COMPOSITIONS, METHODS AND SYSTEMS FOR PROTEIN CORONA ANALYSIS FROM BIOFLUIDS AND USES THEREOF
This disclosure provides methods and compositions for biomolecule corona analysis of biofluids. A biofluid may be contacted with a nanoparticle to form a biomolecule corona, and the composition of the resulting corona may be analyzed. Also provided are methods of preparing a biofluid for corona analysis by serial interrogation.
The present application is a continuation of International Patent Application No. PCT/US2020/024426, filed Mar. 24, 2020, which claims the benefit of U.S. Provisional patent Application No. 62/824,279, filed Mar. 26, 2019, and U.S. Provisional Patent Application No. 62/824,284, filed Mar. 26, 2019, each of which is herein incorporated by reference in its entirety for all purposes.
BACKGROUNDBiofluids contain a wide variety of proteins whose presence and concentrations may be indicative of subject health status. High abundance proteins and other proteins may overshadow the signal of an assay. Protein coronas can form on particles when they are exposed to biological fluids containing proteins. Most work on protein coronas has been performed on fluid from the blood stream (plasma or serum). The interaction of diverse biofluids with particles is largely unknown.
Fractionation may be used to reduce the signal of high abundance proteins when assaying a biological fluid. Currently, various fractionation methods exist, which facilitate the isolation and extraction of proteins. These methods allow for different profiles of proteins in assays to be detected. However, analysis of more diverse proteomics remains desired.
SUMMARYIn various aspects, the present disclosure provides a method of serially interrogating a sample, the method comprising: a) contacting the sample to a first particle type and incubating the first particle type with the sample to form a first biomolecule corona, wherein the first biomolecule corona forms upon incubation of the first particle type with the sample and wherein the first biomolecule corona comprises a protein; b) separating the first particle type comprising the first biomolecule corona from the sample; c) contacting the sample to a second particle type and incubating the second particle type with the sample to form a second biomolecule corona, wherein the second biomolecule corona forms upon incubation of the second particle type with the sample, wherein the second biomolecule corona comprises a protein, and further wherein (i) the first particle type and the second particle type are a same particle type or (ii) the first particle type and the second particle type are different; d) separating the second particle type comprising the second biomolecule corona from the sample; e) assaying the first biomolecule corona and the second biomolecule corona to determine a composition and concentration of a plurality of proteins in the sample based on the assayed first biomolecule corona and the second biomolecule corona.
In some aspects, upon the incubating the first particle type with the sample to form the first biomolecule corona, the dynamic range of the plurality of proteins in the first biomolecule corona is compressed relative to a dynamic range of a plurality of proteins in the sample, as measured by a total protein analysis method.
In some aspects, the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio of: a) a signal produced by a higher abundance protein of the plurality of proteins in the first biomolecule corona; and b) a signal produced by a lower abundance protein of the plurality of proteins in the first biomolecule corona. In some aspects, the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio of a concentration of the highest abundance protein to a concentration of the lowest abundance protein in the plurality of proteins in the first biomolecule corona. In some aspects, the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio of a top decile of proteins to a bottom decile of proteins in the plurality of proteins in the first biomolecule corona. In some aspects, the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio comprising a span of the interquartile range of proteins in the plurality of proteins in the first biomolecule corona. In some aspects, the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio comprising a slope of fitted data in a plot of all concentrations of proteins in the plurality of proteins in the first biomolecule corona versus known concentrations of the same proteins in the sample.
In some aspects, the known concentrations of the same proteins in the sample are obtained from a database. In some aspects, the dynamic range of a plurality of proteins in the sample is a second ratio of: a) a signal produced by a higher abundance protein of the plurality of proteins in the sample, as measured by a total protein analysis method; and b) a signal produced by a lower abundance protein of the plurality of proteins in the sample, as measured by a total protein analysis method. In some aspects, the dynamic range of the plurality of proteins in the sample, as measured by a total protein analysis method, is a second ratio of a concentration of the highest abundance protein to a concentration of the lowest abundance protein in the plurality of proteins in the sample. In some aspects, the dynamic range of the plurality of proteins in the sample, as measured by a total protein analysis method, is a second ratio of a top decile of proteins to a bottom decile of proteins in the plurality of proteins in the sample.
In some aspects, the dynamic range of the plurality of proteins in the sample, as measured by a total protein analysis method, is a second ratio comprising a span of the interquartile range of proteins in the plurality of proteins in the sample. In some aspects, the dynamic range of the plurality of proteins in the sample, as measured by a total protein analysis method, is a second ratio comprising a slope of fitted data in a plot of all concentrations of proteins in the plurality of proteins in the sample versus known concentrations of the same proteins in the sample. In some aspects, the known concentrations of the same proteins in the sample are obtained from a database. In some aspects, the compressing the dynamic range comprises a decreased first ratio relative to the second ratio. In further aspects, the decreased first ratio is at least 1.1-fold, at least 1.2-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 5-fold, or at least 10-fold less than the second ratio.
In some aspects, the method further comprises: determining the composition and concentration of a plurality of proteins in the second biomolecule corona. In some aspects, the determining the composition and concentration of the plurality of proteins in the first biomolecule corona or determining the composition and concentration of the plurality of proteins in the second biomolecule corona comprises performing mass spectrometry. In some aspects, the method further comprising repeating step a), b), and e) with one or more additional particle types to form one or more additional biomolecule coronas. In some aspects, the one or more additional particle types are the same as the first particle type or the second particle type. In some aspects, the one or more additional particle types are different from the first particle type, the second particle type, or a combination thereof.
In some aspects, the one or more additional biomolecule coronas comprise proteins from the sample. In some aspects, the first biomolecule corona, the second biomolecule corona, the one or more additional biomolecule coronas, or any combination thereof comprises at least 100 distinct proteins. In some aspects, the first biomolecule corona, the second biomolecule corona, the one or more additional biomolecule coronas, or any combination thereof comprises at least 200 distinct proteins, at least 300 distinct proteins, at least 400 distinct proteins, at least 500 distinct proteins, at least 1000 distinct proteins, at least 2000 distinct proteins, or at least 5000 distinct proteins.
In some aspects, the first biomolecule corona, the second biomolecule corona, the one or more additional biomolecule coronas, or any combination thereof comprises a different composition of proteins, a different concentration of a subset of proteins, or a combination thereof. In some aspects, upon incubating the one or more additional particle types with the sample to form one or more additional biomolecule coronas, a dynamic range of a plurality of proteins in the one or more additional biomolecule coronas is compressed relative to a dynamic range of a plurality of proteins in the sample, as measured by a total protein analysis method.
In some aspects, the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio of: a) a signal produced by a higher abundance protein of the plurality of proteins in the one or more additional biomolecule coronas; and b) a signal produced by a lower abundance protein of the plurality of proteins in the one or more additional biomolecule coronas.
In some aspects, the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio of a concentration of the highest abundance protein to a concentration of the lowest abundance protein in the plurality of proteins in the one or more biomolecule coronas. In some aspects, the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio of a top decile of proteins to a bottom decile of proteins in the plurality of proteins in the one or more biomolecule coronas. In some aspects, the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio comprising a span of the interquartile range of proteins in the plurality of proteins in the one or more biomolecule coronas.
In some aspects, the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio comprising a slope of fitted data in a plot of all concentrations of proteins in the plurality of proteins in the one or more biomolecule coronas versus known concentrations of the same proteins in the sample. In some aspects, the known concentrations of the same proteins in the sample are obtained from a database. In some aspects, the compressing the dynamic range comprises a decreased additional ratio relative to the second ratio. In further aspects, the decreased first ratio is at least 1.1-fold, at least 1.2-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 5-fold, or at least 10-fold less than the second ratio.
In some aspects, the total protein analysis method comprises direct quantification of the plurality of proteins in the sample by mass spectrometry, gel electrophoresis, or liquid chromatography. In some aspects, the sample comprises a sample volume of no more than about 1000 μL, no more than about 900 μL, no more than about 800 μL, no more than about 700 μL, no more than about 600 μL, no more than about 500 μL, no more than about 400 μL, no more than about 300 μL, no more than about 200 μL, no more than about 100 μL, no more than about 50 μL, no more than about 20 μL, no more than about 10 μL, no more than about 5 μL, no more than about 2 μL, or no more than about 1 μL.
In some aspects, the sample comprises a biological sample. In some aspects, the biological sample comprises a biofluid. In some aspects, the biofluid is selected from the group consisting of plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, fluidized solids, fine needle aspiration samples, tissue homogenates, and cell culture samples. In some aspects, the biofluid is plasma or serum. In some aspects, the biofluid is cerebrospinal fluid. In some aspects, the first particle type, the second particle type, the one or more additional particle types, or any combination thereof are selected from TABLE 1.
In some aspects, the method further comprises removing high abundance proteins from the sample by depleting or fractioning the sample prior to step a). In some aspects, the one or more additional biomolecule coronas comprises a protein. In some aspects, the first biomolecule corona, the second biomolecule corona, the one or more additional biomolecule coronas, or any combination thereof comprises a lipid, a nucleic acid, a polysaccharide, or any combination thereof.
In some aspects, the first particle type, the second particle type, or the one or more additional particle types differ by at least one physicochemical properties. In some aspects, the first particle type and the second particle type differ by at least one physicochemical property and wherein the first biomolecule corona comprises a distinct but overlapping set of proteins relative to the second biomolecule corona. In some aspects, the composition of the plurality of proteins and the concentration of a protein of the plurality of proteins is determined based on the distinct but overlapping set of proteins in the first biomolecule corona and the second biomolecule corona.
In some aspects, the first particle type, the second particle type, the one or more additional particle types, or any combination thereof is selected from the group consisting of a nanoparticle, a microparticle, a micelle, a liposome, an iron oxide particle, a graphene particle, a silica particle, a protein-based particle, a polystyrene particle, a silver particle, a gold particle, a metal particle, a quantum dot, a superparamagnetic particle, or any combination thereof. In some aspects, the first particle type, the second particle type, the one or more additional particle types, or any combination thereof is a superparamagnetic particle.
In some aspects, the first particle type, the second particle type, the one or more additional particle types, or any combination thereof is selected from TABLE 1. In some aspects, the first particle type and the second particle type are the same particle type and wherein at least 70%, at least 80%, at least 90%, or at least 95% of proteins assayed in the first biomolecule corona and the second biomolecule corona are the same. In some aspects, the first particle type and the second particle type are different and wherein no more than 70%, no more than 80%, no more than 90%, or no more than 95% of proteins assayed in the first biomolecule corona and the second biomolecule corona are the same.
In various aspects, the present disclosure provides a high throughput method of analyzing a plurality of biofluids, the method comprising: a) contacting a first biofluid and a second biofluid of the plurality of biofluids with a particle type; b) in a first volume, separating the particle type from a first biofluid of the plurality of biofluids and determining the composition and concentration of a plurality of proteins in a first biomolecule corona corresponding to the particle type; and c) in a second volume, separating the particle type from a second biofluid of the plurality of biofluids and determining the composition and concentration of a plurality of proteins in a second biomolecule corona corresponding to the particle type, wherein the first biofluid and the second biofluid are different biofluids.
In some aspects, a biofluid of the plurality of biofluids is selected from the group consisting of plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, fluidized solids, fine needle aspiration samples, tissue homogenates, and cell culture samples. In further aspects, the biofluid is plasma or serum. In other aspects, the biofluid is cerebrospinal fluid.
In some aspects, a biomolecule corona forms upon contacting the particle type with the sample and wherein the first biomolecule corona comprises a protein. In some aspects, the biomolecule corona comprises a lipid, a nucleic acid, a polysaccharide, or any combination thereof. In some aspects, the method further comprises removing high abundance proteins from the sample by depleting or fractioning the sample prior to step a).
In some aspects, the particle type is selected from the group consisting of a nanoparticle, a microparticle, a micelle, a liposome, an iron oxide particle, a graphene particle, a silica particle, a protein-based particle, a polystyrene particle, a silver particle, a gold particle, a metal particle, a quantum dot, a superparamagnetic particle, or any combination thereof. In some aspects, the particle type is a superparamagnetic particle. In some aspects, the particle type is selected from TABLE 1. In some aspects, the separating comprises magnetic separation, filtration, gravitational separation, or centrifugation. In some aspects, the contacting occurs in vitro. In some aspects, the method further comprises identifying a biological state of the biofluid processing the composition and concentration of the plurality of proteins in the biomolecule corona using a trained algorithm to identify the biological state.
In some aspects, the biofluid is isolated from a subject. In further aspects, the subject is a human. In other aspects, the subject is a non-human animal. In some aspects, the subject has a condition. In further aspects, the condition is a disease state. In still further aspects, the disease state is cancer. In still further aspects, the cancer is prostate cancer, colorectal cancer, lung cancer, or breast cancer. In other aspects, the disease state is Alzheimer's disease. In some aspects, the separating comprises magnetic separation, column-based separation, filtration, spin column-based separation, centrifugation, ultracentrifugation, density or gradient-based centrifugation, gravitational separation, or any combination thereof.
In various aspects, the present disclosure provides a method of analyzing a biofluid, the method comprising: a) contacting a biofluid in a biofluid collection tube with a particle type, wherein the blood collection tube comprises a stabilization reagent, wherein the stabilization reagent stabilizes cell-free nucleic acid molecules in the biofluid; and b) incubating the biofluid and the particle type in the biofluid collection tube to permit binding of proteins of the biofluid to the particle type, thereby forming a biomolecule corona comprising proteins bound to the particle type, wherein the biomolecule corona comprises a population of proteins that is also detected when the particle type is incubated in the biofluid when stored in EDTA and permitted to form a control biomolecule corona; and wherein the biofluid and the particle type are incubated in the biofluid collection tube at from about 20° C. to about 35° C. and wherein 50% or more of the population of proteins of the biomolecule corona is also detectable in the control biomolecule corona.
In some aspects, 60% or more, 70% or more, 80% or more, or 90% or more of the population of proteins of the biomolecule corona is also detectable in the control biomolecule corona. In some aspects, at least a subset of the population of proteins is detected at a higher abundance than when the particle type is incubated in the biofluid when stored in EDTA. In some aspects, at least 5% of the population of proteins is detected at a higher abundance than when the particle type is incubated in the biofluid when stored in EDTA. In some aspects, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or 100% of the population of proteins is detected at a higher abundance than when the particle type is incubated in the biofluid when stored in EDTA.
In some aspects, the method further comprises assaying the proteins in the biomolecule corona at a lower limit of detection than when the particle type is incubated in the biofluid when stored in EDTA. In some aspects, the incubating comprises incubating at room temperature. In some aspects, the incubating comprises incubating for up to 14 days, up to 13 days, up to 12 days, up to 11 days, up to 10 days, up to 9 days, up to 8 days, up to 7 days, up to 6 days, up to 5 days, up to 4 days, or up to 3 days. In some aspects, the incubating comprises incubating for up to 14 days. In some aspects, the biomolecule corona comprises a unique protein that is absent from the control biomolecule corona. In some aspects, the biomolecule corona comprises at least 100 distinct proteins, at least 200 distinct proteins, at least 300 distinct proteins, at least 400 distinct proteins, at least 500 distinct proteins, at least 1000 distinct proteins, at least 2000 distinct proteins, or at least 5000 distinct proteins. In some aspects, the particle type binds 100 or more distinct proteins.
In further aspects, the biofluid comprises plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, fluidized solids, fine needle aspiration samples, tissue homogenates, or cell culture samples. In further aspects, the biofluid is plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, a fluid from swabbing, a bronchial aspirant, a fluidized solid, a fine needle aspiration sample, a tissue homogenate, or a cell culture sample.
In some aspects, the method further comprises separating the particle type from the biofluid. In some aspects, the separating comprises magnetic separation, filtration, gravitational separation, or centrifugation. In some aspects, the method further comprises determining the composition and concentration of proteins in the biomolecule corona. In some aspects, the method further comprises determining the composition and concentration of proteins in the control biomolecule corona. In some aspects, the determining the composition and concentration of proteins comprises mass spectrometry, gel electrophoresis, or liquid chromatography.
In some aspects, the stabilization reagent comprises a metabolic inhibitor, a protease inhibitor, a phosphatase inhibitor, a nuclease inhibitor, a preservative agent, or a combination thereof. In some aspects, the metabolic inhibitor comprises glyceraldehyde, dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, 1,3-bisphosphoglycerate, 3-phosphoglycerate, 2-phosphoglycerate, phosphoenolpyruvate, pyruvate and glycerate dihydroxyacetate, sodium fluoride, or K2C2O4. In some aspects, the protease inhibitor comprises antipain, aprotinin, chymostatin, elastatinal, phenylmethylsulfonyl fluoride (PMSF), APMSF, TLCK, TPCK, leupeptin, soybean trypsin inhibitor, indoleacetic acid (IAA), E-64, EDTA, pepstatin, VdLPFFVdL, 1,10-phenanthroline, phosphoramodon, amastatin, bestatin, diprotin A, diprotin B, alpha-2-macroglobulin, lima bean trypsin inhibitor, pancreatic protease inhibitor, or egg white ovostatin egg white cystatin.
In some aspects, the phosphatase inhibitor comprises calyculin A, nodularin, NIPP-1, microcystin LR, tautomycin, okadaic acid, cantharidin, microcystin LR, okadaic acid, fostriecin, tautomycin, cantharidin, endothall, nodularin, cyclosporin A, FK 506/immunophilin complexes, cypermethrin, deltamethrin, fenvalerate, bpV(phen), dephostatin, mpV(pic) DMHV, or sodium orthovanadate. In some aspects, the nuclease inhibitor comprises diethyl pyrocarbonate, ethanol, aurintricarboxylic acid (ATA), formamide, vanadyl-ribonucleoside complexes, macaloid, ethylenediamine tetraacetic acid (EDTA), proteinase K, heparin, hydroxylamine-oxygen-cupric ion, bentonite, ammonium sulfate, dithiothreitol (DTT), beta-mercaptoethanol, cysteine, dithioerythritol, tris(2-carboxyethyl) phosphene hydrochloride, or a divalent cation such as Mg+2, Mn+2, Zn+2, Fe+2, Ca+2, or Cu+2.
