections 00146, 00408, and 00420 for example. As recited the metes and bounds of the claim cannot be determined. It is suggested that the term “same sample volume” is defined in the claim in order to obviate the rejection. Appropriate correction is required.
B. Claim 39 is ambiguous because the protein coronas appear to have two different concentrations prior to contact. It is not clear as to how the protein coronas will be both less than 100ng/ml and greater than 100ng/ml at the same time. Appropriate clarification is required.
Claim Rejections - 35 USC § 103
9. The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
A. Claims 30-35, 37-42, 48, and 49 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hajipour et al. (Biomater. Sci., 2014, 2, 1210-1221) in view of Walkey, et al. (ACS Nano, 2014, 8, 2439-2455) and further in view of Cai et al., “Characterization of Carbon Nanotube Protein Corona by Using Quantitative Proteomics,” Nanomedicine: Nanotechnology, Biology and Medicine 9 (2013) 583-593, with its supplementary data (Table S2), submitted on IDS filed 10/31/4.
Hajipour incubated two different nanoparticles (“NPs”) (polystyrene and silica — having surfaces with different physicochemical properties) with plasma from human subjects with different diseases and determined a pattern of binding proteins that varied in a “personalized protein corona’ (“PPC) manner correlated with the type of disease (abstract).
Hajipour teaches that “we found that changes in plasma protein concentrations and structures (mediated by different disease states) affect the formation of the protein corona on a NP” (p. 1219).
Hajipour defines a biomolecule fingerprint representative of the proteins that bind to the NPs and associates the fingerprint with the biological state — i.e. Fig. 2 SDS-PAGE of plasma proteins obtained from polystyrene and silica associated with breast cancer vs. healthy (the proteins are separated from the particles). Hajipour teaches identification of the proteins at 3.1.3 (page 1214) including albumin.
Hajipour et al. do not specifically teach the measurement of the biomolecule fingerprint by mass spectrometry (a method taught by the disclosure to measure a broad dynamic range of at least 6 magnitude – see section 00176).
However, Walkey teaches that protein corona fingerprinting of nanoparticles can be characterized by mass spectrometry (p. 2441-42) and Fig 1. Walkey also teaches on p. 2447 and in figure 6; that fingerprinting can be used to predict a variety of physiologically relevant markers:
“The protein corona fingerprinting strategy can be extended to predict the association of nanoparticles with other physiologically relevant cell types, such as endothelial cells, macrophages, and hepatocytes.
Since nanoparticle--cell interactions determine downstream cellular responses, the protein corona finger print may also predict the activation of intracellular signaling cascades, cytokine secretion, gene expression, toxicity, and, by extension, in vivo pharmacokinetics, biodistribution, and organ response, Provided the appropriate models have been established, it is theoretically possible to predict multiple biological interactions and responses from a single characterization of the protein corona fingerprint.
Moreover, since a protein corona forms around silica, metal oxide, lipid, and polymer nanoparticles, protein corona fingerprinting is applicable across nanoparticle classes,”
Thus, one of ordinary skill in the art following the teaching of Hajipour would reasonably consider applying the teaching of Walkey and utilize the well-known technique of characterizing proteins using mass spectrometry.
One of ordinary skill in the art would have a reasonable expectation of success in combining the references and arriving at the claimed invention because the prior art references both relate to the application of protein corona analysis in biological systems. Therefore, claims 30-35, 37-42, 48, and 49 are prima facie obvious.
The Supreme Court stated in KSR "if a technique has been used to improve one device, and a person of ordinary skill in the art would recognize that it would improve similar devices in the same way, using the technique is obvious unless its actual application is beyond that person's skill." KSR Intern. Co. v. Teleflex Inc., 127 S.Ct. 1727, 1731 (2007).
Because utilizing well-known mass spectrometry, NPs, and classification techniques is routinely used in methods similar to those claimed here, the application of the same technique would be obvious.
Hajipour et al. (Biomater. Sci., 2014, 2, 1210-1221) in view of Walkey, et al. (ACS Nano, 2014, 8, 2439-2455) differ from the instant invention in not specifically reciting “proteins comprising concentrations varying across a dynamic range of more than 6 orders of magnitude”.
