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 .
Status of the Claims
Claims 1-4 are pending and examined herein.
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed in parent Application No. CN 202311846546.4, filed on December 29, 2023.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Should applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d) prior to declaration of an interference, a certified English translation of the foreign application must be submitted in reply to this action. 37 CFR 41.154(b) and 41.202(e). Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Information Disclosure Statement
No Information Disclosure Statement has been filed in the present application.
Claim Interpretation
Claims 1-3 recite biomarkers “for severity of ischemic stroke.” For purposes of examination, the phrase “for severity of ischemic stroke” is interpreted as reciting the intended purpose or use of the claimed biomarkers. The body of the claims defines the claimed subject matter by reciting the respective protein markers, small molecule metabolite markers, and lipid metabolite markers. The recitation “for severity of ischemic stroke” does not further structurally distinguish the recited markers. Where the body of a claim fully and intrinsically sets forth the limitations of the claimed invention and the preamble merely states the purpose or intended use of the invention, the preamble does not constitute an additional limitation of the claim. See MPEP § 2111.02.
The transitional phrase “comprising” is interpreted as open-ended. Accordingly, the claims do not exclude the presence of additional, unrecited components; however, each expressly recited component remains a limitation of the respective claim.
Claim Objections
Claims 2 and 3 are objected to because of informalities. Claims 2 and 3 recite “ischemic strokeaccording to claim 1,” wherein the words “stroke” and “according” are improperly joined. Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 2 and 3 are rejected under 35 U.S.C. 112(a) because the specification, while being enabling for certain aspects of the claimed invention, does not reasonably enable a person skilled in the art to make and use the full scope of the claimed invention without undue experimentation.
Claim 2 depends from claim 1 and further recites a specifically identified set of small-molecule metabolite markers as biomarkers for severity of ischemic stroke.
Claim 3 depends from claim 1 and further recites a specifically identified set of lipid metabolite markers as biomarkers for severity of ischemic stroke.
The specification describes enrolling ischemic-stroke patients, grouping the patients according to disease severity using National Institutes of Health Stroke Scale (NIHSS) scores, obtaining plasma samples, performing LC-MS/MS analysis, processing the resulting data, and applying a random-forest machine-learning classifier to identify molecules having predictive importance. See, e.g., Specification paragraphs [0028]-[0042] and [0043]-[0056]. The specification therefore provides substantial direction regarding the discovery methodology by which the recited small-molecule and lipid markers were identified.
However, the disclosure provides comparatively limited guidance or experimental evidence establishing that the specifically recited molecules, individually or collectively as the claimed sets, reliably function as biomarkers of ischemic-stroke severity. In particular, the disclosure does not describe independent validation of the claimed biomarker signatures in an external patient cohort, targeted analytical validation of the specifically recited markers, or sufficient confirmatory testing establishing that the identified molecules reproducibly correspond to ischemic-stroke severity. Rather, the recited molecules are identified as potential biomarkers following high-throughput molecular analysis and machine-learning feature selection.
The need for further experimentation is particularly significant because the claimed sets comprise chemically and biologically heterogeneous molecules. Examination of the recited compounds indicates that the sets include endogenous biological molecules as well as compounds reported in the art as pharmaceutical agents or metabolites, synthetic compounds, chemical/reaction components, and other molecular species having substantially different known biological origins or uses. For example, claim 2 recites 1R-cis-3,3,5-Trimethylcyclohexyl ester 5-oxo-L-proline (crilvastatin), an HMG-CoA reductase inhibitor known for its cholesterol-lowering activity. Claim 3 recites N-(2-fluoro-ethyl) arachidonoyl amine, a synthetic arachidonoyl amine compound used in research relating to cannabinoid/endocannabinoid activity. These known uses and contexts do not themselves establish their asserted function as biomarkers of ischemic-stroke severity and illustrate the chemically and biologically diverse nature of the recited metabolite markers. The identities and known uses or contexts of the remaining metabolite markers recited in claims 2 and 3 are summarized in Tables 1 and 2 below. The specification does not provide sufficient guidance explaining the relationship between these heterogeneous molecules and ischemic-stroke severity or establishing that each of the specifically recited molecules represents an operative and reproducible biomarker rather than a candidate molecular feature identified during the discovery analysis.