In some aspects, the preservative agent comprises diazolidinyl urea, imidazolidinyl urea, dimethoylol-5,5-dimethylhydantoin, dimethylol urea, 2-bromo-2-nitropropane-1,3-diol, oxazolidines, sodium hydroxymethyl glycinate, 5-hydroxymethoxymethyl-1-1aza-3,7-dioxabicyclo[3.3.0]octane, 5-hydroxymethyl-1-1aza-3,7dioxabicyclo[3.3.0]octane, 5-hydroxypoly[methyleneoxy]methyl-1-1aza-3,7dioxabicyclo[3.3.0]octane, or quaternary adamantine. In some aspects, the biofluid collection tube is a blood collection tube. In some aspects, the particle type is a nanoparticle or a microparticle.
In some aspects, the particle type is selected from the group consisting of a nanoparticle, a microparticle, a micelle, a liposome, an iron oxide particle, a graphene particle, a silica particle, a protein-based particle, a polystyrene particle, a silver particle, a gold particle, a metal particle, a quantum dot, a superparamagnetic particle, and any combination thereof. In some aspects, the particle type is selected from TABLE 1.
In some aspects, the method further comprises contacting the biofluid with one or more additional particle types, incubating the biofluid with the one or more additional particle types to permit binding of proteins of the biofluid to the one or more additional particle type, thereby forming one or more additional biomolecule coronas comprising proteins bound to the one or more additional particle types. In some aspects, the one or more additional particle types binds a population of proteins that is distinct but overlapping with the population of proteins in the biomolecule proteins of the particle type. In some aspects, the contacting the biofluid with the one or more additional particle types occurs after the contacting the biofluid with the particle type.
The present disclosure analyzes the protein corona from the interaction of nanoparticles and diverse fluids such as CSF, urine, tear and saliva. Various biofluids, including CSF, urine, tear and saliva are used to incubate with nanoparticles. The resulted protein coronas were separated and analyzed with mass spectrometry. The present disclosure provides how proteins from diverse biofluids will interact with nanoparticles. The proteins (or biomarkers) identified from these protein corona may be used in the discovery of advanced diagnostic tools as well as therapeutic targets.
In some aspects, the present disclosure provides a method of analyzing of a plurality of biofluids, the method comprising: (a) separately contacting each biofluid of the plurality of biofluids with a nanoparticle; (b) isolating the first nanoparticle and analyzing a first protein corona corresponding to a first biofluid of the plurality of biofluids; and (c) isolating the second nanoparticle and analyzing a second protein corona corresponding to a second biofluid of the plurality of biofluids, wherein step (b) and step (c) occur simultaneously.
In some embodiments, the method further comprises contacting the plurality of biofluids with a third nanoparticle. In some embodiments, the method further comprises contacting the plurality of biofluids with a fourth nanoparticle. In some embodiments, the method further comprises contacting the plurality of biofluids with a fifth nanoparticle. In some embodiments, the first nanoparticle and the second nanoparticle are the same.
In some embodiments, the method further comprises contacting the plurality of biofluids with up to 10 different nanoparticles.
In some embodiments, the nanoparticle is made of a material selected from a lipid, a polymer, a metal, or any combination thereof. In some embodiments, the polymer comprises PS, PLA, PGA, PLGA, or PVP. In some embodiments, the lipid comprises EPC, DOPC, DOPG, or DPPG. In some embodiments, the metal comprises iron oxide, gold, or silver. In some embodiments, the nanoparticle comprises a positive surface charge. In some embodiments, the nanoparticle comprises a negative surface charge. In some embodiments, the nanoparticle comprises a neutral surface charge.
In some embodiments, the nanoparticle comprises a size of 1-400 nm.
In some embodiments, the biofluid comprises plasma, serum, CSF, urine, tear, or saliva.
In some embodiments, the method further comprises comparing the first protein corona to a first control protein corona identified by contacting the first biofluid with the first nanoparticle. In some embodiments, the method further comprises comparing the second protein corona to a second control protein corona identified by contacting the second biofluid with the second nanoparticle.
In some embodiments, the method further comprises correlating the first protein corona to a first biological state. In some embodiments, the method further comprises correlating the second protein corona to a second biological state.
The present disclosure provides methods and systems for analyzing diverse proteomics. As disclosed herein, abundant proteins are first removed by fractionation or by nanoparticle depletion, thereby generating a depleted sample. The depleted sample is then incubated with a nanoparticle, which leads to the formation of a protein corona with high affinity low abundant proteins. The methods and systems disclosed herein provided a diverse protein corona profile, which may be used in the discovery of advanced diagnostic tools as well as therapeutic targets.
In some aspects, the present disclosure provides a method of identifying a biological state of a sample of a subject, the method comprising: incubating the sample with a depletion nanoparticle, thereby generating a depleted sample; incubating the depleted sample with a first nanoparticle to generate a protein corona; generating protein data corresponding to a protein in the protein corona associated with the first nanoparticle; and processing the protein data using a trained algorithm to identify the biological state of the subject.
In some embodiments, incubating the sample with the depletion nanoparticle comprises the incubating the sample with the depletion nanoparticle for at least about 30 minutes and extracting the depletion nanoparticle from the sample. In some embodiments, incubating the sample with the depletion nanoparticle for at least about 30 min and extracting the depletion nanoparticle from the sample removes at least about 80% of high abundance proteins from the sample.
In some embodiments, the method further comprises analyzing a protein corona associated with the depletion nanoparticle. In some embodiments, incubating the sample with the depletion nanoparticle comprises incubating the sample with the depletion nanoparticle for at least about 60 minutes and extracting the depletion nanoparticle from the sample at least two times. In some embodiments, incubating the sample with the depletion nanoparticle for at least about 60 minutes and removing the depletion nanoparticle from the sample at least two times removes 99% of high abundance proteins.
In some embodiments, the depletion nanoparticle comprises at least one different physicochemical property from the first nanoparticle. The different physicochemical property may comprise size, surface charge, or a chemical moiety.
In some embodiments, processing the protein data comprises analyzing the protein corona, analyzing the sample prior to depletion, or analyzing the depleted sample.
In some aspects, the present disclosure provides a method of identifying a biological state of a protein sample from a subject, the method comprising: fractionating the protein sample, thereby generating a fractionated sample comprising a subset of proteins in the protein sample; incubating the depleted sample with a first nanoparticle to generate a protein corona; generating protein data corresponding to a protein of the protein corona associated with the first nanoparticle; and processing the protein data using a trained algorithm to identify the biological state of the subject, wherein fractionating the sample comprises separating high abundance proteins with a method selected from the group consisting of Cohn's method, column chromatograph, ion-exchange chromatography, affinity chromatography, size exclusion chromatography, centrifugation, filtration, ultrafiltration and cryo-precipitation.
In some embodiments, processing the protein data comprises analyzing the protein corona, analyzing the protein sample prior to fractionation, or analyzing the fractionated sample.
In some embodiments for the methods disclosed herein, a concentration of the first nanoparticle in the depleted sample is from 1-50 mg/mL. In some embodiments, generating protein data corresponding to the protein in the protein corona associated with the first nanoparticle comprises determining a concentration of each unique protein in the protein corona and correlating the concentration of each unique protein in the protein corona to the biological state. In some embodiments, processing the protein data using a trained algorithm to identify the biological state of the subject comprises associating the biological state with a biomolecule fingerprint. In some embodiments, the sample is plasma or serum.
In some aspects, the present disclosure provides a method for assaying a biological sample, comprising (a) obtaining a biological sample comprising a plurality of biomolecules, which plurality of biomolecules comprises protein; (b) enriching said biological sample based on one or more features selected from the group consisting of: size, charge, hydrophobicity, structure and affinity, to yield a processed biological sample; (c) generating at least a first subset of biomolecules and a second subset of biomolecules from said processed biological sample of (b) with the aid of one or more nanoparticles, wherein said first subset of biomolecules associates with said one or more nanoparticles and said second subset of biomolecules does not associate with said one or more nanoparticles; and (d) separately conducting one or more assays on at least said first subset of biomolecules or said second subset of biomolecules.
In some embodiments, the method further comprises (e) isolating said first subset of biomolecules from said second subset of biomolecules.
In some embodiments, the one or more assays comprise an assay selected from the group consisting of: mass spectrometry and enzyme-linked immunosorbent assay (ELISA). In some embodiments, the one or more assays comprise mass spectrometry.
In some embodiments, enriching said biological sample comprises fractionation to yield said processed biological sample. In some embodiments, the fractionation comprises separating high abundance proteins with a method selected from the group consisting of Cohn's method, ion-exchange chromatography, affinity chromatography, size exclusion chromatography, centrifugation, filtration, ultrafiltration and cryo-precipitation. In some embodiments, enriching said biological sample to yield said processed biological sample comprises depleting one or more proteins.
In some embodiments, in (b), one or more depletion nanoparticles are used to yield said processed biological sample. In some embodiments, the one or more depletion nanoparticles of (b) are different from said one or more nanoparticles of (c).
In some embodiments, the one or more assays are conducted on said first subset, which assay is ELISA.
In some embodiments, the biological sample is a biofluid selected from the group consisting of: plasma, serum, urine, cerebrospinal fluid, tears, saliva, whole blood, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, pericrevicular fluid, semen, prostatic fluid, sputum, synovial fluid, fecal matter, trabecular fluid, bronchial lavage, fluid from swabbings, and bronchial aspirants.
In some embodiments, the one or more assays yields proteomic data, and further comprising processing said proteomic data to predict a biological state. In some embodiments, processing said proteomic data comprises use of a trained algorithm, which trained algorithm is trained using an independent set of biological samples.
In some embodiments, the first subset of biomolecules associates with said one or more nanoparticles upon incubation with said one or more nanoparticles to form protein coronas.
In some embodiments, the biological sample is depleted prior to (a).
In some embodiments, the first subset of biomolecules and said second subset of biomolecules comprise protein.
INCORPORATION BY REFERENCEAll publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:
Provided herein are compositions of particles that may be incubated with various biological samples. Various particle types, alone or in combination, can be incubated with a wide range of biological samples to analyze the proteins present in said biological sample based on binding to particle surface to form protein coronas. A single particle type may be used to assay the proteins in a particular biological sample or multiple particle types can be used together to assay the proteins in the biological sample. A protein corona analysis may be performed on a biological sample (e.g., a biofluid) by contacting the biological sample with a plurality of particles, incubating the biological sample with the plurality of particles to form a protein corona, separating the particles from the biological sample, and analyzing the protein corona to determine the composition of the protein corona. In some embodiments, analyzing the protein corona is performed using mass spectrometry. Interrogation of a sample with a plurality of particles followed by analysis of the protein corona formed on the plurality of particles may be referred to herein as “protein corona analysis.” A biological sample may be interrogated with one or more particle types. The protein corona of each particle type may be analyzed separately. In some embodiments, the protein corona of one or more particle types may be analyzed in combination.
The present disclosure provides several biological samples that can be assayed using the particles disclosed herein and the methods provided herein. For example, a biological sample may be a biofluid sample such as cerebral spinal fluid (CSF), synovial fluid (SF), urine, plasma, serum, tears, crevicular fluid, semen, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, sweat or saliva. A biofluid may be a fluidized solid, for example a tissue homogenate, or a fluid extracted from a biological sample. A biological sample may be, for example, a tissue sample or a fine needle aspiration (FNA) sample. In some embodiments a biological sample may be a cell culture sample. In some embodiments, a biofluid is a fluidized biological sample. For example, a biofluid may be a fluidized cell culture extract.
Also provided herein are methods of depleting a sample of highly abundant proteins and compositions for doing so. In some embodiments, depletion can comprise using one or more particles to deplete a biological sample (e.g., a biofluid) of highly abundant proteins. Depletion of a sample with particles may include one or more rounds of depletion of the sample with a one or more particle types (e.g., a particle with a unique material composition). In other cases, plasma depletion kits, columns, chromatography, centrifugation, or other systems may be used to deplete a biological sample of highly abundant proteins. Any of these methods of depletion can be followed up by serial interrogation of the sample using the various particle types disclosed herein and corona analysis of said various particle types, as disclosed herein.
Example workflows of the present disclosure are illustrated in
A first example of a workflow is provided in
A second example of a workflow is provided in
A third example of a workflow is provided in
A fourth example of a workflow is provided in
A fifth example of a workflow is provided in
A sixth example of a workflow is provided in
While examples of workflows are provided in
The present disclosure also provides methods and compositions for fractioning a biological sample, such as a biofluid. A biofluid may be separated into fractions by sequentially contacting the fluid or a supernatant of the fluid to different types of particles. A biofluid may be contacted with a first particle type, and the first particle type may be separated from the biological sample (e.g., by centrifugation or magnetic separation) along with any biological molecules (e.g., proteins) bound to the first particle type. The separated first particle type and bound biological molecules may constitute a first fraction. The remaining biofluid (e.g., a supernatant) may be contacted with a second particle type, and the second particle type may be separated from the biological sample along with any biological molecules bound to the second particle type. This process may be repeated with additional particle types, thereby fractioning the biofluid. In some embodiments, a biological sample may be fractionated using a chromatography, centrifugation, precipitation, electrophoresis, or any other method of biochemical separation. After fractioning a sample, the sample may be assayed for proteins using the methods of serial interrogation with various particle types, as disclosed herein.
The particles, compositions, and methods disclosed herein are compatible with various sample collection and stabilization methods and compositions. The protein corona analysis methods provided herein may be performed on a stabilized biological sample. A stabilized biological sample may comprise a biological sample (e.g., a biofluid) that has been treated with a stabilizing reagent (e.g., a preservative). In some embodiments, a biological sample may be treated with a liquid preservative that maintains cellular antigen expression. The stabilizing reagent may be contained within a sample collection container (e.g., a blood collection tube). The stabilized biological sample may be analyzed by protein corona analysis using any of the particles, compositions, or methods disclosed herein. In some embodiments, the stabilized biological sample may be stored unrefrigerated prior to protein corona analysis.
Particle TypesParticle types consistent with the methods disclosed herein can be made from various materials. For example, particle materials consistent with the present disclosure include metals, polymers, magnetic materials, and lipids. Magnetic particles may be iron oxide particles. Examples of metal materials include any one of or any combination of gold, silver, copper, nickel, cobalt, palladium, platinum, iridium, osmium, rhodium, ruthenium, rhenium, vanadium, chromium, manganese, niobium, molybdenum, tungsten, tantalum, iron and cadmium, or any other material described in U.S. Pat. No. 7,749,299. In some embodiments, a particle may be a superparamagnetic iron oxide nanoparticle (SPION).
Examples of polymers include any one of or any combination of polyethylenes, polycarbonates, polyanhydrides, polyhydroxyacids, polypropylfumerates, polycaprolactones, polyamides, polyacetals, polyethers, polyesters, poly(orthoesters), polycyanoacrylates, polyvinyl alcohols, polyurethanes, polyphosphazenes, polyacrylates, polymethacrylates, polycyanoacrylates, polyureas, polystyrenes, or polyamines, a polyalkylene glycol (e.g., polyethylene glycol (PEG)), a polyester (e.g., poly(lactide-co-glycolide) (PLGA), polylactic acid, or polycaprolactone), or a copolymer of two or more polymers, such as a copolymer of a polyalkylene glycol (e.g., PEG) and a polyester (e.g., PLGA). In some embodiments, the polymer is a lipid-terminated polyalkylene glycol and a polyester, or any other material disclosed in U.S. Pat. No. 9,549,901.
Examples of lipids that can be used to form the particles of the present disclosure include cationic, anionic, and neutrally charged lipids. For example, particles can be made of any one of or any combination of dioleoylphosphatidylglycerol (DOPG), diacylphosphatidylcholine, diacylphosphatidylethanolamine, ceramide, sphingomyelin, cephalin, cholesterol, cerebrosides and diacylglycerols, dioleoylphosphatidylcholine (DOPC), dimyristoylphosphatidylcholine (DMPC), and dioleoylphosphatidylserine (DOPS), phosphatidylglycerol, cardiolipin, diacylphosphatidylserine, diacylphosphatidic acid, N-dodecanoyl phosphatidylethanolamines, N-succinyl phosphatidylethanolamines, N-glutarylphosphatidylethanolamines, lysylphosphatidylglycerols, palmitoyloleyolphosphatidylglycerol (POPG), lecithin, lysolecithin, phosphatidylethanolamine, lysophosphatidylethanolamine, dioleoylphosphatidylethanolamine (DOPE), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DMPE), distearoyl-phosphatidyl-ethanolamine (DSPE), palmitoyloleoyl-phosphatidylethanolamine (POPE) palmitoyloleoylphosphatidylcholine (POPC), egg phosphatidylcholine (EPC), distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), palmitoyloleyolphosphatidylglycerol (POPG), 16-O-monomethyl PE, 16-O-dimethyl PE, 18-1-trans PE, palmitoyloleoyl-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-phosphatidyethanolamine (SOPE), phosphatidylserine, phosphatidylinositol, sphingomyelin, cephalin, cardiolipin, phosphatidic acid, cerebrosides, dicetylphosphate, and cholesterol, or any other material listed in U.S. Pat. No. 9,445,994, which is incorporated herein by reference in its entirety.
Examples of particles of the present disclosure are provided in TABLE 1.
A particle of the present disclosure may be synthesized, or a particle of the present disclosure may be purchased from a commercial vendor. For example, particles consistent with the present disclosure may be purchased from commercial vendors including Sigma-Aldrich, Life Technologies, Fisher Biosciences, nanoComposix, Nanopartz, Spherotech, and other commercial vendors. In some embodiments, a particle of the present disclosure may be purchased from a commercial vendor and further modified, coated, or functionalized.
Particles that are consistent with the present disclosure can be made and used in methods of forming protein coronas after incubation in a biofluid at a wide range of sizes. In some embodiments, a particle of the present disclosure may be a nanoparticle. In some embodiments, a nanoparticle of the present disclosure may be from about 10 nm to about 1000 nm in diameter. For example, the nanoparticles disclosed herein can be at least 10 nm, at least 100 nm, at least 200 nm, at least 300 nm, at least 400 nm, at least 500 nm, at least 600 nm, at least 700 nm, at least 800 nm, at least 900 nm, from 10 nm to 50 nm, from 50 nm to 100 nm, from 100 nm to 150 nm, from 150 nm to 200 nm, from 200 nm to 250 nm, from 250 nm to 300 nm, from 300 nm to 350 nm, from 350 nm to 400 nm, from 400 nm to 450 nm, from 450 nm to 500 nm, from 500 nm to 550 nm, from 550 nm to 600 nm, from 600 nm to 650 nm, from 650 nm to 700 nm, from 700 nm to 750 nm, from 750 nm to 800 nm, from 800 nm to 850 nm, from 850 nm to 900 nm, from 100 nm to 300 nm, from 150 nm to 350 nm, from 200 nm to 400 nm, from 250 nm to 450 nm, from 300 nm to 500 nm, from 350 nm to 550 nm, from 400 nm to 600 nm, from 450 nm to 650 nm, from 500 nm to 700 nm, from 550 nm to 750 nm, from 600 nm to 800 nm, from 650 nm to 850 nm, from 700 nm to 900 nm, or from 10 nm to 900 nm in diameter. In some embodiments, a nanoparticle may be less than 1000 nm in diameter.