However, Cai discloses a method to “utili[ze] stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics to characterize the binding of human cellular proteins to two forms of carbon nanoparticles: namely multi-walled carbon nanotubes (MWCNTs) and carbon black (CB).” Abstract, 583. Cai further discloses: “[i]n the present study we exposed CNTs [carbon nanotubes] to a complex protein mixture, and report the large-scale identification of the resulting corona proteins. A complete protein lysate of HeLa cells was used as an archetypal human proteome, which provided the representative inventory of proteins for the binding assay.” 591; see also 585 (“To test the binding of complex mixtures of proteins, we incubated multi-wall CNTs (MCWNTs) with a mean diameter of 20-40 nm with a cell lysate prepared from the human cell line HeLa. Proteins from HeLa cells were chosen because they provide a representative source of the human proteome.”); 584 (“Cell lysates were incubated….” ); 586 & FIG. 1 (below, depicting “Protein binding assay to study MWCNT- and CB-protein corona”).
Cai also discloses analysis of the protein coronas that formed around the CNTs and CB during the incubation period resulting in the CNTs and CB being bound to the HeLa cell lysate. 583-589 (sections entitled “Protein corona of carbon nanoparticles,” “Systematic characterization of carbon nanoparticle-protein corona,” “Functional classification of the carbon nanotube-protein corona,” “Physiochemical properties of CNT-binding proteins”). For example, Cai discloses that “[a] comparison of the gel electrophoretic profiles of total HeLa cell lysate and the proteins pulled down by MWCNTs indicated that some proteins were selectively enriched into the CNT protein corona.586.
Cai also discloses “the formation of protein corona” as a result of the protein binding. 585; see also 584, 586, 589, FIGs. 1B, 3. Cai further discloses that CNTs—such as those used in its process—“are known to absorb a mixture of proteins to form a ‘protein corona’.” 583.
Cai discloses that “[i]t is important to identify the proteins that bind to MWCNTs specifically,” and to do so “we performed proteomics analysis to identify[] the proteins that selectively bind to MWCNT of diameters of 20-40 nm.” 586. The proteins that selectively bound to MWCNTs of diameters of 20-40 nm are a subset of proteins that were removed from the biological sample. Cai further discloses that “[t]he mixtures were then separated by SDS-PAGE, and analyzed with the ‘gel-LCMS/MS’ approach.” 586-87.
Cai further discloses multiple methods of assaying the isolated protein coronas taken from the bound carbon nanoparticles, including gel electrophoresis, LC-MS/MS with SILAC encoding and Western Blotting. 586-87, FIG. 1(B).
A person of ordinary skill in the art would have understood that the various disclosed methods are performed using devices to detect, assay, and characterize proteins. Cai discloses to perform “[m]ass spectrometry… on an LTQ-orbitrap mass spectrometer system (ThermoElectron, Bremen, Germany) coupled to a Dionex 3000 nano-LC system (Camberley, UK) A 100×0.075 mm Agilent C18 column (3.5 μm particle diameter)….” 585. Additionally, Cai discloses that “[s]ome of the proteins with the highest binding efficiencies… are low abundance proteins… suggest[ing] that protein binding to MWCNT is unlikely to be non-specific aggregation of the highly abundant proteins…. [i]nstead, the binding of proteins to MWCNT and CB appears to be
protein-selective.” 587 In other words, a person of ordinary skill in the art would have understood that these results were from assaying the biological sample using MS across a range large enough to detect both low abundant and high abundant proteins in the biological sample.
Cai also discloses the results of the “MS analysis confirmed that the number of proteins enriched by MWCNT-binding is much higher than that enriched by CB,” and that “[t]he relative abundance of the MWCNT-binding proteins spread over 8 orders of magnitude.” 587. Therefore, a person of ordinary skill in the art would have understood that the relative abundance of bound proteins “spread over 8 orders of magnitude” as demonstrated by Cai’s MS analysis detecting protein concentrations in the subset across a dynamic range comprising the claimed “at least 6 orders of magnitude,” which is further confirmed by the concentrations detected in Cai.
Absent evidence to the contrary the measurement of ‘”at least 6 orders of magnitude is deemed obvious.
KSR forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness. See recent Board decision Ex parte Smith,— USPQ2d—, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007)(citing KSR, 82 USPQ2d at 1396).
B. Claims 43, 44, 46-47, 52 and 53 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hajipour et al. (Biomater. Sci., 2014, 2, 1210-1221) in view of Walkey, et al. (ACS Nano, 2014, 8, 2439-2455) and further in view of Cai et al., “Characterization of Carbon Nanotube Protein Corona by Using Quantitative Proteomics,” Nanomedicine: Nanotechnology, Biology and Medicine 9 (2013) 583-593, with its supplementary data (Table S2), submitted on IDS filed 10/31/4 and Hadjidemetriou et al. (Vol.9, No.8, pages 8142-8156, 2015).