Table 1. Small Molecule Metabolite Markers Recited in Claim 2
Claimed Compound
Common/ Recognized Identity
Known Use/Context
Supporting Reference/Source
Valylleucine
It appears naturally as a breakdown product in animal tissues, including poultry, pork, and other meats. Scientists sometimes track it as a dietary biomarker.
Valylleucine (Val-Leu) | Dipeptide | MedChemExpress
(1S,2R,4As,6aS,6bR,8R,9R,10R,11R,12aR,12bR,14bS)-8,10,11-trihydroxy-9-(hydroxymethyl)-1,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid
madecassic acid
Softener and conditioner
Madecassic Acid | C30H48O6 | CID 73412 - PubChem
1R-cis-3,3,5-Trimethylcyclohexyl ester 5-oxo-L-proline
Crilvastatin
Cholesterol-lowering agent
1R-cis-3,3,5-trimethylcyclohexyl ester5-oxo-L-proline | C14H23NO3 | CID 9859832 - PubChem
Olopatadine n-oxide
An anti-allergic medication by-product
CAS No : 173174-07-7 | Product Name : (Z)-Olopatadine N-Oxide
Tetramethylene sulfoxide
A chemical solvent, reaction reagent, and extraction medium
Tetramethylene sulfoxide | C4H8OS | CID 1128 - PubChem
Phenylacetaldehyde
Perfumes and Scents
Phenylacetaldehyde | C8H8O | CID 998 - PubChem
Pentrinitrol
An antianginal medication
Pentaerythritol | C(CH2OH)4 | CID 8285 - PubChem
13-OxoODE
Used as internal standards to measure lipid levels using mass spectrometry
The Michael addition of thiols to 13-oxo-octadecadienoate (13-oxo-ODE) with implications for LC-MS analysis of glutathione conjugation - ScienceDirect
2-[[(2S)-1-[[(2S)-2-Carboxy-2-hydroxyethyl]amino]-1-oxo-3-phenylpropan-2-yl]amino]-4-phenylbutanoic acid
This compound has been identified in human blood as reported by (PMID: 31557052) It is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives
(2S)-2-[[(2S)-1-[[(2S)-2-carboxypropyl]amino]-1-oxo-3-(4-phenylphenyl)propan-2-yl]amino]-4-phenylbutanoic acid | C29H32N2O5 | CID 56683924 - PubChem
Beta-Citryl-L-glutamic acid
β-citrylglutamate
An endogenous acidic dipeptide found naturally in the central nervous system, particularly in developing mammalian brains
β-Citryl-L-glutamate acts as an iron carrier to activate aconitase activity - PubMed
Desmethylmianserin
An active metabolite (a substance formed when the body breaks down a drug) of the tetracyclic antidepressant
Pharmacological aspects of mianserin - PubMed
N,N-Didesmethyltramadol
is an opioid derivative which is one of two active metabolites of the opioid analgesic medication tramadol
Desmetramadol Has the Safety and Analgesic Profile of Tramadol Without Its Metabolic Liabilities: Consecutive Randomized, Double-Blind, Placebo-and Active Comparator-Controlled Trials - PMC
Triethylene glycol dimethacrylate
A thinning agent and cross-linking component in dental composites, plastics, and adhesives
Triethylene Glycol Dimethacrylate (TEGDMA) Monomer | Polysciences
Uracil mustard
An oral alkylating chemotherapy drug
Uracil Mustard | C8H11Cl2N3O2 | CID 6194 - PubChem
Table 2. Lipid Metabolite Markers Recited in Claim 3
Claimed Compound
Common/Recognized Identity
Known Use/Context
Supporting Reference/Source
2-eicosyl-3-hydroxy-34-carboxy-tetratriacontanoic acid,
dicarboxylic mycolic acid
Mycolic acids are unique structural hallmarks of pathogenic bacteria like Mycobacterium tuberculosis. main relevance and uses involving humans are within medical diagnostics, drug development, and immunological research.