In some embodiments, a particle of the present disclosure may be a microparticle. A microparticle may be a particle that is from about 1 μm to about 1000 μm in diameter. For example, the microparticles disclosed here can be at least 1 μm, at least 10 μm, at least 100 μm, at least 200 μm, at least 300 μm, at least 400 μm, at least 500 μm, at least 600 μm, at least 700 μm, at least 800 μm, at least 900 μm, from 10 μm to 50 μm, from 50 μm to 100 μm, from 100 μm to 150 μm, from 150 μm to 200 μm, from 200 μm to 250 μm, from 250 μm to 300 μm, from 300 μm to 350 μm, from 350 μm to 400 μm, from 400 μm to 450 μm, from 450 μm to 500 μm, from 500 μm to 550 μm, from 550 μm to 600 μm, from 600 μm to 650 μm, from 650 μm to 700 μm, from 700 μm to 750 μm, from 750 μm to 800 μm, from 800 μm to 850 μm, from 850 μm to 900 μm, from 100 μm to 300 μm, from 150 μm to 350 μm, from 200 μm to 400 μm, from 250 μm to 450 μm, from 300 μm to 500 μm, from 350 μm to 550 μm, from 400 μm to 600 μm, from 450 μm to 650 μm, from 500 μm to 700 μm, from 550 μm to 750 μm, from 600 μm to 800 μm, from 650 μm to 850 μm, from 700 μm to 900 μm, or from 10 μm to 900 μm in diameter. In some embodiments, a microparticle may be less than 1000 μm in diameter.
A particle of the present disclosure may be contacted with a biological sample (e.g., a biofluid) to form a biomolecule corona. The particle and biomolecule corona may be separated from the biological sample, for example by centrifugation, magnetic separation, filtration, or gravitational separation. The particle types and biomolecule corona may be separated from the biological sample using a number of separation techniques. Non-limiting examples of separation techniques include comprises magnetic separation, column-based separation, filtration, spin column-based separation, centrifugation, ultracentrifugation, density or gradient-based centrifugation, gravitational separation, or any combination thereof. A protein corona analysis may be performed on the separated particle and biomolecule corona. A protein corona analysis may comprise identifying one or more proteins in the biomolecule corona, for example by mass spectrometry. In some embodiments, a single particle type (e.g., a particle of a type listed in TABLE 1) may be contacted to a biological sample. In some embodiments, a plurality of particle types (e.g., a plurality of the particle types provided in TABLE 1) may be contacted to a biological sample. The plurality of particle types may be combined and contacted to the biological sample in a single sample volume. The plurality of particle types may be sequentially contacted to a biological sample and separated from the biological sample prior to contacting a subsequent particle type to the biological sample. Protein corona analysis of the biomolecule corona may compress the dynamic range of the analysis compared to a total protein analysis method.
The particles of the present disclosure may be used to serially interrogate a sample by incubating a first particle type with the sample to form a biomolecule corona on the first particle type, separating the first particle type, incubating a second particle type with the sample to form a biomolecule corona on the second particle type, separating the second particle type, and repeating the interrogating (by incubation with the sample) and the separating for any number of particle types. In some embodiments, the biomolecule corona on each particle type used for serial interrogation of a sample may be analyzed by protein corona analysis. In some embodiments, the biomolecule content of the supernatant may be analyzed following serial interrogation with one or more particle types.
In some embodiments, a particle type of the present disclosure can be used to serially interrogate a sample followed by corona analysis of proteins in the protein corona formed upon incubation of the particle type with the sample. Serial interrogation may be performed with two particle types in a round-by-round fashion. Serial interrogation may also include subsequent interrogation with additional particle times. In some embodiments, a particle of the present disclosure may be used to deplete a sample prior to the above described method of serial interrogation. A particle type may be contacted to a sample to form biomolecule corona on a surface of the particle type, and the particle may be separated from the sample, thereby depleting the sample. This strategy may be used to deplete one or more proteins (e.g., one or more high abundance proteins) from a sample. In some embodiments, the biomolecule content of the supernatant of a depleted sample may be analyzed. In some embodiments, the supernatant of the depleted sample may be used in any of the protein corona analysis methods disclosed herein.
An example of a particle type of the present disclosure may be a carboxylate (Citrate) superparamagnetic iron oxide nanoparticle (SPION), a phenol-formaldehyde coated SPION, a silica-coated SPION, a polystyrene coated SPION, a carboxylated poly(styrene-co-methacrylic acid) coated SPION, a N-(3-Trimethoxysilylpropyl)diethylenetriamine coated SPION, a poly(N-(3-(dimethylamino)propyl) methacrylamide) (PDMAPMA)-coated SPION, a 1,2,4,5-Benzenetetracarboxylic acid coated SPION, a poly(Vinylbenzyltrimethylammonium chloride) (PVBTMAC) coated SPION, a carboxylate, PAA coated SPION, a poly(oligo(ethylene glycol) methyl ether methacrylate) (POEGMA)-coated SPION, a carboxylate microparticle, a polystyrene carboxyl functionalized particle, a carboxylic acid coated particle, a silica particle, a carboxylic acid particle of about 150 nm in diameter, an amino surface microparticle of about 0.4-0.6 μm in diameter, a silica amino functionalized microparticle of about 0.1-0.39 μm in diameter, a Jeffamine surface particle of about 0.1-0.39 μm in diameter, a polystyrene microparticle of about 2.0-2.9 μm in diameter, a silica particle, a carboxylated particle with an original coating of about 50 nm in diameter, a particle coated with a dextran based coating of about 0.13 μm in diameter, or a silica silanol coated particle with low acidity.
Sample Collection and Extraction MethodsA variety of samples may be assayed in accordance with the methods and compositions of this disclosure. The samples disclosed herein may be analyzed by protein corona analysis after serially interrogating the sample with various particle types. In some embodiments, a sample may be fractioned prior to protein corona analysis. In some embodiments, a sample may be depleted prior to protein corona analysis. In some embodiments, a method of this disclosure may comprise contacting a sample with one or more particle types and performing a protein corona analysis on the sample.
A sample may be a biological sample. For example, a biological sample may be a biofluid sample such as cerebrospinal fluid (CSF), synovial fluid (SF), urine, plasma, serum, tear, crevicular fluid, semen, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, sweat or saliva. A biofluid may be a fluidized solid, for example a tissue homogenate, or a fluid extracted from a biological sample. A biological sample may be, for example, a tissue sample or a fine needle aspiration (FNA) sample. In some embodiments a biological sample may be a cell culture sample. For example, a sample that may be used in the methods disclosed herein can either include cells grow in cell culture or can include acellular material taken from cell cultures. In some embodiments, a biofluid is a fluidized biological sample. For example, a biofluid may be a fluidized cell culture extract. In some embodiments, a sample may be extracted from a fluid sample, or a sample may be extracted from a solid sample. For example, a sample may comprise gaseous molecules extracted from a fluidized solid (e.g., a volatile organic compound).
The protein corona analysis methods described herein may comprise assaying proteins in a sample of the present disclosure across a wide dynamic range. The dynamic range of proteins assayed in a sample may be a range of measured signals of protein abundances as measured by an assay method (e.g., mass spectrometry, chromatography, gel electrophoresis, spectroscopy, or immunoassays) for the proteins contained within a sample. For example, an assay capable of detecting proteins across a wide dynamic range may be capable of detecting proteins of very low abundance to proteins of very high abundance. The dynamic range of an assay may be directly related to the slope of assay signal intensity as a function of protein abundance. For example, an assay with a low dynamic range may have a low (but positive) slope of the assay signal intensity as a function of protein abundance, e.g., the ratio of the signal detected for a high abundance protein to the ratio of the signal detected for a low abundance protein may be lower for an assay with a low dynamic range than an assay with a high dynamic range. The protein corona analysis methods described herein may compress the dynamic range of an assay. The dynamic range of an assay may be compressed relative to another assay if the slope of the assay signal intensity as a function of protein abundance is lower than that of the other assay. For example, a plasma sample assayed using protein corona analysis with mass spectrometry may have a compressed dynamic range compared to a plasma sample assayed using mass spectrometry alone, directly on the sample or compared to provided abundance values for plasma proteins in databases (e.g., the database provided in Keshishian et al., Mol. Cell Proteomics 14, 2375-2393 (2015), also referred to herein as the “Carr database”), as shown in
Compression of a dynamic range of an assay may enable the detection of low abundance proteins using the methods disclosed herein (e.g., serial interrogation with a particle followed by an assay for quantitating protein abundance such as mass spectrometry). For example, an assay (e.g., mass spectrometry) may be capable of detecting a dynamic range of 3 orders of magnitude. In a sample comprising five proteins, A, B, C, D, and E, in abundances of 1 ng/mL, 10 ng/mL, 100 ng/mL, 1,000 ng/mL, and 10,000 ng/mL, respectively, the assay (e.g., mass spectrometry) may detect proteins B, C, D, and E. However, using the methods disclosed herein of incubating the sample with a particle, proteins A, B, C, D, and E may have different affinities for the particle surface and may adsorb to the surface of the particle to form the biomolecule corona at different abundancies than present in the sample. For example, proteins A, B, C, D, and E may be present in the biomolecule corona at abundancies of 1 ng/mL, 231 ng/mL, 463 ng/mL, 694 ng/mL, and 926 ng/mL, respectively. Thus, using the particles disclosed herein in methods of interrogating a sample results in compressing the dynamic range to 2 orders of magnitude and the resulting assay (e.g., mass spectrometry) can detect all five proteins.
Multiple biofluids may be processed in parallel using the methods and compositions of this disclosure. A protein corona analysis may be performed in parallel on multiple biological samples by performing each step of a protein corona analysis assay on multiple biological samples at the same time. For example, a protein corona analysis may be performed in parallel on multiple biological samples by performing a first step of a protein corona analysis assay on the multiple biological samples simultaneously, performing a second step of a protein corona analysis assay on the multiple biological samples simultaneously, and performing a third step of a protein corona analysis assay on the multiple biological samples simultaneously. Simultaneous performance of each step of a protein corona analysis on the multiple biological samples may be repeated until all steps of a protein corona analysis assay have been performed on the multiple biological samples. In some instances, the multiple biological samples may be obtained from the same subject. These samples may be portions of a sample obtained from a subject (e.g., multiple aliquots of a plasma sample). These samples may be different biofluids collected from the same subject.
In some embodiments, a protein corona analysis may be performed in parallel on multiple biological samples by sequentially performing a first step of a protein corona analysis assay on each sample of a plurality of biological samples, sequentially performing a second step of a protein corona analysis assay on each sample of a plurality of biological samples, and sequentially performing a third step of a protein corona analysis assay on each sample of a plurality of biological samples. Sequential performance of each step of a protein corona analysis may be performed on each sample of a plurality of biological samples may be repeated until all steps of a protein corona analysis assay have been performed on each biological sample of the plurality of biological samples.
A protein of interest (e.g., a low abundance protein) may be enriched in a biomolecule corona relative to the untreated sample (e.g., a sample that is not assayed using particles). In some embodiments, a level of enrichment may be the percent increase or fold increase in concentration of the protein of interest relative to the total protein concentration in the biomolecule corona as compared to the untreated sample. A protein of interest may be enriched in a biomolecule corona by increasing the concentration of the protein of interest in the biomolecule corona as compared to the sample that has not been contacted to a particle. A protein of interest may be enriched by decreasing the concentration of a high abundance protein in the biomolecule corona as compared to the sample that has not been contacted to a particle. A protein corona analysis assay may be used to rapidly identify low abundance proteins in a biological sample (e.g., a biofluid). In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a biological sample in no more than about 8 hours from first contacting the biological sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a biological sample in no more than about 8 hours from first contacting the biological sample with a particle. In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a biological sample in no more than about 4 hours from first contacting the biological sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a biological sample in no more than about 4 hours from first contacting the biological sample with a particle.
A biological sample may be collected in a sample collection tube comprising a stabilizing reagent. The stabilizing reagent may stabilize nucleated cells in a biofluid sample or other biomolecules in the biofluid sample, such as proteins or nucleic acids (e.g., RNA or DNA, including cell free RNA or DNA). In some embodiments, a sample collection tube may comprise a metabolic inhibitor, a protease inhibitor, a phosphatase inhibitor, a nuclease inhibitor, a preservative agent, a polyamide, or a combination thereof. A metabolic inhibitor may comprise glyceraldehyde, dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, 1,3-bisphosphoglycerate, 3-phosphoglycerate, 2-phosphoglycerate, phosphoenolpyruvate, pyruvate and glycerate dihydroxyacetate, sodium fluoride, or K2C2O4. A protease inhibitor may comprise antipain, aprotinin, chymostatin, elastatinal, phenylmethylsulfonyl fluoride (PMSF), APMSF, TLCK, TPCK, leupeptin, soybean trypsin inhibitor, indoleacetic acid (IAA), E-64, EDTA, pepstatin, VdLPFFVdL, 1,10-phenanthroline, phosphoramodon, amastatin, bestatin, diprotin A, diprotin B, alpha-2-macroglobulin, lima bean trypsin inhibitor, pancreatic protease inhibitor, or egg white ovostatin egg white cystatin. A phosphatase inhibitor may comprise calyculin A, nodularin, NIPP-1, microcystin LR, tautomycin, okadaic acid, cantharidin, microcystin LR, okadaic acid, fostriecin, tautomycin, cantharidin, endothall, nodularin, cyclosporin A, FK 506/immunophilin complexes, cypermethrin, deltamethrin, fenvalerate, bpV(phen), dephostatin, mpV(pic) DMHV, or sodium orthovanadate. A nuclease inhibitor may comprise diethyl pyrocarbonate, ethanol, aurintricarboxylic acid (ATA), formamide, vanadyl-ribonucleoside complexes, macaloid, ethylenediamine tetraacetic acid (EDTA), proteinase K, heparin, hydroxylamine-oxygen-cupric ion, bentonite, ammonium sulfate, dithiothreitol (DTT), beta-mercaptoethanol, cysteine, dithioerythritol, tris(2-carboxyethyl) phosphene hydrochloride, or a divalent cation such as Mg+2, Mn+2, Zn+2, Fe+2, Ca+2, or Cu+2. A preservative agent may comprise diazolidinyl urea, imidazolidinyl urea, dimethoylol-5,5-dimethylhydantoin, dimethylol urea, 2-bromo-2-nitropropane-1,3-diol, oxazolidines, sodium hydroxymethyl glycinate, 5-hydroxymethoxymethyl-1-1aza-3,7-dioxabicyclo[3.3.0]octane, 5-hydroxymethyl-1-1aza-3,7dioxabicyclo[3.3.0]octane, 5-hydroxypoly[methyleneoxy]methyl-1-1aza-3,7dioxabicyclo[3.3.0]octane, or quaternary adamantine. A sample collection tube may comprise stabilizing agents disclosed in U.S. Pat. Nos. 8,304,187, 8,586,306, 9,657,227, 9,926,590, 10,144,955, and 10,294,513, and U.S. application Ser. No. 16/377,344, each of which is incorporated herein by reference in its entirety, and other protein separation techniques.
Cerebrospinal Fluid (CSF) Sample. The present disclosure provides methods of assaying for proteins in a cerebrospinal fluid sample using one or more of the particles disclosed herein (e.g., and one or more of the particles disclosed in TABLE 1). The relatively low abundance of proteins in CSF may confound protein detection using traditional means (e.g., ELISA, immunofluorescence, gel electrophoresis, or chromatography). The methods and compositions disclosed herein may be well suited for detecting proteins in samples with low protein concentration. For example, the protein corona analysis assays disclosed herein may be capable of detecting proteins in samples with no more than about 1.0 mg/mL, no more than about 0.9 mg/mL, no more than about 0.8 mg/mL, no more than about 0.7 mg/mL, no more than about 0.6 mg/mL, no more than about 0.5 mg/mL, no more than about 0.4 mg/mL, no more than about 0.3 mg/mL, no more than about 0.2 mg/mL, or no more than about 0.1 mg/mL total protein concentration.
Sample collection volumes of CSF may be small, ranging from about 1 mL to about 10 mL, limiting the number of assays that may be performed with each sample. The methods and compositions disclosed herein may be well suited for detecting proteins in small sample volumes. For example, the protein corona analysis assays disclosed herein may be capable of detecting proteins in sample volumes of no more than about 1000 μL, no more than about 900 μL, no more than about 800 μL, no more than about 700 μL, no more than about 600 μL, no more than about 500 μL, no more than about 400 μL, no more than about 300 μL, no more than about 200 μL, no more than about 100 μL, no more than about 50 μL, no more than about 20 μL, no more than about 10 μL, no more than about 5 μL, no more than about 2 μL, or no more than about 1 μL.
A protein corona analysis assay may be used to rapidly identify low abundance proteins in a CSF sample. A protein corona analysis may identify low abundance proteins in a CSF sample in no more than about 2 hours, no more than about 2.5 hours, no more than about 3 hours, no more than about 3.5 hours, no more than about 4 hours, no more than about 4.5 hours, no more than about 5 hours, no more than about 5.5 hours, no more than about 6 hours, no more than about 6.5 hours, no more than about 7 hours, no more than about 7.5 hours, no more than about 8 hours, no more than about 8.5 hours, no more than about 9 hours, no more than about 9.5 hours, or no more than about 10 hours from first contacting the CSF sample with a particle.
In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a CSF sample in no more than about 8 hours from first contacting the biological sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a CSF sample in no more than about 8 hours from first contacting the CSF sample with a particle. In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a CSF sample in no more than about 4 hours from first contacting the CSF sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a CSF sample in no more than about 4 hours from first contacting the CSF sample with a particle.