Please see Hajipour et al. in view of Walkey et al. and Cai et al. as set forth above.
Hajipour et al. in view of Walkey et al. and Cai et al. do not specifically teach functionalizing the particles to measure proteins at concentrations > 1mg/ml and <10ng/ml, measuring ratios and coronas at least 15nm thick.
However, Hadjidemetrious et al. disclose that PEG coating had a minor effect on the molecular consistency of the protein coronas. The targeted liposome systems that contained a full IgG MoAb at the distal end of the PEG chains led to corona formation of higher total protein content.
And the association of more proteins onto the surface of NPs in the presence of large molecular weight biological targeting ligands may also be relevant to other clinically used targeted, PEGylated constructs. See page 8152 2nd column, 1st paragraph.
In vivo protein corona formed onto intravenously injected, clinically used liposomes, based on the composition of the PEGylated liposomal formulation that constitutes the anticancer agent Doxil.
The formation of in vivo protein corona was determined after the recovery of the liposomes from the blood circulation of CD-1 mice 10 min postinjection (claim 13). In comparison, in vitro protein corona was formed by the incubation of liposomes in CD-1 mouse plasma. The in vivo and in vitro formed protein coronas were compared in terms of morphology, composition and cellular internalization. The protein coronas on bare (non-PEGylated) and monoclonal antibody (IgG) targeted liposomes of the same lipid composition were also comparatively investigated. A network of linear fibrillary structures constituted the in vitro formed protein corona, whereas the in vivo corona had a different morphology but did not appear to coat the liposome surface entirely. Even though the total amount of protein attached on circulating liposomes correlated with that observed from in vitro incubations, the variety of molecular species in the in vivo corona were considerably wider.
Both in vitro and in vivo formed protein coronas were found to significantly reduce receptor binding and cellular internalization of antibody-conjugated liposomes; however, the in vivo corona formation did not lead to complete ablation of their targeting capability. See abstract.
With respect to proteins at concentrations > 1mg/ml and <10ng/ml, measuring ratios, and coronas at least 15nm thick; these limitations are found at least in figures 1, 2, and 5.
Therefore, it would have been prima facie obvious to one of ordinary skill in the art at the effective filing date of the instant invention to include the PEG functionalized nanoparticles taught by Hadjidemetriou et al. in the method of Hajipour et al. in view of Walkey et al. and Cai et al. because Hadjidemetriou et al. demonstrated that PEG coating had a minor effect on the molecular consistency of the protein coronas.
The targeted liposome systems that contained a full IgG MoAb at the distal end of the PEG chains led to corona formation of higher total protein content.
One skilled in the art would have been motivated to employ the functionalized PEG particles in order to achieve in vitro and/or in vivo NP’s for protein analyzes and treatment. See Hadjidemetriou et al. abstract.
Response to Argument
Applicant contends that unlike the reference to Cai et al., the claimed method starts with a sample comprising proteins varying in concentration across a dynamic range of more than 6 orders of magnitude, and results in a significant increase in the number and range of both low- and high-abundance proteins which can be identified in the sample by mass spectrometry. See for example, FIG. 12 of the application, showing a wide concentration range for the input sample and a reduced range of concentrations after performing the method of the invention. This argument was carefully considered but not found persuasive because the claimed method does not clearly set forth this distinction.
Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Applicant also contends that Cai further does not contact particles with the biological sample in a same volume of the biological sample, as presently claimed. Instead, Cai separately treats lysates using either carbon nanotube “CNT” particles or carbon black “CB” particles (see, e.g., Cai at Figure 1B, Figure 3). Similarly, neither Hajipour nor Walkey remedy these deficiencies, relying instead on separate incubation of particles with different volumes of sample. This argument was carefully considered but was not found persuasive because the claimed “same volume” is vague and indefinite.
Finally, none of Cai, Hajipour, or Walkey disclose the use of particles comprising iron oxide to perform the method as claimed. In response to iron oxide particles, it is noted that the limitation is deemed a routine design choice that is recognized by the prior art and optimizing for assay measurement. Absent evidence to the contrary the use of an iron oxide particles is deemed obvious.
11. For reasons aforementioned, no claims are allowed.
12. 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.
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to LISA V COOK whose telephone number is (571)272-0816. The examiner works a flexible schedule but can normally be reached on Monday-Friday from 9am to 5pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Samira Jean-Louis, can be reached at telephone number 571-270-3503. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Lisa V. Cook
Patent Examiner
Art Unit 1642
571-272-0816
10/18/25
/LISA V COOK/Primary Examiner, Art Unit 1642