LIPID MAPS
3beta-hydroxy-4beta-methyl-5alpha-cholest-7-ene-4alpha-carboxylic acid
natural chemical intermediate used by cells to build sterols and steroids
Gene Set - 3-beta-Hydroxy-4-beta-methyl-5-alpha-cholest-7-ene-4-alpha-carboxylate
6-pentadecyl salicylic acid
6SA
primarily used in scientific research as an experimental compound studied for its potential anti-cancer, anti-inflammatory, and immune-boosting properties
Anacardic 6-pentadecyl salicylic acid induces apoptosis in breast cancer tumor cells, immunostimulation in the host and decreases blood toxic effects of taxol in an animal model - PubMed
AC2SGL(16:0/28:0(2Me[S],4Me[S],6Me[S],8Me[R],10Me[R],11OH))
specialized diacylated sulfoglycolipid
It is primarily used in biomedical research regarding tuberculosis (TB) immunology, diagnostics, and vaccine design
Diacylated sulfoglycolipids are novel mycobacterial antigens stimulating CD1-restricted T cells during infection with Mycobacterium tuberculosis - PubMed
Am-PE(16:0/20:5(5Z,8Z,11Z,14Z,17Z))
An Amadori-glycated phosphatidylethanolamine that serves as an endogenous lipid metabolite and potential biomarker for early non-enzymatic glycation
Human Metabolome Database: Showing metabocard for PE(16:0/20:5(5Z,8Z,11Z,14Z,17Z)) (HMDB0008939)
Am-PE(18:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z))
functioning as a structural component of cell membranes and a participant in lipid signaling and metabolism in humans.
Human Metabolome Database: Showing metabocard for PE(18:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) (HMDB0009012)
Artonin P
used as a laboratory research chemical to study its potential anticancer (cytotoxic) and antioxidant properties
Artonin E induces p53-independent G1 cell cycle arrest and apoptosis through ROS-mediated mitochondrial pathway and livin suppression in MCF-7 cells - PMC
CL(1'-[16:0/18:0],3'-[16:0/16:0])
Cardiolipin
It functions naturally as a structural component of mitochondrial membranes in human cells.
Human Metabolome Database: Showing metabocard for CL(16:0/18:1(9Z)/18:1(9Z)/16:0) (HMDB0056661)
DG(21:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/0:0)[iso2]
Diacylglycerol
A specific diacylglycerol (DG) lipid molecule used primarily as a reference and biomarker in lipidomics research and metabolomics studies.
Comparative Metabolomics Reveals Phosphine-Induced Metabolic Disruptions in Planococcus citri (Risso) - PMC
ethyl 2E,4Z-decadienoate
pear ester
Flavorings and fragrances
Ethyl 2,4-decadienoate, (2E,4Z)- | C12H20O2 | CID 5281162 - PubChem
LacCer(d18:1/18:1(9Z))
lactosylceramide
It helps modulate cell membrane fluidity
LacCer(d18:1/18:1(9Z)) | C48H89NO13 | CID 53480999 - PubChem
LacCer(d18:1/22:0)
lactosylceramide
A research reagent to study cell signaling, membrane dynamics, and lipid metabolism
Bovine Metabolome Database: Showing metabocard for Lactosylceramide (d18:1/22:0) (BMDB0011594)
lanosteryloleate
A precursor for all animal and fungal steroids, including cholesterol
Lanosterol | C30H50O | CID 246983 - PubChem
N-(2-fluoro-ethyl) arachidonoyl amine
A synthetic chemical copy of anandamide, a natural signaling molecule in the body
Arachidonoyl-2'-Fluoroethylamide (2'-fluoro AEA, 2'-fluoro Anandamide, CAS Number: 166100-37-4) | Cayman Chemical
PC(O-20:0/19:1(9Z))
A glycerophospholipid metabolite used primarily as a structural component of cell membranes and as a biomarker in lipidomics and metabolomics research.
Dynamic Changes of Plasma Metabolome in Response to Severe Feed Restriction in Pregnant Ewes - PMC
PI(O-20:0/0:0), PIM1(16:0/18:0)
A biomarker in lipidomics research and as structural components of cell membranes
Human Metabolome Database: Showing metabocard for PE(20:0/20:0) (HMDB0009229)
PS(14:1(9Z)/18:3(6Z,9Z,12Z))
A structural building block in cell membranes
Human Metabolome Database: Showing metabocard for PS(14:1(9Z)/18:3(6Z,9Z,12Z)) (HMDB0112308)
Sitostanyl-22:0
A plant-based compound used primarily to lower blood cholesterol levels and reduce the risk of heart disease
Sitostanol administered in lecithin micelles potently reduces cholesterol absorption in humans - PubMed
The state of the art further demonstrates the distinction between discovery of candidate biomarker signatures using non-targeted, high-throughput analysis and validation of those signatures for diagnostic application. Diaz-Uriarte et al., Ten quick tips for biomarker discovery and validation analyses using machine learning, PLOS Computational Biology 18(8):e1010357 (2022), explains that biomarker signatures obtained using non-targeted, high-throughput measurement approaches generally require further validation, including validation in an external cohort and translation from the original high-throughput measurement approach to a more targeted and sensitive measurement technology, before development into a clinically validated diagnostic test. See Diaz-Uriarte et al., Tip 10.