The methods disclosed herein are superior to other methods of assaying for proteins in CSF and provide sampling of proteins in CSF across a wide dynamic range in a short period of time. In some embodiments, the methods disclosed herein utilize one or more of the particles to rapidly enrich for proteins in a CSF sample. For example, in some embodiments, one or more of the particle types disclosed herein can be used in a method of assaying for a protein of interest (high abundance protein, medium abundance protein, or low abundance protein) in a CSF sample, the method including incubating said one or more particle types in the CSF sample allowing for formation of a biomolecule corona on the particle and enrichment of proteins in the CSF sample, separating the particle from unbound biomolecules in the CSF sample (e.g., by magnetic separation), and trypsinizing and analyzing the biomolecules in the corona for the protein of interest. Further, using said methods allows for efficient enrichment of the protein of interest in the biomolecule coronas formed around the particle type. A protein of interest may be enriched in a biomolecule corona by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 100% relative to the CSF sample that has not been contacted to a particle. A protein of interest may be enriched in a biomolecule corona by at least about 1.1-fold, at least about 1.2-fold, at least about 1.3-fold, at least about 1.4-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 4.5-fold, at least about 5-fold, at least about 5.5-fold, at least about 6-fold, at least about 6.5-fold, at least about 7-fold, at least about 7.5-fold, at least about 8-fold, at least about 8.5-fold, at least about 9-fold, at least about 9.5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold relative to the CSF sample that has not been contacted to a particle. In some embodiments, any one or more of the particles disclosed herein (e.g., any one or more of the particle types disclosed in TABLE 1) can result in capturing at least about 500, at least about 600, at least about 650, at least about 700, at least about 750, at least about 800, at least about 850, at least about 900, at least about 950, at least about 1000 proteins, at least about 1050 proteins, at least about 1100 proteins, at least about 1150 proteins, or at least about 1200 distinct proteins from a CSF sample.
Synovial Fluid Sample. The present disclosure provides methods of assaying for proteins in a synovial fluid sample using one or more of the particles disclosed herein (e.g., and one or more of the particles disclosed in TABLE 1). The relatively high concentration of high abundance proteins (e.g., albumin) relative to total protein in SF may confound protein detection using traditional means (e.g., ELISA, immunofluorescence, gel electrophoresis, or chromatography). The methods and compositions disclosed herein may be well suited for detecting low abundance proteins in samples with high concentrations of high abundance proteins. For example, the protein corona analysis assays disclosed herein may be capable of detecting low abundance proteins in samples with at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, or at least about 70% by weight of a high abundance protein relative to total protein content. In some embodiments, the protein corona analysis assays disclosed herein may be performed on a sample comprising a relatively high concentration of high abundance proteins without the need for additional fractionation or depletion steps.
Sample collection volumes of SF may be small, ranging from about 2 mL to about 20 mL, limiting the number of assays that may be performed with each sample. The methods and compositions disclosed herein may be well suited for detecting proteins in small sample volumes. For example, the protein corona analysis assays disclosed herein may be capable of detecting proteins in sample volumes of no more than about 1000 μL, no more than about 900 μL, no more than about 800 μL, no more than about 700 μL, no more than about 600 μL, no more than about 500 μL, no more than about 400 μL, no more than about 300 μL, no more than about 200 μL, no more than about 100 μL, no more than about 50 μL, or no more than about 20 μL, no more than about 10 μL, no more than about 5 μL, no more than about 2 μL, or no more than about 1 μL.
A protein corona analysis assay may be used to rapidly identify low abundance proteins in a SF sample. A protein corona analysis may identify low abundance proteins in a SF sample in no more than about 2 hours, no more than about 2.5 hours, no more than about 3 hours, no more than about 3.5 hours, no more than about 4 hours, no more than about 4.5 hours, no more than about 5 hours, no more than about 5.5 hours, no more than about 6 hours, no more than about 6.5 hours, no more than about 7 hours, no more than about 7.5 hours, no more than about 8 hours, no more than about 8.5 hours, no more than about 9 hours, no more than about 9.5 hours, or no more than about 10 hours from first contacting the SF sample with a particle.
In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a SF sample in no more than about 8 hours from first contacting the biological sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a SF sample in no more than about 8 hours from first contacting the SF sample with a particle. In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a SF sample in no more than about 4 hours from first contacting the SF sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a SF sample in no more than about 4 hours from first contacting the SF sample with a particle.
The methods disclosed herein are superior to other methods of assaying for proteins in synovial fluid and provide sampling of proteins in synovial fluid across a wide dynamic range in a short period of time. In some embodiments, the methods disclosed herein utilize one or more of the particles to rapidly enrich for proteins in a synovial fluid sample. For example, in some embodiments, one or more of the particle types disclosed herein can be used in a method of assaying for a protein of interest (high abundance protein, medium abundance protein, or low abundance protein) in a synovial fluid sample, the method including incubating said one or more particle types in the synovial fluid sample allowing for formation of a biomolecule corona on the particle and enrichment of proteins in the synovial fluid sample, separating the particle from unbound biomolecules in the synovial fluid sample (e.g., by magnetic separation), and trypsinizing and analyzing the biomolecules in the corona for the protein of interest. Further, using said methods allows for efficient enrichment of the protein of interest in the biomolecule coronas formed around the particle type. A protein of interest may be enriched in a biomolecule corona by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 100% relative to the SF sample that has not been contacted to a particle. A protein of interest may be enriched in a biomolecule corona by at least about 1.1-fold, at least about 1.2-fold, at least about 1.3-fold, at least about 1.4-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 4.5-fold, at least about 5-fold, at least about 5.5-fold, at least about 6-fold, at least about 6.5-fold, at least about 7-fold, at least about 7.5-fold, at least about 8-fold, at least about 8.5-fold, at least about 9-fold, at least about 9.5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold relative to the SF sample that has not been contacted to a particle. In some embodiments, any one or more of the particles disclosed herein (e.g., any one or more of the particle types disclosed in TABLE 1) can result in enrichment of at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about 1800, at least about 1900, at least about 2000, at least about 2100, at least about 2200, at least about 2300, at least about 2400, at least about 2500, at least about 2750, at least about 3000, at least about 3250, at least about 3500, at least about 3750, or at least about 4000 from a synovial fluid sample.
Urine Sample. The present disclosure provides methods of assaying for proteins in a urine sample using one or more of the particles disclosed herein (e.g., and one or more of the particles disclosed in TABLE 1). The relatively low abundance of proteins in urine may confound protein detection using traditional means (e.g., ELISA, immunofluorescence, gel electrophoresis, or chromatography). The methods and compositions disclosed herein may be well suited for detecting proteins in samples with low protein concentration. For example, the protein corona analysis assays disclosed herein may be capable of detecting proteins in samples with no more than about 10 mg/mL, no more than about 5.0 mg/mL, no more than about 4.0 mg/mL, no more than about 3.0 mg/mL, no more than about 2.0 mg/mL, no more than about 1.0 mg/mL, no more than about 0.9 mg/mL, no more than about 0.8 mg/mL, no more than about 0.7 mg/mL, no more than about 0.6 mg/mL, no more than about 0.5 mg/mL, no more than about 0.4 mg/mL, no more than about 0.3 mg/mL, no more than about 0.2 mg/mL, no more than about 0.1 mg/mL, no more than about 0.05 mg/mL, or no more than about 0.02 mg/mL total protein concentration.
The relatively high concentration of high abundance proteins (e.g., albumin) relative to total protein in urine may confound protein detection using traditional means. The methods and compositions disclosed herein may be well suited for detecting low abundance proteins in samples with high concentrations of high abundance proteins. For example, the protein corona analysis assays disclosed herein may be capable of detecting low abundance proteins in samples with at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95% by weight of a high abundance protein relative to total protein content. In some embodiments, the protein corona analysis assays disclosed herein may be performed on a sample comprising a relatively high concentration of high abundance proteins without the need for additional fractionation or depletion steps.
A protein corona analysis assay may be used to rapidly identify low abundance proteins in a urine sample. A protein corona analysis may identify low abundance proteins in a urine sample in no more than about 2 hours, no more than about 2.5 hours, no more than about 3 hours, no more than about 3.5 hours, no more than about 4 hours, no more than about 4.5 hours, no more than about 5 hours, no more than about 5.5 hours, no more than about 6 hours, no more than about 6.5 hours, no more than about 7 hours, no more than about 7.5 hours, no more than about 8 hours, no more than about 8.5 hours, no more than about 9 hours, no more than about 9.5 hours, or no more than about 10 hours from first contacting the urine sample with a particle.
In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a urine sample in no more than about 8 hours from first contacting the biological sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a urine sample in no more than about 8 hours from first contacting the urine sample with a particle. In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a urine sample in no more than about 4 hours from first contacting the urine sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a urine sample in no more than about 4 hours from first contacting the urine sample with a particle.
The methods disclosed herein are superior to other methods of assaying for proteins in urine and provide sampling of proteins in urine across a wide dynamic range in a short period of time. In some embodiments, the methods disclosed herein utilize one or more of the particles to rapidly enrich for proteins in a urine sample. For example, in some embodiments, one or more of the particle types disclosed herein can be used in a method of assaying for a protein of interest (high abundance protein, medium abundance protein, or low abundance protein) in a urine sample, the method including incubating said one or more particle types in the urine sample allowing for formation of a biomolecule corona on the particle and enrichment of proteins in the urine sample, separating the particle from unbound biomolecules in the urine sample (e.g., by magnetic separation), and trypsinizing and analyzing the biomolecules in the corona for the protein of interest. Further, using said methods allows for efficient enrichment of the protein of interest in the biomolecule coronas formed around the particle type. A protein of interest may be enriched in a biomolecule corona by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 100% relative to the urine sample that has not been contacted to a particle. A protein of interest may be enriched in a biomolecule corona by at least about 1.1-fold, at least about 1.2-fold, at least about 1.3-fold, at least about 1.4-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 4.5-fold, at least about 5-fold, at least about 5.5-fold, at least about 6-fold, at least about 6.5-fold, at least about 7-fold, at least about 7.5-fold, at least about 8-fold, at least about 8.5-fold, at least about 9-fold, at least about 9.5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold relative to the urine sample that has not been contacted to a particle. In some embodiments, any one or more of the particles disclosed herein (e.g., any one or more of the particle types disclosed in TABLE 1) can result in enrichment of at least about 291, at least about 294, at least about 300, at least about 350, at least about 400, at least about 450, at least about 470, at least about 500, at least about 550, at least about 600, at least about 618, at least about 650, at least about 700, at least about 709, at least about 718, at least about 750, at least about 800, at least about 838, at least about 840, at least about 847, at least about 850, at least about 900, at least about 950, at least about 984, at least about 1000, at least about 1050, at least about 1100, at least about 1150, or at least about 1200 from a urine sample.
Fluidized Solid Sample. The present disclosure provides methods of assaying for proteins in a fluidized solid sample using one or more of the particles disclosed herein (e.g., and one or more of the particles disclosed in TABLE 1). A fluidized solid (e.g., a tissue homogenate) may comprise inhomogeneities, which may confound protein detection using traditional means (e.g., ELISA, immunofluorescence, gel electrophoresis, or chromatography). The methods and compositions disclosed herein may be well suited for detecting proteins in heterogeneous samples. For example, the protein corona analysis assays disclosed herein may be performed on a fluidized solid without the need for additional purification, fractionation, or depletion steps.
The methods disclosed herein are superior to other methods of assaying for proteins in fluidized solid and provide sampling of proteins in fluidized solid across a wide dynamic range in a short period of time. In some embodiments, the methods disclosed herein utilize one or more of the particles to rapidly enrich for proteins in a fluidized solid sample. For example, in some embodiments, one or more of the particle types disclosed herein can be used in a method of assaying for a protein of interest (high abundance protein, medium abundance protein, or low abundance protein) in a fluidized solid sample, the method including incubating said one or more particle types in the fluidized solid sample allowing for formation of a biomolecule corona on the particle and enrichment of proteins in the fluidized solid sample, separating the particle from unbound biomolecules in the fluidized solid sample (e.g., by magnetic separation), and trypsinizing and analyzing the biomolecules in the corona for the protein of interest. Further, using said methods allows for efficient enrichment of the protein of interest in the biomolecule coronas formed around the particle type. A protein of interest may be enriched in a biomolecule corona by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 100% relative to the fluidized solid sample that has not been contacted to a particle. A protein of interest may be enriched in a biomolecule corona by at least about 1.1-fold, at least about 1.2-fold, at least about 1.3-fold, at least about 1.4-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 4.5-fold, at least about 5-fold, at least about 5.5-fold, at least about 6-fold, at least about 6.5-fold, at least about 7-fold, at least about 7.5-fold, at least about 8-fold, at least about 8.5-fold, at least about 9-fold, at least about 9.5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold relative to the fluidized solid sample that has not been contacted to a particle. In some embodiments, any one or more of the particles disclosed herein (e.g., any one or more of the particle types disclosed in TABLE 1) can result in enrichment of at least about 291, at least about 294, at least about 300, at least about 350, at least about 400, at least about 450, at least about 470, at least about 500, at least about 550, at least about 600, at least about 618, at least about 650, at least about 700, at least about 709, at least about 718, at least about 750, at least about 800, at least about 838, at least about 840, at least about 847, at least about 850, at least about 900, at least about 950, at least about 984, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about 1800, at least about 1900, at least about 2000, at least about 2100, at least about 2200, at least about 2300, at least about 2400, at least about 2500, at least about 2750, at least about 3000, at least about 3250, at least about 3500, at least about 3750, or at least about 4000 from a fluidized solid sample.
A protein corona analysis assay may be used to rapidly identify low abundance proteins in a fluidized solid sample. A protein corona analysis may identify low abundance proteins in a fluidized solid sample in no more than about 2 hours, no more than about 2.5 hours, no more than about 3 hours, no more than about 3.5 hours, no more than about 4 hours, no more than about 4.5 hours, no more than about 5 hours, no more than about 5.5 hours, no more than about 6 hours, no more than about 6.5 hours, no more than about 7 hours, no more than about 7.5 hours, no more than about 8 hours, no more than about 8.5 hours, no more than about 9 hours, no more than about 9.5 hours, or no more than about 10 hours from first contacting the fluidized solid sample with a particle.
In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a fluidized solid sample in no more than about 8 hours from first contacting the biological sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a fluidized solid sample in no more than about 8 hours from first contacting the fluidized solid sample with a particle. In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a fluidized solid sample in no more than about 4 hours from first contacting the fluidized solid sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a fluidized solid sample in no more than about 4 hours from first contacting the fluidized solid sample with a particle.
Cell Culture Sample. The present disclosure provides methods of assaying for proteins in a cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample) using one or more of the particles disclosed herein (e.g., and one or more of the particles disclosed in TABLE 1). A cell culture sample may comprise inhomogeneities, which may confound protein detection using traditional means (e.g., ELISA, immunofluorescence, gel electrophoresis, or chromatography). The methods and compositions disclosed herein may be well suited for detecting proteins in heterogeneous samples. For example, the protein corona analysis assays disclosed herein may be performed on a cell culture sample without the need for additional purification, fractionation, or depletion steps.
The methods disclosed herein are superior to other methods of assaying for proteins in a cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample) and provide sampling of proteins in a cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample) across a wide dynamic range in a short period of time. In some embodiments, the methods disclosed herein utilize one or more of the particles to rapidly enrich for proteins in a cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample). For example, in some embodiments, one or more of the particle types disclosed herein can be used in a method of assaying for a protein of interest (high abundance protein, medium abundance protein, or low abundance protein) in a cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample), the method including incubating said one or more particle types in the cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample) allowing for formation of a biomolecule corona on the particle and enrichment of proteins in the cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample), separating the particle from unbound biomolecules in the a cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample) (e.g., by magnetic separation), and trypsinizing and analyzing the biomolecules in the corona for the protein of interest. Further, using said methods allows for efficient enrichment of the protein of interest in the biomolecule coronas formed around the particle type. A protein of interest may be enriched in a biomolecule corona by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 100% relative to the cell culture sample that has not been contacted to a particle. A protein of interest may be enriched in a biomolecule corona by at least about 1.1-fold, at least about 1.2-fold, at least about 1.3-fold, at least about 1.4-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 4.5-fold, at least about 5-fold, at least about 5.5-fold, at least about 6-fold, at least about 6.5-fold, at least about 7-fold, at least about 7.5-fold, at least about 8-fold, at least about 8.5-fold, at least about 9-fold, at least about 9.5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold relative to the cell culture sample that has not been contacted to a particle. In some embodiments, any one or more of the particles disclosed herein (e.g., any one or more of the particle types disclosed in TABLE 1) can result in capturing at least about 100, at least about 200, at least about 300, at least about 350, at least about 400, at least about 450, at least about 470, at least about 500, at least about 550, at least about 600, at least about 618, at least about 650, at least about 700, at least about 709, at least about 718, at least about 750, at least about 800, at least about 838, at least about 840, at least about 847, at least about 850, at least about 900, at least about 950, at least about 984, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about 1800, at least about 1900, at least about 2000, at least about 2100, at least about 2200, at least about 2300, at least about 2400, at least about 2500, at least about 2750, at least about 3000, at least about 3250, at least about 3500, at least about 3750, or at least about 4000 proteins from a cell culture sample (a cellular sample, a cell permeated sample, or an extracellular sample) in the corona that forms on the surface of the particle type upon incubation with the cell culture sample.
A protein corona analysis assay may be used to rapidly identify low abundance proteins in a cell culture sample. A protein corona analysis may identify low abundance proteins in a cell culture sample in no more than about 2 hours, no more than about 2.5 hours, no more than about 3 hours, no more than about 3.5 hours, no more than about 4 hours, no more than about 4.5 hours, no more than about 5 hours, no more than about 5.5 hours, no more than about 6 hours, no more than about 6.5 hours, no more than about 7 hours, no more than about 7.5 hours, no more than about 8 hours, no more than about 8.5 hours, no more than about 9 hours, no more than about 9.5 hours, or no more than about 10 hours from first contacting the cell culture sample with a particle.
In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a cell culture sample in no more than about 8 hours from first contacting the biological sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a cell culture sample in no more than about 8 hours from first contacting the cell culture sample with a particle. In some embodiments, a protein corona analysis may identify at least about 500 low abundance proteins in a cell culture sample in no more than about 4 hours from first contacting the cell culture sample with a particle. In some embodiments, a protein corona analysis may identify at least about 1000 low abundance proteins in a cell culture sample in no more than about 4 hours from first contacting the cell culture sample with a particle.
The biological samples of this disclosure may be collected may many different techniques. A tissue sample may be collected through a biopsy, dissection, fine needle aspiration, or surgical excision. A tissue sample may be fluidized, for example by homogenization or centrifugation. A fluid sample (e.g., blood, serum, plasma, urine, or semen) may be collected in a sample collection tube. Commercially available collection tubes may be used for the collection of a fluid sample. For example, commercially available collection tubes that may be used to collect a sample of this disclosure include EDTA collection tubes, collection tubes comprising a nucleic acid stabilizing agent (e.g., Streck tubes), serum-separating tubes (SST), sodium citrate collection tubes, citrate, theophylline, adenosine and dipyridamole (CTAD) collection tubes, lithium/sodium heparin collection tubes, sodium fluoride collection tubes, acid citrate dextrose (ACD) collection tubes, or sodium polyanethol sulfonate (SPS) collection tubes.
In some embodiments, a biofluid may be collected in a sample collection tube comprising stabilizing reagents (e.g., preservatives, protease inhibitors, phosphatase inhibitors, or crosslinkers). The stabilizing reagents may stabilize the biofluid to be stored unfrozen. The biofluid may be stored at an ambient temperature, at a room temperature, or at any temperature from 0° C. to 37° C. For example, the biofluid collected in the sample collection tube comprising a stabilizing reagent may be stored unfrozen (e.g., at a temperature of from 0° C. to 37° C.) for up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, up to 9, up to 10, up to 11, up to 12, up to 13, or up to 14 days. Following storage at room temperature, the biofluid may be analyzed (e.g., via corona analysis) or frozen for later use. For example, a biofluid sample may be collected in a collection tube comprising a nucleic acid stabilizing agent (e.g., a Streck tube) and stored at room temperature overnight, or the biofluid sample may be collected in the blood collection tube comprising a nucleic acid stabilizing agent and shipped without ice or dry ice. The unfrozen biofluid may be processed at separate facility from where the sample was collected.
The biofluids collected in collection tubes and stored unfrozen may be suitable for analysis by protein corona analysis. Following storage at a temperature from 0° C. to 37° C., at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1100, at least 1200, at least 1300, at least 1400, or at least 1500 proteins may be detected in the biofluid using corona analysis. In some embodiments, following storage at a temperature from 0° C. to 37° C., at least 1000, at least 1100, at least 1200, at least 1300, at least 1400, at least 1500, at least 1600, at least 1700, at least 1800, at least 1900, at least 2000, at least 2500, at least 3000, at least 3500, at least 4000, at least 4500, or at least 5000 peptides may be detected in the biofluid using corona analysis. In some embodiments, following storage at a temperature from 0° C. to 37° C., at least 5000, at least 6000, at least 7000, at least 7100, at least 7200, at least 7300, at least 7400, at least 7500, at least 7600, at least 7700, at least 7800, at least 7900, at least 8000, at least 8500, or at least 9000 protein features may be detected in the biofluid using corona analysis. A frozen biofluid may be shipped on ice, on dry ice, or with liquid nitrogen. The frozen biofluid may be thawed and processed at separate facility from where the sample was collected. For example, a biofluid may be collected in a tube comprising a nucleic acid stabilizing agent (e.g., a Streck tube) at a medical facility and shipped under ambient conditions to a research facility for corona analysis.
In some embodiments, a biofluid may be collected in a sample collection tube and frozen. A biofluid may be frozen within about 10 minutes, about 20 minutes, about 30 minutes, about 40 minutes, about 50 minutes, about 60 minutes, about 1 hour, about 2 hours, about 3 hours, about 4 hours, about 5 hours, or about 6 hours. Biofluids that have been collected in sample collection tubes and frozen may be suitable for analysis by protein corona analysis. Following frozen storage (e.g., storage at a temperature below 0° C.), at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1100, at least 1200, at least 1300, at least 1400, or at least 1500 proteins may be detected in the biofluid using corona analysis. In some embodiments, following storage at a temperature below 0° C., at least 1000, at least 1100, at least 1200, at least 1300, at least 1400, at least 1500, at least 1600, at least 1700, at least 1800, at least 1900, at least 2000, at least 2500, at least 3000, at least 3500, at least 4000, at least 4500, or at least 5000 peptides may be detected in the biofluid using corona analysis. In some embodiments, following storage at a temperature below 0° C., at least 5000, at least 6000, at least 7000, at least 7100, at least 7200, at least 7300, at least 7400, at least 7500, at least 7600, at least 7700, at least 7800, at least 7900, at least 8000, at least 8500, or at least 9000 protein features may be detected in the biofluid using corona analysis.
In some embodiments, the methods disclosed herein provide for collection of a biofluid in a Streck blood collection tube, incubation with particles to form coronas, and subsequent analysis of the proteins in the coronas at a later time point (e.g., up to 14 days after incubation of said sample in the Streck blood collection tube at room temperature).
Protein Corona Analysis in Biological SamplesThe particles and methods of use thereof disclosed herein can bind a large number of unique proteins in a biological sample (e.g., a biofluid). Non-limiting examples of biological samples that may be analyzed using the protein corona analysis methods described herein include biofluid samples (e.g., cerebral spinal fluid (CSF), synovial fluid (SF), urine, plasma, serum, tears, semen, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, sweat or saliva), fluidized solids (e.g., a tissue homogenate), or samples derived from cell culture. For example, a particle disclosed herein can be incubated with any biological sample disclosed herein to form a protein corona comprising at least 100 unique proteins, at least 120 unique proteins, at least 140 unique proteins, at least 160 unique proteins, at least 180 unique proteins, at least 200 unique proteins, at least 220 unique proteins, at least 240 unique proteins, at least 260 unique proteins, at least 280 unique proteins, at least 300 unique proteins, at least 320 unique proteins, at least 340 unique proteins, at least 360 unique proteins, at least 380 unique proteins, at least 400 unique proteins, at least 420 unique proteins, at least 440 unique proteins, at least 460 unique proteins, at least 480 unique proteins, at least 500 unique proteins, at least 520 unique proteins, at least 540 unique proteins, at least 560 unique proteins, at least 580 unique proteins, at least 600 unique proteins, at least 620 unique proteins, at least 640 unique proteins, at least 660 unique proteins, at least 680 unique proteins, at least 700 unique proteins, at least 720 unique proteins, at least 740 unique proteins, at least 760 unique proteins, at least 780 unique proteins, at least 800 unique proteins, at least 820 unique proteins, at least 840 unique proteins, at least 860 unique proteins, at least 880 unique proteins, at least 900 unique proteins, at least 920 unique proteins, at least 940 unique proteins, at least 960 unique proteins, at least 980 unique proteins, at least 1000 unique proteins, from 100 to 1000 unique proteins, from 150 to 950 unique proteins, from 200 to 900 unique proteins, from 250 to 850 unique proteins, from 300 to 800 unique proteins, from 350 to 750 unique proteins, from 400 to 700 unique proteins, from 450 to 650 unique proteins, from 500 to 600 unique proteins, from 200 to 250 unique proteins, from 250 to 300 unique proteins, from 300 to 350 unique proteins, from 350 to 400 unique proteins, from 400 to 450 unique proteins, from 450 to 500 unique proteins, from 500 to 550 unique proteins, from 550 to 600 unique proteins, from 600 to 650 unique proteins, from 650 to 700 unique proteins, from 700 to 750 unique proteins, from 750 to 800 unique proteins, from 800 to 850 unique proteins, from 850 to 900 unique proteins, from 900 to 950 unique proteins, from 950 to 1000 unique proteins. In some embodiments, several different types of particles can be used, separately or in combination, to identify large numbers of proteins in a particular biological sample. In other words, particles can be multiplexed in order to bind and identify large numbers of proteins in a biological sample. Protein corona analysis of the biomolecule corona may compress the dynamic range of the analysis compared to a total protein analysis method.
The compositions and methods disclosed herein can be used to identify various biological states in a particular biological sample. For example, a biological state can refer to an elevated or low level of a particular protein or a set of proteins. In other examples, a biological state can refer to identification of a disease, such as cancer. One or more particle types can be incubated with CSF, allowing for formation of a protein corona. Said protein corona can then be analyzed by gel electrophoresis or mass spectrometry in order to identify a pattern of proteins. Analysis of protein corona (e.g., by mass spectrometry or gel electrophoresis) may be referred to as corona analysis. The pattern of proteins can be compared to the same methods carried out on a control sample. Upon comparison of the patterns of proteins, it may be identified that the first CSF sample comprises an elevated level of markers corresponding to a particular type of brain cancer. The particles and methods of use thereof, can thus be used to diagnose a particular disease state.
Corona Analysis by Serial InterrogationProvided herein are several methods for compressing the dynamic range of a proteomic analysis assay to facilitate the detection of low abundance proteins relative to high abundance proteins. As used herein, the phrase “dynamic range” is the ratio of the highest concentration of a molecule in a sample to the lowest concentration of a molecule in a sample. The dynamic range may be quantified by a number of methods consistent with evaluating the ratio of the highest concentration of a molecule in a sample to the lowest concentration of a molecule in a sample. For example, the dynamic range may be quantified as a ratio of the top decile of proteins in a sample to the bottom decile of proteins in the sample. The dynamic range may be quantified by a ratio of the concentration of the highest concentration detectable in a sample to the lowest concentration detectable in the sample. The dynamic range may be quantified as a span of the interquartile range (a ratio of the 75th percentile and 25th percentile) of proteins in a sample. The dynamic range may be quantified by measuring the slope of fitted data in a plot of all concentrations of proteins detected in a sample (e.g., using a method disclosed herein such as serial interrogation with a particle) against published concentrations of said proteins (e.g., using the Carr database of plasma proteins). The dynamic range may be quantified by measuring the slope between any two points in a plot of protein concentration detected in a sample (e.g., using a method disclosed herein such as serial interrogation with a particle) against published concentrations of said protein (e.g., using the Carr database of plasma proteins). Thus, the dynamic range captures the range of concentrations, or orders of magnitude, at which a molecule is detectable in the sample. For example, “dynamic range” may refer to the ratio of the highest detectable concentration of a protein in a sample to the lowest detectable concentration of another protein in the sample. Thus, in this example, the dynamic range captures the range of concentrations, or orders of magnitude, at which proteins are detectable in the sample. As used herein, the phrase “compressing the dynamic range” or “compression of the dynamic range” refers to a decrease in the ratio of the highest concentration of a molecule in a sample to the lowest concentration of a molecule in a sample. Thus, the dynamic range is compressed when the range of concentrations, or orders of magnitude, at which a molecule is detectable in a sample is decreased. For example, a particle type of the present disclosure can be used to serially interrogate a sample. Upon incubation of the particle type in the sample, a biomolecule corona comprising forms on the surface of the particle type. If proteins are directly detected in the sample without the use of said particle types, for example by direct mass spectrometric analysis of the sample, the dynamic range may span a wider range of concentrations, or more orders of magnitude, than if the proteins are directed on the surface of the particle type. Thus, using the particle types disclosed herein compresses the dynamic range of proteins in a sample. Without being limited by theory, this effect may be observed due to more capture of higher affinity, lower abundance proteins in the biomolecule corona of the particle type and less capture of lower affinity, higher abundance proteins in the biomolecule corona of the particle type. A dynamic range of a proteomic analysis assay may be the slope of a plot of a protein signal measured by the proteomic analysis assay as a function of total abundance of the protein in the sample. Compressing the dynamic range may comprise decreasing the slope of the plot of a protein signal measured by a proteomic analysis assay as a function of total abundance of the protein in the sample relative to the slope of the plot of a protein signal measured by a second proteomic analysis assay as a function of total abundance of the protein in the sample. The protein corona analysis assays disclosed herein may compress the dynamic range relative to the dynamic range of a total protein analysis method (e.g., mass spectrometry, gel electrophoresis, or liquid chromatography).
In some embodiments, the dynamic range of a proteomic analysis assay may be the ratio of the signal produced by highest abundance proteins (e.g., the highest 10% of proteins by abundance) to the signal produced by the lowest abundance proteins (e.g., the lowest 10% of proteins by abundance). Compressing the dynamic range of a proteomic analysis may comprise decreasing the ratio of the signal produced by the highest abundance proteins to the signal produced by the lowest abundance proteins for a first proteomic analysis assay relative to that of a second proteomic analysis assay. The protein corona analysis assays disclosed herein may compress the dynamic range relative to the dynamic range of a total protein analysis method (e.g., mass spectrometry, gel electrophoresis, or liquid chromatography).
Compressing the dynamic range of a proteomic analysis may be achieved by serial interrogation. A method for compressing the dynamic range of a proteomic analysis may comprise serially interrogating a sample (e.g., a biological sample) with particles and performing a protein corona analysis of the proteomic data captured by the particles. In some embodiments, a method for compressing the dynamic range of a proteomic analysis may comprise depleting high abundance proteins from a sample or enriching low abundance proteins in a sample, serially interrogating the sample with a single particle type multiple times or various particle types, and performing a protein corona analysis of the particles. In some embodiments, a method for compressing the dynamic range of a proteomic analysis may comprise fractioning a sample and interrogating a fraction that is enriched for low abundance proteins or depleted of high abundance proteins using the methods of serially interrogating the sample with various particle types, as disclosed herein. In some embodiments, serial interrogation of a sample may be performed before, after, or in lieu of sample fractionation or sample depletion.
The serial interrogation methods disclosed herein may increase the detection of low abundance proteins by protein corona analysis. For example, a serial interrogation method may comprise depleting a sample of high abundance proteins that impact the ability to assay for low abundance proteins. The serial interrogation methods disclosed herein may increase the detection of low abundance proteins by protein corona analysis, because the compressed dynamic range of proteins captured in the protein corona allows for locally concentrating a low abundance protein on the particle surface instead of sampling for said low abundance protein directly in the sample where confounding high abundance proteins are present. In another example, a serial interrogation method may comprise enriching low abundance proteins in biomolecule corona formed on particles. The methods disclosed herein for serially interrogating a sample with various sample types may be preceded by depletion or fractionation. These methods of depletion can include depletion using a depletion kit. These methods of depletion can also include depletion with a novel particle disclosed herein (e.g., any one of the particles in TABLE 1).
A corona analysis after serially interrogating a sample with various particle types may be performed on a biological sample that has been depleted prior to corona analysis. A corona analysis after serially interrogating a sample with various particle types may be performed on individual fractions of fractionated biological sample. A corona analysis after serially interrogating a sample with various particle types may be performed on one or more of the particle types separated from a serially interrogated sample. Fractionation may be used to deplete a sample, and serial interrogation of the sample with various particle types and corona analysis may be performed on the sample that has been fractioned. Fractionation or depletion of a biological sample prior to corona analysis may increase the sensitivity, accuracy, or specificity of the corona analysis. In some embodiments, serial interrogation, fractionation, or depletion of a biological sample prior to corona analysis may enable detection of one or more biological molecules that could not be detected in a sample that is directly assayed for total protein content (e.g., by a gel analysis or mass spectrometry). Serial interrogation of a sample with various particle types and corona analysis of an individual fraction of a fractioned sample may enable detection of a desired subset of biological molecules. A sample may be depleted then serially interrogated with various particle types, which are then analyzed by protein corona analysis. In another example, a sample may be fractioned, and one or more fractions may be serially interrogated with various particle types, which are then analyzed by protein corona analysis.
Serial Interrogation. A sample (e.g., a biological sample) may be serially interrogated with one or more particle types of the present disclosure. A particle type may be separated from the sample, and a protein corona analysis may be performed. Serial interrogation may comprise contacting a sample with a particle type to forming protein corona on the particle, separating the particle type, and repeating the contacting and the separating one or more times on the same sample with the same particle type, a different particle type, or a combination thereof. A protein corona analysis may be performed on one or more of the separated particle types. Serial interrogation of a sample may be well suited for small sample sizes. For example, a protein corona analysis using a panel of particle types (e.g., a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more particle types) may be performed using a sample volume as low as about of no more than about 1000 μL, no more than about 900 μL, no more than about 800 μL, no more than about 700 μL, no more than about 600 μL, no more than about 500 μL, no more than about 400 μL, no more than about 300 μL, no more than about 200 μL, no more than about 100 μL, no more than about 50 μL, or no more than about 20 μL, no more than about 10 μL, no more than about 5 μL, no more than about 2 μL, or no more than about 1 μL. This may provide an advantage over other protein corona analysis methods that involve dividing a sample prior to contacting with one or more particle types. Serial interrogation of a sample may increase the number of proteins that can be identified by protein corona analysis as compared to interrogation of the sample with a single particle type.
A biomolecule composition of a sample may not change substantially during serial interrogation. For example, the biomolecule composition of a sample prior to contacting the sample with first particle type may be substantially the same as the biomolecule composition of the sample following separation of the first particle type from the sample. In some embodiments, the biomolecule composition of a sample prior to contacting the sample with first particle type may be substantially the same as the biomolecule composition of the sample following separation of the second particle type, the third particle type, the fourth particle type, the fifth particle type, or more particle types, from the sample. The biomolecule composition of the sample may be substantially the same if the total biomolecule mass changes by no more than about 1% by mass, no more than about 2% by mass, no more than about 3% by mass, no more than about 4% by mass, no more than about 5% by mass, no more than about 6% by mass, no more than about 7% by mass, no more than about 8% by mass, no more than about 9% by mass, no more than about 10% by mass, no more than about 11% by mass, no more than about 12% by mass, no more than about 13% by mass, no more than about 14% by mass, or no more than about 15% by mass. In some embodiments, the total biomolecule mass of the sample may change by less than about 1% by mass. The biomolecule composition of the sample may be substantially the same if a mass of a subset of biomolecules changes by no more than about 1% by mass, no more than about 2% by mass, no more than about 3% by mass, no more than about 4% by mass, no more than about 5% by mass, no more than about 6% by mass, no more than about 7% by mass, no more than about 8% by mass, no more than about 9% by mass, no more than about 10% by mass, no more than about 11% by mass, no more than about 12% by mass, no more than about 13% by mass, no more than about 14% by mass, or no more than about 15% by mass. In some embodiments, the subset of biomolecules may comprise a medium abundance protein. In some embodiments, the subset of biomolecules may comprise a low abundance protein.
In some embodiments, serial interrogation may be performed by contacting the sample with a first particle type, allowing biological molecules to bind to the first particle type, and separating the first particle type along with the bound biological molecules from the biofluid. For example, the particles may be separated from the biofluid using centrifugation or magnetic separation. The biofluid may be further interrogated by contacting the fluid with a second particle type, allowing biological molecules to bind to the second particle type, and separating the second particle type along with the bound biological molecules from the biofluid. In some embodiments, serial interrogation may be performed by sequentially contacting a biological sample with the same or different particle types, allowing biological molecules to bind to the particle type, and separating each particle type and the bound biological molecules before adding the next particle type. Each separated particle type and bound biological molecules may constitute a fraction. In some embodiments, serial interrogation may be performed with at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 particle types. In some embodiments, serial interrogation with a particle type may be repeated using the sample particle type. In some embodiments, corona analysis may be performed on a fraction of the serially interrogated biological sample. In some embodiments, corona analysis may be performed on a remaining supernatant of the biological sample following serial interrogation.