In determining whether undue experimentation would be required, the factors set forth in In re Wands (858 F.2d 731 737 Fed. Cir. 1988) have been considered. The claims encompass specifically identified but chemically and biologically heterogeneous sets of small-molecule and lipid markers (breadth of the claims and nature of the invention). The identification and validation of biomarkers associated with disease severity involves an art having a significant degree of biological and analytical unpredictability (state of the prior art and predictability of the art). Although the specification provides substantial direction and working examples concerning patient grouping, plasma preparation, LC-MS/MS analysis, data processing, and random-forest selection of candidate markers (amount of direction or guidance and existence of working examples), it provides comparatively limited guidance or experimental evidence establishing that the specifically recited molecules, individually or as the claimed sets, reliably function as biomarkers of ischemic-stroke severity.
Consequently, even taking into account the level of skill of one of ordinary skill in the relevant art, practicing the claimed subject matter would require additional experimentation to confirm the identities and reproducibility of the recited analytes and to establish that the specifically recited molecules reliably correspond to ischemic-stroke severity (level of ordinary skill and quantity of experimentation). Such experimentation would require more than merely following the disclosed LC-MS/MS and machine-learning protocols because the skilled artisan would have to determine whether the identified candidate molecules are operative and reproducible biomarkers and establish their relationship to ischemic-stroke severity. The specification does not provide sufficient guidance from which those determinations could be made without undue experimentation.
Accordingly, considering the Wands factors and the evidence as a whole, the amount of experimentation necessary to make and use the full scope of the claimed subject matter would be undue. Claims 2 and 3 are therefore rejected under 35 U.S.C. 112(a) for lack of enablement.
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.
Claim 4 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 4 recites “use of the biomarkers for severity of ischemic stroke according to claim 1 in the preparation of a diagnostic kit for assessing the severity of ischemic stroke”. The claim is indefinite because it merely recites a use of the biomarkers without setting forth active, positive steps delimiting how the recited use is actually practiced. It is unclear whether claim 4 is intended to define a process of preparing a diagnostic kit, a process of using the biomarkers in preparation of a diagnostic kit, or another form of subject matter. Specifically, the claim does not positively recite the steps by which the biomarkers are used in preparation of the diagnostic kit. Accordingly, the scope of the claimed subject matter cannot be determined with reasonable certainty. See MPEP § 2173.05(q) (“Use” Claims); Ex parte Erlich, 3 USPQ2d 1011 (Bd. Pat. App. & Inter. 1986).
Claim 4 is therefore rejected under 35 U.S.C. 112(b).
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.
Claims 1-3 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to a judicial exception (product of nature) without reciting additional elements sufficient to integrate the judicial exception into a practical application or amount to significantly more than the judicial exception.
Regarding claim 1, the claim recites biomarkers comprising the specifically recited protein markers ACOX3, CAP1, GRIPAP1, MAN1A1, UQCRC1, SULT1A2, VNN1, BPGM, COPS8, HLA-DRB3, SPATS2L, VPS26A, and DOCK1. The specification describes identifying the recited proteins from biological samples using proteomic analysis and selecting proteins associated with the severity of ischemic stroke. The recited proteins are nature-based products, and the claim does not recite that the claimed nature-based combination possesses markedly different structural, functional, or other characteristics relative to the naturally occurring counterparts. Accordingly, the claimed nature-based subject matter does not exhibit markedly different characteristics and constitutes a product-of-nature judicial exception. See MPEP §§ 2106.04(b) and 2106.04(c).
The additional recitation that the biomarkers are “for severity of ischemic stroke” states the intended purpose or use of the biomarkers but does not require a particular assay, measurement, diagnostic procedure, treatment, or other practical application of the recited biomarkers. Thus, the claim does not integrate the product-of-nature exception into a practical application.
Regarding claim 2, the claim incorporates all of the limitations of claim 1 and further recites specifically identified small-molecule metabolite markers. To the extent the additionally recited small-molecule markers are nature-based products, the markedly different characteristics analysis applies to the nature-based product limitations. To the extent claim 2 recites non-nature-based components, those components are considered as additional elements in determining whether the claim as a whole integrates the product-of-nature exception into a practical application. The additionally recited molecular markers do not require a particular assay, measurement, diagnostic procedure, treatment, or other practical application of the nature-based biomarkers. Rather, claim 2 further defines the claimed biomarkers by reciting additional molecular markers. Considered individually and as an ordered combination, the additional elements do not integrate the product-of-nature exception into a practical application.
Regarding claim 3, the claim incorporates all of the limitations of claim 1 and further recites specifically identified lipid metabolite markers. To the extent the additionally recited lipid markers are nature-based products, the markedly different characteristics analysis applies to the nature-based product limitations. To the extent claim 3 recites non-nature-based components, those components are considered as additional elements in determining whether the claim as a whole integrates the product-of-nature exception into a practical application. The additionally recited molecular markers do not require a particular assay, measurement, diagnostic procedure, treatment, or other practical application of the nature-based biomarkers. Rather, claim 3 further defines the claimed biomarkers by reciting additional molecular markers. Considered individually and as an ordered combination, the additional elements do not integrate the product-of-nature exception into a practical application.
Claims 1–3 do not recite additional elements that amount to significantly more than the judicial exception. The claims do not positively recite a particular assay, measurement procedure, diagnostic process, treatment step, device, transformation, or other meaningful application of the recited biomarkers. Rather, the claims are directed to the recited biomarkers themselves, with the disease-severity language identifying their intended purpose or use.
Accordingly, claims 1-3 are not eligible for patent protection under 35 U.S.C. 101. See MPEP §§ 2106.04(b), 2106.04(c), 2106.04(d), and 2106.05.
Claim 4 is rejected under 35 U.S.C. 101 because the claimed invention is not directed to one of the four statutory categories of patent-eligible subject matter.
Claim 4 recites “use of the biomarkers” according to claim 1 in preparation of a diagnostic kit for the severity of ischemic stroke. The recited “use” per se does not fall within any of the four statutory categories identified in 35 U.S.C. 101, namely, a process, machine, manufacture, or composition of matter. The claim does not positively recite a process comprising acts or steps for preparing the diagnostic kit, nor does the claim recite a machine, manufacture, or composition of matter.
Accordingly, claim 4 fails to comply with 35 U.S.C. 101 because the claimed subject matter does not fall within one of the statutory categories. See MPEP § 2106.03 and § 2173.05(q).
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.
Claim 1 is rejected under 35 U.S.C. 103 as being unpatentable over Brown et al. (WO 2012/174282 A2) in view of Cheng et al., “Serum Proteomic Analysis by Tandem Mass Tag-Based Quantitative Proteomics in Pediatric Obstructive Sleep Apnea,” Frontiers in Molecular Biosciences, Vol. 9, Article 762336, April 11, 2022; Jiang et al., “Clinical Characterization and Proteomic Profiling of Lean Nonalcoholic Fatty Liver Disease,” Frontiers in Endocrinology, Vol. 14, Article 1171397, November 16, 2023; Comabella et al., “CSF Chitinase 3–Like 2 Is Associated With Long-term Disability Progression in Patients With Progressive Multiple Sclerosis,” Neurology: Neuroimmunology & Neuroinflammation, Vol. 8, No. 6, Article e1082, 2021; Ramesha et al., “Human Plasma Proteomics for Biomarker Discovery for Ischemic Stroke and TIA,” 2020 Society of Vascular and Interventional Neurology Annual Meeting Abstract Book; Kean et al. (WO 2019/079360 A1); Shoemaker et al. (U.S. Patent No. 9,770,170 B2); Schutzer et al. (WO 2011/142827 A2); and Valkirs et al. (US 2003/0109420 A1).
Brown teaches biomarker compositions and methods for characterizing biological and disease states using one or more biomarkers and teaches that biomarkers may provide biosignatures useful for diagnosis, prognosis, assessment of disease stage, and disease progression. Brown further teaches the use of combinations of biomarkers in such biosignatures. Brown identifies CAP1 (Table 20, p. 203), GRIPAP1 (Table 20, p. 201), UQCRC1 (Table 20, p. 201), SULT1A2 (Table 22, p. 204), BPGM (Table 20, p. 202), and HLA-DRB3 (Table 22, p. 204).