Depletion. Provided herein are methods of depleting a sample of highly abundant proteins and compositions for doing so. These methods of depleting a sample of high abundance proteins can be carried out prior to the methods described herein of serially interrogating a sample with various particle types, which are then analyzed using the protein corona analysis methods disclosed herein. In some embodiments, one or more nanoparticles can be used to deplete a biological sample of highly abundant proteins. Depletion of a sample with particles may include round-by-round depletion of the sample, wherein within each round, a different type of particle (e.g., a particle with a unique material composition) may be used for the depletion. In other cases, plasma depletion kits, columns, chromatography, or other systems may be used to deplete a biological sample of highly abundant proteins. Depletion followed by serial interrogation of the sample with various particle types and protein corona analysis may increase the number of proteins that can be identified as compared to carrying out the same method in an undepleted sample. However, depletion may not be necessary and serial interrogation of the sample with various particle types and protein corona analysis may be used to identify various proteins in a shorter assay time than if the sample was depleted first.
Sample depletion may comprise reducing a level of at least one biological molecule (e.g., a protein) in the biofluid sample. For example, sample depletion may comprise reducing a level of a highly abundant protein in the sample. The highly abundant protein may be albumin, IgG, or a ribosomal protein. In some embodiments, sample depletion may be performed by contacting the biofluid with a first particle type, allowing biological molecules to bind to the first particle type, and separating the first particle type along with the bound biological molecules from the biofluid. For example, the particles may be separated from the biofluid using centrifugation or magnetic separation. The biofluid may be further depleted by contacting the fluid with a second particle type, allowing biological molecules to bind to the second particle type, and separating the second particle type along with the bound biological molecules from the biofluid. Depletion may be performed on a biofluid by contacting the biofluid with different particle types and separating each particle type before contacting the biofluid with the next particle type, in a round-by-round manner. In some embodiments, depletion may be performed with at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 particle types. In some embodiments, sample depletion may be performed using chromatography or electrophoresis.
In some embodiments, sample depletion may comprise depleting the sample using a commercially available kit. A kit that may be used to deplete a sample may be a spin column-based depletion kit, an albumin depletion kit, an immunodepletion kit, or an abundant protein depletion kit. Non-limiting examples of kits that may be used for sample depletion include a PureProteome™ Human Albumin/Immunoglobulin depletion kit (EMD Millipore Sigma), a ProteoPrep® Immunoaffinity Albumin & IgG Depletion Kit (Millipore Sigma), a Seppro® Protein Depletion kit (Millipore Sigma), Top 12 Abundant Protein Depletion Spin Columns (Pierce), or a Proteome Purify™ Immunodepletion Kit (R&D Systems). While these kits are listed by way of example, one of skill in the art could envision numerous other kits that may be used for sample depletion.
A kit of the present disclosure may comprise a particle type to serially interrogate a sample. The kit may be pre-packaged in discrete aliquots. In another example, the kit can comprise a plurality of different particle types that can be used to serially interrogate a sample. The plurality of particle types can be pre-packaged where each particle type of the plurality is packaged separately. Alternately, the plurality of particle types can be packaged together to contain combination of particle types in a single package.
Depleting a sample may comprise precipitating a component from a sample. In some embodiments, depleting a sample may comprise precipitating an undesired component (e.g. a high abundance protein). An undesired component may be precipitated, and the supernatant may be further processed (e.g., by protein corona analysis, serial interrogation, fractionation, or depletion). In some embodiments, a precipitated undesired component may be removed from the supernatant by filtration, centrifugation, ultracentrifugation, or gravitational separation. Methods of precipitating an undesired component may comprise cryo-precipitation or chemical precipitation (e.g., Cohn process or ethanol precipitation). In some embodiments, depleting a sample may comprise precipitating a desired component (e.g., a low abundance protein). A desired component may be precipitated, the supernatant may be discarded, and the precipitate may be resuspended for further processing (e.g., serial interrogation with various particle types, which are then assayed by protein corona analysis, fractionation, or depletion). In some embodiments, a precipitated desired component may be separated from the supernatant by filtration, centrifugation, ultracentrifugation, or gravitational separation. Methods of precipitating a desired component may comprise cryo-precipitation or chemical precipitation (e.g., Cohn process or ethanol precipitation). In some embodiments, an untreated sample may comprise an undesired precipitate. An undesired precipitate may be removed from the supernatant by filtration, centrifugation, ultracentrifugation, or gravitational separation.
Depleting a sample may comprise separating and undesired component from a desired component (e.g., separating a high abundance protein from a low abundance protein). In some embodiments, components may be separated based on a biochemical property (e.g., binding affinity, charge, or size). In some embodiments, depletion may be performed using chromatography or gel electrophoresis. In some embodiments, a sample may be separated into two or more fractions based on a biochemical property. A first fraction may comprise a desired component, and a second fraction may comprise an undesired component. Fractions comprising desired components may be further processed (e.g., by serial interrogation with various particle types and corona analysis, further fractionation, or depletion). Fractions comprising undesired components may be discarded. Non-limiting examples of depletion methods may include ion-exchange chromatography, affinity chromatography, size exclusion chromatography, gel electrophoresis, or reverse phase chromatography. While these methods are listed by way of example, one of skill in the art could envision numerous other methods that may be used for sample depletion.
Using the compositions and methods disclosed herein, depletion can result in removal of at least 50%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, 100%, from 5% to 20%, from 5% to 100%, from 10% to 95%, from 15% to 90%, from 20% to 85%, from 25% to 80%, from 30% to 75%, from 35% to 70%, from 40% to 65%, from 45% to 60%, from 50% to 55%, from 60% to 70%, from 60% to 80%, or from 50% to 90% of high abundance proteins from a biological sample. In some embodiments, the methods of depletion disclosed herein and the compositions used to deplete a sample can remove all, or 100%, of a highly abundant protein. A corona analysis may be performed on the depleted biological sample.
Fractionation. Provided herein are methods of separating components of a sample (e.g., a biological sample) into fractions. A first fraction may differ from a second fraction in biomolecule composition. For example, a first fraction may be enriched in high abundance proteins, and a second fraction may be enriched in low abundance proteins, relative to the unfractioned sample. A fraction may be further interrogated using the methods and compositions disclosed herein (e.g., serially interrogating the sample followed by protein corona analysis of each particle type used in the serial interrogation). In some embodiments, fractionation may facilitate protein corona analysis by separating high abundance proteins from low abundance proteins, thereby increasing the detection of low abundance proteins. In some embodiments, fractionation may facilitate protein corona analysis by separating a sample into fractions that are well-suited for a particular particle type. For example, a first fraction may be interrogated with a first particle type, and a second fraction may be interrogated with a second particle type. Fractionation followed by protein corona analysis may increase the number of proteins that can be identified as compared to protein corona analysis of an unfractioned sample.
Sample fractionation may comprise separating components of a biological sample. In some embodiments, components may be separated based on a biochemical property (e.g., binding affinity, charge, or size). In some embodiments, fractionation may be performed using chromatography or gel electrophoresis. One or more fractions may be further processed (e.g., by serially interrogating the sample followed by protein corona analysis of each particle type used in the serial interrogation, further fractionation, or depletion). Non-limiting examples of fractionation methods may include ion-exchange chromatography, affinity chromatography, size exclusion chromatography, gel electrophoresis, or reverse phase chromatography. While these methods are listed by way of example, one of skill in the art could envision numerous other methods that may be used for sample fractionation.
Protein Corona Analysis MethodsThe methods disclosed herein include isolating one or more particle types from one or more than one sample (e.g., a biological sample or a serially interrogated sample). The particle types can be rapidly isolated or separated from the sample using a magnetic. Moreover, multiple samples that are spatially isolated can be processed in parallel. Thus, the methods disclosed herein provide for isolating or separating a particle type from unbound protein in a sample. A particle type may be separated by a variety of means, including but not limited to magnetic separation, centrifugation, filtration, or gravitational separation. In some embodiments, particle panels may be incubated with a plurality of spatially isolated samples, wherein each spatially isolated sample is in a well in a well plate (e.g., a 96-well plate). In some embodiments, after incubation, the particle types in each of the wells of the well plate can be separated from unbound protein present in the spatially isolated samples by placing the entire plate on a magnet. This simultaneously pulls down the superparamagnetic particles in the particle panel. The supernatant in each sample can be removed to remove the unbound protein. These steps (incubate, pull down) can be repeated to effectively wash the particles, thus removing residual background unbound protein that may be present in a sample. This is one example, but one of skill in the art could envision numerous other scenarios in which superparamagnetic particles are rapidly isolated from one or more than one spatially isolated samples at the same time.
In some embodiments, the methods and compositions of the present disclosure provide identification and measurement of particular proteins in the biological samples by processing of the proteomic data via digestion of coronas formed on the surface of particles. Examples of proteins that can be identified and measured include highly abundant proteins, proteins of medium abundance, and low-abundance proteins. A low abundance protein may be present in a sample at concentrations at or below about 10 ng/mL. A high abundance protein may be present in a sample at concentrations at or above about 10 μg/mL. A protein of moderate abundance may be present in a sample at concentrations between about 10 ng/mL and about 10 μg/mL. Examples of proteins that are highly abundant proteins include albumin, IgG, and the top 14 proteins in abundance that contribute 95% of the mass in plasma. Additionally, any proteins that may be purified using a conventional depletion column may be directly detected in a sample using the particle panels disclosed herein. Examples of proteins may be any protein listed in published databases such as Keshishian et al. (Mol Cell Proteomics. 2015 September; 14(9):2375-93. doi: 10.1074/mcp.M114.046813. Epub 2015 Feb. 27.), Farr et al. (J Proteome Res. 2014 Jan. 3; 13(1):60-75. doi: 10.1021/pr4010037. Epub 2013 Dec. 6.), or Pernemalm et al. (Expert Rev Proteomics. 2014 August; 11(4):431-48. doi: 10.1586/14789450.2014.901157. Epub 2014 Mar. 24.).
In some embodiments, examples of proteins that can be measured and identified using the methods and compositions disclosed herein include albumin, IgG, lysozyme, CEA, HER-2/neu, bladder tumor antigen, thyroglobulin, alpha-fetoprotein, PSA, CA125, CA19.9, CA 15.3, leptin, prolactin, osteopontin, IGF-II, CD98, fascin, sPigR, 14-3-3 eta, troponin I, B-type natriuretic peptide, BRCA1, c-Myc, IL-6, fibrinogen. EGFR, gastrin, PH, G-CSF, desmin. NSE, FSH, VEGF, P21, PCNA, calcitonin, PR, CA125, LH, somatostatin. S100, insulin. alpha-prolactin, ACTH, Bcl-2, ER alpha, Ki-67, p53, cathepsin D, beta catenin. VWF, CD15, k-ras, caspase 3, EPN, CD10, FAS, BRCA2. CD30L, CD30, CGA, CRP, prothrombin, CD44, APEX, transferrin, GM-CSF, E-cadherin, IL-2, Bax, IFN-gamma, beta-2-MG, TNF alpha, c-erbB-2, trypsin, cyclin D1, MG B, XBP-1, HG-1, YKL-40, S-gamma, NESP-55, netrin-1, geminin, GADD45A, CDK-6, CCL21, BrMS1, 17betaHDI, PDGFRA, Pcaf, CCLS, MMP3, claudin-4, and claudin-3. In some embodiments, other examples of proteins that can be measured and identified using the particle panels disclosed herein are any proteins or protein groups listed in the open targets database for a particular disease indication of interest (e.g., prostate cancer, lung cancer, or Alzheimer's disease).
The proteomic data of the biological sample can be identified, measured, and quantified using a number of different analytical techniques. For example, proteomic data can be analyzed using SDS-PAGE or any gel-based separation technique. Peptides and proteins can also be identified, measured, and quantified using an immunoassay, such as ELISA. Alternatively, proteomic data can be identified, measured, and quantified using mass spectrometry, high performance liquid chromatography, LC-MS/MS, Edman Degradation, immunoaffinity techniques, methods disclosed in EP3548652, WO2019083856, WO2019133892, each of which is incorporated herein by reference in its entirety, and other protein separation techniques.
Computer Control SystemsThe present disclosure provides computer control systems that are programmed to implement methods of the disclosure.
The computer system 901 includes a central processing unit (CPU, also “processor” and “computer processor” herein) 905, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system 901 also includes memory or memory location 910 (e.g., random-access memory, read-only memory, flash memory), electronic storage unit 915 (e.g., hard disk), communication interface 920 (e.g., network adapter) for communicating with one or more other systems, and peripheral devices 925, such as cache, other memory, data storage and/or electronic display adapters. The memory 910, storage unit 915, interface 920 and peripheral devices 925 are in communication with the CPU 905 through a communication bus (solid lines), such as a motherboard. The storage unit 915 can be a data storage unit (or data repository) for storing data. The computer system 901 can be operatively coupled to a computer network (“network”) 930 with the aid of the communication interface 920. The network 930 can be the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet. The network 930 in some cases is a telecommunication and/or data network. The network 930 can include one or more computer servers, which can enable distributed computing, such as cloud computing. The network 930, in some cases with the aid of the computer system 901, can implement a peer-to-peer network, which may enable devices coupled to the computer system 901 to behave as a client or a server.
The CPU 905 can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory 910. The instructions can be directed to the CPU 905, which can subsequently program or otherwise configure the CPU 905 to implement methods of the present disclosure. Examples of operations performed by the CPU 905 can include fetch, decode, execute, and writeback.
The CPU 905 can be part of a circuit, such as an integrated circuit. One or more other components of the system 901 can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).
The storage unit 915 can store files, such as drivers, libraries and saved programs. The storage unit 915 can store user data, e.g., user preferences and user programs. The computer system 901 in some cases can include one or more additional data storage units that are external to the computer system 901, such as located on a remote server that is in communication with the computer system 901 through an intranet or the Internet.
The computer system 901 can communicate with one or more remote computer systems through the network 930. For instance, the computer system 901 can communicate with a remote computer system of a user. Examples of remote computer systems include personal computers (e.g., portable PC), slate or tablet PC's (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone, Android-enabled device, Blackberry®), or personal digital assistants. The user can access the computer system 901 via the network 930.
Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system 901, such as, for example, on the memory 910 or electronic storage unit 915. The machine executable or machine readable code can be provided in the form of software. During use, the code can be executed by the processor 905. In some cases, the code can be retrieved from the storage unit 915 and stored on the memory 910 for ready access by the processor 905. In some situations, the electronic storage unit 915 can be precluded, and machine-executable instructions are stored on memory 910.
The code can be pre-compiled and configured for use with a machine having a processer adapted to execute the code, or can be compiled during runtime. The code can be supplied in a programming language that can be selected to enable the code to execute in a pre-compiled or as-compiled fashion.
Aspects of the systems and methods provided herein, such as the computer system 901, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.
Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.
The computer system 901 can include or be in communication with an electronic display 935 that comprises a user interface (UI) 940 for providing, for example a readout of the proteins identified using the methods disclosed herein. Examples of UI's include, without limitation, a graphical user interface (GUI) and web-based user interface.
Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit 905.
Determination, analysis or statistical classification is done by methods known in the art, including, but not limited to, for example, a wide variety of supervised and unsupervised data analysis and clustering approaches such as hierarchical cluster analysis (HCA), principal component analysis (PCA), Partial least squares Discriminant Analysis (PLSDA), machine learning (also known as random forest), logistic regression, decision trees, support vector machine (SVM), k-nearest neighbors, naive bayes, linear regression, polynomial regression, SVM for regression, K-means clustering, and hidden Markov models, among others. The computer system can perform various aspects of analyzing the protein sets or protein corona of the present disclosure, such as, for example, comparing/analyzing the biomolecule corona of several samples to determine with statistical significance what patterns are common between the individual biomolecule coronas to determine a protein set that is associated with the biological state. The computer system can be used to develop classifiers to detect and discriminate different protein sets or protein corona (e.g., characteristic of the composition of a protein corona). Data collected from the presently disclosed sensor array can be used to train a machine learning algorithm, specifically an algorithm that receives array measurements from a patient and outputs specific biomolecule corona compositions from each patient. Before training the algorithm, raw data from the array can be first denoised to reduce variability in individual variables.
Machine learning can be generalized as the ability of a learning machine to perform accurately on new, unseen examples/tasks after having experienced a learning data set. Machine learning may include the following concepts and methods. Supervised learning concepts may include AODE; Artificial neural network, such as Backpropagation, Autoencoders, Hopfield networks, Boltzmann machines, Restricted Boltzmann Machines, and Spiking neural networks; Bayesian statistics, such as Bayesian network and Bayesian knowledge base; Case-based reasoning; Gaussian process regression; Gene expression programming; Group method of data handling (GMDH); Inductive logic programming; Instance-based learning; Lazy learning;
Learning Automata; Learning Vector Quantization; Logistic Model Tree; Minimum message length (decision trees, decision graphs, etc.), such as Nearest Neighbor Algorithm and Analogical modeling; Probably approximately correct learning (PAC) learning; Ripple down rules, a knowledge acquisition methodology; Symbolic machine learning algorithms; Support vector machines; Random Forests; Ensembles of classifiers, such as Bootstrap aggregating (bagging) and Boosting (meta-algorithm); Ordinal classification; Information fuzzy networks (IFN); Conditional Random Field; ANOVA; Linear classifiers, such as Fisher's linear discriminant, Linear regression, Logistic regression, Multinomial logistic regression, Naive Bayes classifier, Perceptron, Support vector machines; Quadratic classifiers; k-nearest neighbor; Boosting; Decision trees, such as C4.5, Random forests, ID3, CART, SLIQ SPRINT; Bayesian networks, such as Naive Bayes; and Hidden Markov models. Unsupervised learning concepts may include; Expectation-maximization algorithm; Vector Quantization; Generative topographic map; Information bottleneck method; Artificial neural network, such as Self-organizing map; Association rule learning, such as, Apriori algorithm, Eclat algorithm, and FPgrowth algorithm; Hierarchical clustering, such as Singlelinkage clustering and Conceptual clustering; Cluster analysis, such as, K-means algorithm, Fuzzy clustering, DBSCAN, and OPTICS algorithm; and Outlier Detection, such as Local Outlier Factor. Semi-supervised learning concepts may include; Generative models; Low-density separation; Graph-based methods; and Co-training. Reinforcement learning concepts may include; Temporal difference learning; Q-learning; Learning Automata; and SARSA. Deep learning concepts may include; Deep belief networks; Deep Boltzmann machines; Deep Convolutional neural networks; Deep Recurrent neural networks; and Hierarchical temporal memory. A computer system may be adapted to implement a method described herein. The system includes a central computer server that is programmed to implement the methods described herein. The server includes a central processing unit (CPU, also “processor”) which can be a single core processor, a multi core processor, or plurality of processors for parallel processing. The server also includes memory (e.g., random access memory, read-only memory, flash memory); electronic storage unit (e.g. hard disk); communications interface (e.g., network adaptor) for communicating with one or more other systems; and peripheral devices which may include cache, other memory, data storage, and/or electronic display adaptors. The memory, storage unit, interface, and peripheral devices are in communication with the processor through a communications bus (solid lines), such as a motherboard. The storage unit can be a data storage unit for storing data. The server is operatively coupled to a computer network (“network”) with the aid of the communications interface. The network can be the Internet, an intranet and/or an extranet, an intranet and/or extranet that is in communication with the Internet, a telecommunication or data network. The network in some cases, with the aid of the server, can implement a peer-to-peer network, which may enable devices coupled to the server to behave as a client or a server.