Brown therefore teaches the use of multiple protein biomarkers for disease characterization and expressly identifies six of the thirteen protein markers recited in claim 1 but does not expressly disclose a biomarker composition comprising all thirteen claimed protein markers.
Cheng et al. teaches quantitative serum proteomic analysis for identification of proteins associated with disease severity. Cheng reports differential expression of VNN1 and MAN1A1 according to severity, including decreased VNN1 in moderate and severe obstructive sleep apnea and increased MAN1A1 in severe obstructive sleep apnea. See Cheng et al., Abstract, p. 1. Cheng therefore teaches that VNN1 and MAN1A1 were proteins selected through proteomic analysis because their measured levels were associated with disease severity.
Jiang et al. teaches plasma proteomic profiling for identification of diagnostically useful disease-associated proteins and identifies CAP1 and VNN1 among differentially expressed proteins exhibiting diagnostic performance. See Jiang et al., Results, “Plasma Proteomic Profiling” and the table 2 reporting differentially expressed proteins and diagnostic AUC values. Jiang therefore further teaches the selection of CAP1 and VNN1 as plasma biomarkers based on measured diagnostic usefulness.
Comabella et al. teaches proteomic analysis directed to disease progression and identifies SPATS2L among proteins selected for further validation based on an association with long-term disability progression in progressive multiple sclerosis. See Comabella et al., Results, “CSF Proteomic Analysis in the Discovery Cohort of Patients With Progressive MS Identifies Proteins Associated With Long-term Disability Progression,” Table 3. Thus, SPATS2L was not merely identified as a known protein but was specifically selected in a proteomic biomarker study based on an observed disease-related association. Comabella does not establish SPATS2L as a validated prognostic biomarker, as SPATS2L could not be detected in the independent validation cohort.
Ramesha et al. teaches plasma proteomic analysis of subjects comprising patients having acute ischemic stroke, TIA, and stroke mimics for identification of plasma proteins and development of diagnostic biomarker panels. Ramesha identifies SPATS2L among the plasma proteins identified by the analysis, specifically identifying SPATS2L among proteins having the highest levels in stroke mimics. Ramesha further teaches that plasma proteomics can identify novel biomarkers and facilitate development of biomarker panels for differentiating relevant clinical conditions. See Ramesha et al., “Human Plasma Proteomics for Biomarker Discovery for Ischemic Stroke and TIA,” 2020 Society of Vascular and Interventional Neurology Annual Meeting Abstract Book, Results.
Kean teaches COPS8 (Table 3, p. 168) and VPS26A (Table 3, p. 240) in its analysis of healthy and diseased tissues. In particular, Kean identifies COPS8 and VPS26A among genes identified in its cell and pathway analyses. Kean therefore teaches COPS8 and VPS26A, which are not expressly disclosed as part of the combination taught by Brown.
Shoemaker teaches analysis of biological samples using protein markers for diagnosing, characterizing, and/or monitoring disease and further teaches ACOX3 (Appendix C, col. 746). Shoemaker therefore teaches ACOX3, which is not expressly disclosed as part of the combination taught by Brown.
Schutzer teaches biological markers useful for diagnosis of disease and identifies DOCK1 (Table 6c, p. 72). Schutzer further teaches the use of combinations of biomarkers in diagnostic signatures. Schutzer therefore teaches DOCK1, which is not expressly disclosed as part of the combination taught by Brown.
Accordingly, the cited art collectively teaches each of the protein markers recited in claim 1 and further demonstrates that several of the specifically claimed proteins had already been selected in the art for disease-related biomarker analysis based on diagnostic performance, disease severity, disease progression, or differentiation of clinically related conditions. In particular, Cheng and Jiang teach disease-associated selection of MAN1A1, VNN1, and CAP1; Comabella teaches the selection of SPATS2L for further validation based on an observed association with disability progression; and Ramesha identifies SPATS2L in a plasma proteomic study directed to ischemic stroke, TIA, and stroke mimics.
Valkirs teaches the use of combinations of markers for disease diagnosis and evaluation and recognizes advantages associated with multimarker analysis, including increased predictive value and improved risk stratification relative to reliance on an individual marker. See, e.g., Valkirs at paragraphs [0017], [0031], [0107], and [0184]. Brown similarly teaches that combinations of biomarkers may form biosignatures useful for characterizing disease, including disease stage and disease progression.
Therefore, one of ordinary skill in the art, seeking to develop or improve a biomarker composition for disease characterization, would have been motivated to consider additional disease-associated protein biomarkers identified through proteomic and diagnostic studies and incorporate such markers into the multimarker biomarker composition taught by Brown. In particular, the prior art provides a reason to select protein markers based on demonstrated association with diagnostic performance, severity, progression, or other disease-related biological information, rather than selecting markers solely because they were known proteins.
One of ordinary skill in the art would further have been motivated to combine such selected biomarkers because Brown and Valkirs teach that disease characterization may be performed using combinations or panels of biomarkers and that the use of multiple markers can provide additional predictive and risk-stratification information relative to reliance on individual markers. Thus, the reason for combining the teachings of the references is not merely that the individual proteins were independently known, but that the art taught both selection of disease-associated biomarkers and the recognized benefit of incorporating multiple selected biomarkers into a multimarker analysis.
The skilled artisan would have had a reasonable expectation of successfully preparing and analyzing such a multimarker composition because the cited references demonstrate established proteomic and biomarker-analysis techniques for detecting the recited types of proteins in biological samples and for evaluating multiple biomarkers together. The proposed combination would have employed the respective protein markers according to their known biomarker function using conventional detection and analysis techniques, and nothing in the cited art indicates that inclusion of the additional selected markers would have prevented detection or analysis of the other markers.
Furthermore, because claim 1 is directed to the biomarkers themselves and the phrase “for severity of ischemic stroke” is interpreted as stating the intended use or purpose of the recited biomarker composition, the prior art need not teach that the identical thirteen-marker combination had already been demonstrated to assess ischemic-stroke severity. Rather, the relevant inquiry is whether one of ordinary skill in the art would have had reason to select and combine the recited protein biomarkers with a reasonable expectation of obtaining and analyzing the claimed biomarker composition. For the reasons discussed above, the combined teachings of Brown, Cheng, Jiang, Comabella, Ramesha, Kean, Shoemaker, Schutzer, and Valkirs provide such a reason.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the biomarker composition of Brown to further include ACOX3, MAN1A1, VNN1, COPS8, SPATS2L, VPS26A, and DOCK1, as taught by the secondary references, in order to obtain a multimarker composition incorporating additional disease-associated protein biomarkers and thereby obtain the recognized benefits of multimarker biomarker analysis taught by Brown and Valkirs.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over the references applied to claim 1 above, further in view of Larner (US 2017/0176460 A1).
The references applied to claim 1 teach or suggest the recited biomarker composition for the reasons set forth above. Claim 4 further recites the use of the biomarkers according to claim 1 in the preparation of a diagnostic kit for assessing the severity of ischemic stroke.
Valkirs teaches kits for determining the diagnosis or prognosis of a patient, comprising devices and reagents for measuring one or more marker levels in a patient sample and instructions for performing the assay. Valkirs further teaches that such kits may contain means for converting marker levels to a diagnosis or prognosis. See Valkirs, paragraphs [0038] and [0110].
Larner teaches biomarker assays and diagnostic kits for detecting biomarkers associated with neurological injury, including the use of protein-biomarker detection reagents and immunoassay techniques. Larner further identifies ischemic stroke among neurological conditions contemplated by its disclosure (¶ 0005).
One of ordinary skill in the art, seeking to implement the multimarker biomarker composition taught by the references applied to claim 1, would have been motivated to employ the diagnostic-kit teachings of Valkirs in view of Larner because Valkirs provides an established format for measuring biomarkers and using measured levels for diagnosis or prognosis, while Larner demonstrates the applicability of protein-biomarker detection assays and kits in the neurological-injury field. The proposed modification would have provided a practical means for detecting and analyzing the selected biomarkers in biological samples using known diagnostic reagents and assay techniques.
The skilled artisan would have had a reasonable expectation of successfully preparing such a kit because the cited references teach established biomarker-detection reagents and assay techniques, and the proposed modification would have involved applying those techniques to the biomarker composition taught by the references applied to claim 1 for their known purpose.
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to employ the biomarker composition taught by the references applied to claim 1 in the preparation of a diagnostic kit according to the teachings of Valkirs and Larner.
Conclusion
For all the reasons discussed above, claims 1-4 are rejected and therefore no claims are allowed.
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/U.S./Examiner, Art Unit 1677 /BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 September 16, 2026
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