The storage unit can store files, such as subject reports, and/or communications with the data about individuals, or any aspect of data associated with the present disclosure.
The computer server can communicate with one or more remote computer systems through the network. The one or more remote computer systems may be, for example, personal computers, laptops, tablets, telephones, Smart phones, or personal digital assistants.
In some applications the computer system includes a single server. In other situations, the system includes multiple servers in communication with one another through an intranet, extranet and/or the internet.
The server can be adapted to store measurement data or a database as provided herein, patient information from the subject, such as, for example, medical history, family history, demographic data and/or other clinical or personal information of potential relevance to a particular application. Such information can be stored on the storage unit or the server and such data can be transmitted through a network.
Methods as described herein can be implemented by way of machine (or computer processor) executable code (or software) stored on an electronic storage location of the server, such as, for example, on the memory, or electronic storage unit. During use, the code can be executed by the processor. In some cases, the code can be retrieved from the storage unit and stored on the memory for ready access by the processor. In some situations, the electronic storage unit can be precluded, and machine-executable instructions are stored on memory. Alternatively, the code can be executed on a second computer system.
Aspects of the systems and methods provided herein, such as the server, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical, and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless likes, optical links, or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” can refer to any medium that participates in providing instructions to a processor for execution.
The computer systems described herein may comprise computer-executable code for performing any of the algorithms or algorithms-based methods described herein. In some applications the algorithms described herein will make use of a memory unit that is comprised of at least one database.
Data relating to the present disclosure can be transmitted over a network or connections for reception and/or review by a receiver. The receiver can be but is not limited to the subject to whom the report pertains; or to a caregiver thereof, e.g., a health care provider, manager, other health care professional, or other caretaker; a person or entity that performed and/or ordered the analysis. The receiver can also be a local or remote system for storing such reports (e.g. servers or other systems of a “cloud computing” architecture). In one embodiment, a computer-readable medium includes a medium suitable for transmission of a result of an analysis of a biological sample using the methods described herein.
Aspects of the systems and methods provided herein can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine readable medium. Machine executable code can be stored on an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide nontransitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.
Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.
Classification of Protein Corona Using Machine LearningThe method of determining a set of proteins associated with the disease or disorder and/or disease state include the analysis of the corona of the at least two samples. This determination, analysis or statistical classification is done by methods known in the art, including, but not limited to, for example, a wide variety of supervised and unsupervised data analysis, machine learning, deep learning, and clustering approaches including hierarchical cluster analysis (HCA), principal component analysis (PCA), Partial least squares Discriminant Analysis (PLS-DA), random forest, logistic regression, decision trees, support vector machine (SVM), k-nearest neighbors, naive bayes, linear regression, polynomial regression, SVM for regression, K-means clustering, and hidden Markov models, among others. In other words, the proteins in the corona of each sample are compared/analyzed with each other to determine with statistical significance what patterns are common between the individual corona to determine a set of proteins that is associated with the disease or disorder or disease state.
Generally, machine learning algorithms are used to construct models that accurately assign class labels to examples based on the input features that describe the example. In some case it may be advantageous to employ machine learning and/or deep learning approaches for the methods described herein. For example, machine learning can be used to associate the protein corona with various disease states (e.g. no disease, precursor to a disease, having early or late stage of the disease, etc.). For example, in some cases, one or more machine learning algorithms are employed in connection with a method of the invention to analyze data detected and obtained by the protein corona and sets of proteins derived therefrom. For example, in one embodiment, machine learning can be coupled with the sensor array described herein to determine not only if a subject has a pre-stage of cancer, cancer or does not have or develop cancer, but also to distinguish the type of cancer.
Unless otherwise defined, all technical terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Any reference to “or” herein is intended to encompass “and/or” unless otherwise stated.
Whenever the term “at least,” “greater than,” or “greater than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “at least,” “greater than” or “greater than or equal to” applies to each of the numerical values in that series of numerical values. For example, greater than or equal to 1, 2, or 3 is equivalent to greater than or equal to 1, greater than or equal to 2, or greater than or equal to 3.
Whenever the term “no more than,” “less than,” “less than or equal to,” or “at most” precedes the first numerical value in a series of two or more numerical values, the term “no more than,” “less than” or “less than or equal to,” or “at most” applies to each of the numerical values in that series of numerical values. For example, less than or equal to 3, 2, or 1 is equivalent to less than or equal to 3, less than or equal to 2, or less than or equal to 1.
Where values are described as ranges, it will be understood that such disclosure includes the disclosure of all possible sub-ranges within such ranges, as well as specific numerical values that fall within such ranges irrespective of whether a specific numerical value or specific sub-range is expressly stated.
Numbered EmbodimentsThe following embodiments recite non-limiting permutations of combinations of features disclosed herein. Other permutations of combinations of features are also contemplated. In particular, each of these numbered embodiments is contemplated as depending from or relating to every previous or subsequent numbered embodiment, independent of their order as listed. 1. A method of serially interrogating a sample, the method comprising: a) contacting the sample to a first particle type and incubating the first particle type with the sample to form a first biomolecule corona, wherein the first biomolecule corona forms upon incubation of the first particle type with the sample and wherein the first biomolecule corona comprises a protein; b) separating the first particle type comprising the first biomolecule corona from the sample; c) contacting the sample to a second particle type and incubating the second particle type with the sample to form a second biomolecule corona, wherein the second biomolecule corona forms upon incubation of the second particle type with the sample, wherein the second biomolecule corona comprises a protein, and further wherein (i) the first particle type and the second particle type are a same particle type or (ii) the first particle type and the second particle type are different; d) separating the second particle type comprising the second biomolecule corona from the sample; e) assaying the first biomolecule corona and the second biomolecule corona to determine a composition and concentration of a plurality of proteins in the sample based on the assayed first biomolecule corona and the second biomolecule corona. 2. The method of embodiment 1, wherein upon the incubating the first particle type with the sample to form the first biomolecule corona, the dynamic range of the plurality of proteins in the first biomolecule corona is compressed relative to a dynamic range of a plurality of proteins in the sample, as measured by a total protein analysis method. 3. The method of embodiment 2, wherein the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio of: a) a signal produced by a higher abundance protein of the plurality of proteins in the first biomolecule corona; and b) a signal produced by a lower abundance protein of the plurality of proteins in the first biomolecule corona. 4. The method of embodiment 2, wherein the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio of a concentration of the highest abundance protein to a concentration of the lowest abundance protein in the plurality of proteins in the first biomolecule corona. 5. The method of embodiment 2, wherein the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio of a top decile of proteins to a bottom decile of proteins in the plurality of proteins in the first biomolecule corona. 6. The method of embodiment 2, wherein the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio comprising a span of the interquartile range of proteins in the plurality of proteins in the first biomolecule corona. 7. The method of embodiment 2, wherein the dynamic range of the plurality of proteins in the first biomolecule corona is a first ratio comprising a slope of fitted data in a plot of all concentrations of proteins in the plurality of proteins in the first biomolecule corona versus known concentrations of the same proteins in the sample. 8. The method of embodiment 7, wherein the known concentrations of the same proteins in the sample are obtained from a database. 9. The method of any one of embodiments 2-8, wherein the dynamic range of a plurality of proteins in the sample is a second ratio of: a) a signal produced by a higher abundance protein of the plurality of proteins in the sample, as measured by a total protein analysis method; and b) a signal produced by a lower abundance protein of the plurality of proteins in the sample, as measured by a total protein analysis method. 10. The method of any one of embodiments 2-8, wherein the dynamic range of the plurality of proteins in the sample, as measured by a total protein analysis method, is a second ratio of a concentration of the highest abundance protein to a concentration of the lowest abundance protein in the plurality of proteins in the sample. 11. The method of any one of embodiments 2-8, wherein the dynamic range of the plurality of proteins in the sample, as measured by a total protein analysis method, is a second ratio of a top decile of proteins to a bottom decile of proteins in the plurality of proteins in the sample. 12. The method of any one of embodiments 2-8, wherein the dynamic range of the plurality of proteins in the sample, as measured by a total protein analysis method, is a second ratio comprising a span of the interquartile range of proteins in the plurality of proteins in the sample. 13. The method of any one of embodiments 2-8, wherein the dynamic range of the plurality of proteins in the sample, as measured by a total protein analysis method, is a second ratio comprising a slope of fitted data in a plot of all concentrations of proteins in the plurality of proteins in the sample versus known concentrations of the same proteins in the sample. 14. The method of embodiment 13, wherein the known concentrations of the same proteins in the sample are obtained from a database. 15. The method of any one of embodiments 9-14, wherein the compressing the dynamic range comprises a decreased first ratio relative to the second ratio. 16. The method of embodiment 15, wherein the decreased first ratio is at least 1.1-fold, at least 1.2-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 5-fold, or at least 10-fold less than the second ratio. 17. The method of any one of embodiments 1-16, wherein the method further comprises: determining the composition and concentration of a plurality of proteins in the second biomolecule corona. 18. The method of any one of embodiments 1-17, wherein the determining the composition and concentration of the plurality of proteins in the first biomolecule corona or determining the composition and concentration of the plurality of proteins in the second biomolecule corona comprises performing mass spectrometry. 19. The method of any one of embodiments 1-18, the method further comprising repeating step a), b), and e) with one or more additional particle types to form one or more additional biomolecule coronas. 20. The method of embodiment 19, wherein the one or more additional particle types are the same as the first particle type or the second particle type. 21. The method of embodiment 19, wherein the one or more additional particle types are different from the first particle type, the second particle type, or a combination thereof 22. The method of any one of embodiments 19-21, wherein the one or more additional biomolecule coronas comprise proteins from the sample. 23. The method of any one of embodiments 19-22, wherein the first biomolecule corona, the second biomolecule corona, the one or more additional biomolecule coronas, or any combination thereof comprises at least 100 distinct proteins. 24. The method of any one of embodiments 19-23, wherein the first biomolecule corona, the second biomolecule corona, the one or more additional biomolecule coronas, or any combination thereof comprises at least 200 distinct proteins, at least 300 distinct proteins, at least 400 distinct proteins, at least 500 distinct proteins, at least 1000 distinct proteins, at least 2000 distinct proteins, or at least 5000 distinct proteins. 25. The method of any one of embodiments 19-24, wherein the first biomolecule corona, the second biomolecule corona, the one or more additional biomolecule coronas, or any combination thereof comprises a different composition of proteins, a different concentration of a subset of proteins, or a combination thereof 26. The method of any one of embodiments 19-25, upon incubating the one or more additional particle types with the sample to form one or more additional biomolecule coronas, a dynamic range of a plurality of proteins in the one or more additional biomolecule coronas is compressed relative to a dynamic range of a plurality of proteins in the sample, as measured by a total protein analysis method. 27. The method of embodiment 26, wherein the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio of: a) a signal produced by a higher abundance protein of the plurality of proteins in the one or more additional biomolecule coronas; and b) a signal produced by a lower abundance protein of the plurality of proteins in the one or more additional biomolecule coronas. 28. The method of embodiment 26, wherein the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio of a concentration of the highest abundance protein to a concentration of the lowest abundance protein in the plurality of proteins in the one or more biomolecule coronas. 29. The method of embodiment 26, wherein the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio of a top decile of proteins to a bottom decile of proteins in the plurality of proteins in the one or more biomolecule coronas. 30. The method of embodiment 26, wherein the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio comprising a span of the interquartile range of proteins in the plurality of proteins in the one or more biomolecule coronas. 31. The method of embodiment 26, wherein the dynamic range of the plurality of proteins in the one or more additional biomolecule coronas is an additional ratio comprising a slope of fitted data in a plot of all concentrations of proteins in the plurality of proteins in the one or more biomolecule coronas versus known concentrations of the same proteins in the sample. 32. The method of embodiment 31, wherein the known concentrations of the same proteins in the sample are obtained from a database. 33. The method of any one of embodiments 27-32, wherein the compressing the dynamic range comprises a decreased additional ratio relative to the second ratio. 34. The method of embodiment 33, wherein the decreased first ratio is at least 1.1-fold, at least 1.2-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 5-fold, or at least 10-fold less than the second ratio. 35. The method of any one of embodiments 2-34, wherein the total protein analysis method comprises direct quantification of the plurality of proteins in the sample by mass spectrometry, gel electrophoresis, or liquid chromatography. 36. The method of any one of embodiments 1-35, wherein the sample comprises a sample volume of no more than about 1000 μL, no more than about 900 μL, no more than about 800 μL, no more than about 700 μL, no more than about 600 μL, no more than about 500 μL, no more than about 400 μL, no more than about 300 μL, no more than about 200 μL, no more than about 100 μL, no more than about 50 μL, no more than about 20 μL, no more than about 10 μL, no more than about 5 μL, no more than about 2 μL, or no more than about 1 μL. 37. The method of any one of embodiments 1-36, wherein the sample comprises a biological sample. 38. The method of embodiment 37, wherein the biological sample comprises a biofluid. 39. The method of embodiment 38, wherein the biofluid is selected from the group consisting of plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, fluidized solids, fine needle aspiration samples, tissue homogenates, and cell culture samples. 40. The method of any one of embodiments 38-39, wherein the biofluid is plasma or serum. 41. The method of any one of embodiments 38-39, wherein the biofluid is cerebrospinal fluid. 42. The method of any one of embodiments 19-41, wherein the first particle type, the second particle type, the one or more additional particle types, or any combination thereof are selected from TABLE 1. 43. The method of any one of embodiments 1-42, comprising removing high abundance proteins from the sample by depleting or fractioning the sample prior to step a). 44. The method of any one of embodiments 19-43, wherein the one or more additional biomolecule coronas comprises a protein. 45. The method of any one of embodiments 19-44, wherein the first biomolecule corona, the second biomolecule corona, the one or more additional biomolecule coronas, or any combination thereof comprises a lipid, a nucleic acid, a polysaccharide, or any combination thereof 46. The method of any one of embodiments 19-45, wherein the first particle type, the second particle type, or the one or more additional particle types differ by at least one physicochemical properties. 47. The method of any one of embodiments 1-46, wherein the first particle type and the second particle type differ by at least one physicochemical property and wherein the first biomolecule corona comprises a distinct but overlapping set of proteins relative to the second biomolecule corona. 48. The method of any one of embodiments 1-47, wherein the composition of the plurality of proteins and the concentration of a protein of the plurality of proteins is determined based on the distinct but overlapping set of proteins in the first biomolecule corona and the second biomolecule corona. 49. The method of any one of embodiments 19-48, wherein the first particle type, the second particle type, the one or more additional particle types, or any combination thereof is selected from the group consisting of a nanoparticle, a microparticle, a micelle, a liposome, an iron oxide particle, a graphene particle, a silica particle, a protein-based particle, a polystyrene particle, a silver particle, a gold particle, a metal particle, a quantum dot, a superparamagnetic particle, or any combination thereof 50. The method of any one of embodiments 1-49, wherein the first particle type, the second particle type, the one or more additional particle types, or any combination thereof is a superparamagnetic particle. 51. The method of any one of embodiments 1-50, wherein the first particle type, the second particle type, the one or more additional particle types, or any combination thereof is selected from TABLE 1. 52. The method of any one of embodiments 1-51, wherein the first particle type and the second particle type are the same particle type and wherein at least 70%, at least 80%, at least 90%, or at least 95% of proteins assayed in the first biomolecule corona and the second biomolecule corona are the same. 53. The method of any one of embodiments 1-52, wherein the first particle type and the second particle type are different and wherein no more than 70%, no more than 80%, no more than 90%, or no more than 95% of proteins assayed in the first biomolecule corona and the second biomolecule corona are the same. 54. A high throughput method of analyzing a plurality of biofluids, the method comprising: a) contacting a first biofluid and a second biofluid of the plurality of biofluids with a particle type; b) in a first volume, separating the particle type from a first biofluid of the plurality of biofluids and determining the composition and concentration of a plurality of proteins in a first biomolecule corona corresponding to the particle type; and c) in a second volume, separating the particle type from a second biofluid of the plurality of biofluids and determining the composition and concentration of a plurality of proteins in a second biomolecule corona corresponding to the particle type, wherein the first biofluid and the second biofluid are different biofluids. 55. The method of embodiment 54, wherein a biofluid of the plurality of biofluids is selected from the group consisting of plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, fluidized solids, fine needle aspiration samples, tissue homogenates, and cell culture samples. 56. The method of embodiment 55, wherein the biofluid is plasma or serum. 57. The method of embodiment 55, wherein the biofluid is cerebrospinal fluid. 58. The method of any one of embodiments 54-57, wherein a biomolecule corona forms upon contacting the particle type with the sample and wherein the first biomolecule corona comprises a protein. 59. The method of embodiment 58, wherein the biomolecule corona comprises a lipid, a nucleic acid, a polysaccharide, or any combination thereof 60. The method of any one of embodiments 54-59, comprising removing high abundance proteins from the sample by depleting or fractioning the sample prior to step a). 61. The method of any one of embodiments 54-60, wherein the particle type is selected from the group consisting of a nanoparticle, a microparticle, a micelle, a liposome, an iron oxide particle, a graphene particle, a silica particle, a protein-based particle, a polystyrene particle, a silver particle, a gold particle, a metal particle, a quantum dot, a superparamagnetic particle, or any combination thereof 62. The method of any one of embodiments 54-61, wherein the particle type is a superparamagnetic particle. 63. The method of any one of embodiments 54-62, wherein the particle type is selected from TABLE 1. 64. The method of any one of embodiments 1-63, wherein the separating comprises magnetic separation, filtration, gravitational separation, or centrifugation. 65. The method of any one of embodiments 1-64, wherein the contacting occurs in vitro. 66. The method of any one of embodiments 38-53 or 55-65, wherein the method further comprises identifying a biological state of the biofluid processing the composition and concentration of the plurality of proteins in the biomolecule corona using a trained algorithm to identify the biological state. 67. The method of any one of embodiments 38-53 or 55-66, wherein the biofluid is isolated from a subject. 68. The method of embodiment 67, wherein the subject is a human. 69. The method of embodiment 67, wherein the subject is a non-human animal. 70. The method of any one of embodiments 67-69, wherein the subject has a condition. 71. The method of embodiment 70, wherein the condition is a disease state. 72. The method of embodiment 71, wherein the disease state is cancer. 73. The method of embodiment 72, wherein the cancer is prostate cancer, colorectal cancer, lung cancer, or breast cancer. 74. The method of embodiment 71, wherein the disease state is Alzheimer's disease. 75. The method of any one of embodiments 1-74, wherein the separating comprises magnetic separation, column-based separation, filtration, spin column-based separation, centrifugation, ultracentrifugation, density or gradient-based centrifugation, gravitational separation, or any combination thereof 76. A method of analyzing a biofluid, the method comprising: a) contacting a biofluid in a biofluid collection tube with a particle type, wherein the blood collection tube comprises a stabilization reagent, wherein the stabilization reagent stabilizes cell-free nucleic acid molecules in the biofluid; and b) incubating the biofluid and the particle type in the biofluid collection tube to permit binding of proteins of the biofluid to the particle type, thereby forming a biomolecule corona comprising proteins bound to the particle type, wherein the biomolecule corona comprises a population of proteins that is also detected when the particle type is incubated in the biofluid when stored in EDTA and permitted to form a control biomolecule corona; and wherein the biofluid and the particle type are incubated in the biofluid collection tube at from about 20° C. to about 35° C. and wherein 50% or more of the population of proteins of the biomolecule corona is also detectable in the control biomolecule corona. 77. The method of embodiment 76, wherein 60% or more, 70% or more, 80% or more, or 90% or more of the population of proteins of the biomolecule corona is also detectable in the control biomolecule corona. 78. The method of any one of embodiments 76-77, wherein at least a subset of the population of proteins is detected at a higher abundance than when the particle type is incubated in the biofluid when stored in EDTA. 79. The method of any one of embodiments 76-78, wherein at least 5% of the population of proteins is detected at a higher abundance than when the particle type is incubated in the biofluid when stored in EDTA. 80. The method of any one of embodiments 76-79, wherein at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or 100% of the population of proteins is detected at a higher abundance than when the particle type is incubated in the biofluid when stored in EDTA. 81. The method of any one of embodiments 76-80, further comprising assaying the proteins in the biomolecule corona at a lower limit of detection than when the particle type is incubated in the biofluid when stored in EDTA. 82. The method of any one of embodiments 76-81, wherein the incubating comprises incubating at room temperature. 83. The method of any one of embodiments 76-82, wherein the incubating comprises incubating for up to 14 days, up to 13 days, up to 12 days, up to 11 days, up to 10 days, up to 9 days, up to 8 days, up to 7 days, up to 6 days, up to 5 days, up to 4 days, or up to 3 days. 84. The method of any one of embodiments 76-83, wherein the incubating comprises incubating for up to 14 days. 85. The method of any one of embodiments 76-84, wherein the biomolecule corona comprises a unique protein that is absent from the control biomolecule corona. 86. The method of any one of embodiments 76-85, wherein the biomolecule corona comprises at least 100 distinct proteins, at least 200 distinct proteins, at least 300 distinct proteins, at least 400 distinct proteins, at least 500 distinct proteins, at least 1000 distinct proteins, at least 2000 distinct proteins, or at least 5000 distinct proteins. 87. The method of any one of embodiments 76-86, wherein the particle type binds 100 or more distinct proteins 88. The method of any one of embodiments 86-87, wherein the biofluid comprises plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, fluidized solids, fine needle aspiration samples, tissue homogenates, or cell culture samples. 89. The method of any one of embodiments 86-88, wherein the biofluid is plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, a fluid from swabbing, a bronchial aspirant, a fluidized solid, a fine needle aspiration sample, a tissue homogenate, or a cell culture sample. 90. The method of any one of embodiments 76-89, further comprising separating the particle type from the biofluid. 91. The method of embodiment 90, wherein separating comprises magnetic separation, filtration, gravitational separation, or centrifugation. 92. The method of any one of embodiments 76-91, further comprising determining the composition and concentration of proteins in the biomolecule corona. 93. The method of any one of embodiments 76-92, further comprising determining the composition and concentration of proteins in the control biomolecule corona. 94. The method of any one of embodiments 76-93, wherein the determining the composition and concentration of proteins comprises mass spectrometry, gel electrophoresis, or liquid chromatography. 95. The method of any one of embodiments 76-94, wherein the stabilization reagent comprises a metabolic inhibitor, a protease inhibitor, a phosphatase inhibitor, a nuclease inhibitor, a preservative agent, or a combination thereof 96. The method of embodiment 95, wherein the metabolic inhibitor comprises glyceraldehyde, dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, 1,3-bisphosphoglycerate, 3-phosphoglycerate, 2-phosphoglycerate, phosphoenolpyruvate, pyruvate and glycerate dihydroxyacetate, sodium fluoride, or K2C2O4. 97. The method of embodiment 95 or embodiment 96, wherein the protease inhibitor comprises antipain, aprotinin, chymostatin, elastatinal, phenylmethylsulfonyl fluoride (PMSF), APMSF, TLCK, TPCK, leupeptin, soybean trypsin inhibitor, indoleacetic acid (IAA), E-64, EDTA, pepstatin, VdLPFFVdL, 1,10-phenanthroline, phosphoramodon, amastatin, bestatin, diprotin A, diprotin B, alpha-2-macroglobulin, lima bean trypsin inhibitor, pancreatic protease inhibitor, or egg white ovostatin egg white cystatin. 98. The method of any one of embodiments 95-97, wherein the phosphatase inhibitor comprises calyculin A, nodularin, NIPP-1, microcystin LR, tautomycin, okadaic acid, cantharidin, microcystin LR, okadaic acid, fostriecin, tautomycin, cantharidin, endothall, nodularin, cyclosporin A, FK 506/immunophilin complexes, cypermethrin, deltamethrin, fenvalerate, bpV(phen), dephostatin, mpV(pic) DMHV, or sodium orthovanadate. 99. The method of any one of embodiments 95-98, wherein the nuclease inhibitor comprises diethyl pyrocarbonate, ethanol, aurintricarboxylic acid (ATA), formamide, vanadyl-ribonucleoside complexes, macaloid, ethylenediamine tetraacetic acid (EDTA), proteinase K, heparin, hydroxylamine-oxygen-cupric ion, bentonite, ammonium sulfate, dithiothreitol (DTT), beta-mercaptoethanol, cysteine, dithioerythritol, tris(2-carboxyethyl) phosphene hydrochloride, or a divalent cation such as Mg+2, Mn+2, Zn+2, Fe+2, Ca+2, or Cu+2. 100. The method of any one of embodiments 95-99, wherein the preservative agent comprises diazolidinyl urea, imidazolidinyl urea, dimethoylol-5,5-dimethylhydantoin, dimethylol urea, 2-bromo-2-nitropropane-1,3-diol, oxazolidines, sodium hydroxymethyl glycinate, 5-hydroxymethoxymethyl-1-1aza-3,7-dioxabicyclo[3.3.0]octane, 5-hydroxymethyl-1-1aza-3,7dioxabicyclo[3.3.0]octane, 5-hydroxypoly[methyleneoxy]methyl-1-1aza-3,7dioxabicyclo[3.3.0]octane, or quaternary adamantine. 101. The method of any one of embodiments 76-100, wherein the biofluid collection tube is a blood collection tube. 102. The method of any one of embodiments 76-101, wherein the particle type is a nanoparticle or a microparticle. 103. The method of any one of embodiments 76-102, wherein the particle type is selected from the group consisting of a nanoparticle, a microparticle, a micelle, a liposome, an iron oxide particle, a graphene particle, a silica particle, a protein-based particle, a polystyrene particle, a silver particle, a gold particle, a metal particle, a quantum dot, a superparamagnetic particle, and any combination thereof 104. The method of any one of embodiments 76-103, wherein the particle type is selected from TABLE 1. 105. The method of any one of embodiments 76-104, further comprising contacting the biofluid with one or more additional particle types, incubating the biofluid with the one or more additional particle types to permit binding of proteins of the biofluid to the one or more additional particle type, thereby forming one or more additional biomolecule coronas comprising proteins bound to the one or more additional particle types. 106. The method of embodiment 105, wherein the one or more additional particle types binds a population of proteins that is distinct but overlapping with the population of proteins in the biomolecule proteins of the particle type. 107. The method of any one of embodiments 105-106, wherein the contacting the biofluid with the one or more additional particle types occurs after the contacting the biofluid with the particle type. 1. A method of analyzing of a plurality of biofluids, the method comprising: (a) separately contacting each biofluid of the plurality of biofluids with a nanoparticle (b) isolating the first nanoparticle and analyzing a first protein corona corresponding to a first biofluid of the plurality of biofluids; and (c) isolating the second nanoparticle and analyzing a second protein corona corresponding to a second biofluid of the plurality of biofluids, wherein step (b) and step (c) occur simultaneously. 2. The method of embodiment 1, the method further comprising contacting the plurality of biofluids with a third nanoparticle. 3. The method of any one of embodiments 1-2, the method further comprising contacting the plurality of biofluids with a fourth nanoparticle. 4. The method of any one of embodiments 1-3, the method further comprising contacting the plurality of biofluids with a fifth nanoparticle. 5. The method of embodiment 1, wherein the first nanoparticle and the second nanoparticle are the same. 6. The method of embodiment 1, the method further comprising contacting the plurality of biofluids with up to 10 different nanoparticles. 7. The method of embodiment 1, wherein the nanoparticle is made of a material selected from a lipid, a polymer, a metal, or any combination thereof 8. The method of embodiment 7, wherein the polymer comprises PS, PLA, PGA, PLGA, or PVP. 9. The method of embodiment 7, wherein the lipid comprises EPC, DOPC, DOPG, or DPPG. 10. The method of embodiment 7, wherein the metal comprises iron oxide, gold, or silver. 11. The method of embodiment 1, wherein the nanoparticle comprises a positive surface charge. 12. The method of embodiment 1, wherein the nanoparticle comprises a negative surface charge. 13. The method of embodiment 1, wherein the nanoparticle comprises a neutral surface charge. 14. The method of embodiment 1, wherein the nanoparticle comprises a size of 1-400 nm. 15. The method of embodiment 1, wherein biofluid comprises plasma, serum, CSF, urine, tear, or saliva. 16. The method of embodiment 1, wherein the method further comprises comparing the first protein corona to a first control protein corona identified by contacting the first biofluid with the first nanoparticle. 17. The method of embodiment 1, wherein the method further comprising comparing the second protein corona to a second control protein corona identified by contacting the second biofluid with the second nanoparticle. 18. The method of embodiment 1, wherein the method further comprises correlating the first protein corona to a first biological state. 19. The method of embodiment 1, wherein the method further comprises correlating the second protein corona to a second biological state. 1. A method of identifying a biological state of a sample of a subject, the method comprising: incubating the sample with a depletion nanoparticle, thereby generating a depleted sample; incubating the depleted sample with a first nanoparticle to generate a protein corona; generating protein data corresponding to a protein in the protein corona associated with the first nanoparticle; and processing the protein data using a trained algorithm to identify the biological state of the subject. 2. A method of identifying a biological state of a protein sample from a subject, the method comprising: fractionating the protein sample, thereby generating a fractionated sample comprising a subset of proteins in the protein sample; incubating the depleted sample with a first nanoparticle to generate a protein corona; generating protein data corresponding to a protein of the protein corona associated with the first nanoparticle; and processing the protein data using a trained algorithm to identify the biological state of the subject, wherein fractionating the sample comprises separating high abundance proteins with a method selected from the group consisting of Cohn's method, column chromatograph, ion-exchange chromatography, affinity chromatography, size exclusion chromatography, centrifugation, filtration, ultrafiltration and cryo-precipitation. 3. The method of embodiment 1, wherein incubating the sample with the depletion nanoparticle comprises the incubating the sample with the depletion nanoparticle for at least about 30 minutes and extracting the depletion nanoparticle from the sample. 4. The method of embodiment 3, wherein incubating the sample with the depletion nanoparticle for at least about 30 min and the extracting the depletion nanoparticle from the sample removes at least about 80% of high abundance proteins from the sample. 5. The method of embodiment 1, further comprising analyzing a protein corona associated with the depletion nanoparticle. 6. The method of embodiment 1, wherein the incubating the sample with the depletion nanoparticle comprises incubating the sample with the depletion nanoparticle for at least about 60 minutes and extracting the depletion nanoparticle from the sample at least two times. 7. The method of embodiment 6, wherein the incubating the sample with the depletion nanoparticle for at least about 60 minutes and removing the depletion nanoparticle from the sample at least two times removes 99% of high abundance proteins. 8. The method of embodiment 1 or 2, wherein a concentration of the first nanoparticle in the depleted sample is from 1-50 mg/mL. 9. The method of embodiment 1 or 2, wherein a concentration of the first nanoparticle in the depleted sample is from 2.5-10 mg/mL. 10. The method of embodiment 1, wherein the depletion nanoparticle comprises at least one different physicochemical property from the first nanoparticle. 11. The method of embodiment 10, wherein the different physicochemical property comprises size, surface charge, or a chemical moiety. 12. The method of embodiment 1 or 2, wherein the generating protein data corresponding to the protein in the protein corona associated with the first nanoparticle comprises determining a concentration of each unique protein in the protein corona and correlating the concentration of each unique protein in the protein corona to the biological state. 13. The method of embodiment 1 or 2, wherein processing the protein data using a trained algorithm to identify the biological state of the subject comprises associating the biological state with a biomolecule fingerprint. 14. The method of embodiment 1 or 2, wherein the sample is plasma or serum. 15. The method of embodiment 1, wherein processing the protein data comprises analyzing the protein corona, analyzing the sample prior to depletion, or analyzing the depleted sample. 16. The method of embodiment 2, wherein processing the protein data comprises analyzing the protein corona, analyzing the protein sample prior to fractionation, or analyzing the fractionated sample. 17. A method for assaying a biological sample, comprising (a) obtaining a biological sample comprising a plurality of biomolecules, which plurality of biomolecules comprises protein; (b) enriching said biological sample based on one or more features selected from the group consisting of: size, charge, hydrophobicity, structure and affinity, to yield a processed biological sample; (c) generating at least a first subset of biomolecules and a second subset of biomolecules from said processed biological sample of (b) with the aid of one or more nanoparticles, wherein said first subset of biomolecules associates with said one or more nanoparticles and said second subset of biomolecules does not associate with said one or more nanoparticles; and (d) separately conducting one or more assays on at least said first subset of biomolecules or said second subset of biomolecules. 18. The method of embodiment 17, further comprising (e) isolating said first subset of biomolecules from said second subset of biomolecules. 19. The method of embodiment 17, wherein said one or more assays comprises an assay selected from the group consisting of: mass spectrometry and enzyme-linked immunosorbent assay (ELISA). 20. The method of embodiment 17, wherein said one or more assays comprise mass spectrometry. 21. The method of embodiment 17, wherein the enriching said biological sample comprises fractionation to yield said processed biological sample. 22. The method of embodiment 21, wherein the fractionation comprises separating high abundance proteins with a method selected from the group consisting of Cohn's method, ion-exchange chromatography, affinity chromatography, size exclusion chromatography, centrifugation, filtration, ultrafiltration and cryo-precipitation. 23. The method of embodiment 17, wherein the enriching said biological sample to yield said processed biological sample comprises depleting one or more proteins. 24. The method of embodiment 17, wherein, in (b), one or more depletion nanoparticles are used to yield said processed biological sample. 25. The method of embodiment 24, wherein said one or more depletion nanoparticles of (b) are different from said one or more nanoparticles of (c). 26. The method of embodiment 17, wherein said one or more assays are conducted on said first subset, which assay is ELISA. 27. The method of embodiment 17, wherein said biological sample is a biofluid selected from the group consisting of: plasma, serum, urine, cerebrospinal fluid, tears, saliva, whole blood, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, pericrevicular fluid, semen, prostatic fluid, sputum, synovial fluid, fecal matter, trabecular fluid, bronchial lavage, fluid from swabbings, and bronchial aspirants. 28. The method of embodiment 17, wherein said one or more assays yields proteomic data, and further comprising processing said proteomic data to predict a biological state. 29. The method of embodiment 28, wherein said processing said proteomic data comprises use of a trained algorithm, which trained algorithm is trained using an independent set of biological samples. 30. The method of embodiment 17, wherein said first subset of biomolecules associates with said one or more nanoparticles upon incubation with said one or more nanoparticles to form protein coronas. 31. The method of embodiment 17, wherein said biological sample is depleted prior to (a). 32. The method of embodiment 17, said first subset of biomolecules and said second subset of biomolecules comprise protein.
EXAMPLESThe following examples are illustrative and non-limiting to the scope of the devices, methods, systems, and kits described herein.
Example 1 Identification of Proteins in Cerebrospinal Fluid (CSF) Protein CoronaThis example describes the identification of proteins in cerebrospinal fluid (CSF) protein corona.
To produce protein coronas from a cerebrospinal fluid (CSF) sample, about 100 μL of P39 particles were mixed with about 100 μL of neat CSF in microtiter plates. The plates were sealed and incubated at about 37° C. for about 1 hour with shaking at 300 rpm. After incubation, the plate was placed on top of magnetic collection for about 5 minutes to pellet down the particles. Unbound proteins in biological samples were pipetted out. The protein corona was further washed with about 200 μL of PBS for three times with magnetic separation.
To digest the proteins bound onto particles, a trypsin digestion kit (iST 96X, PreOmics, Germany) was used according to the protocols provided. Briefly, after the last round of wash buffer was pipetted out from the plate, about 50 μL of lyse buffer was added to each well and the sample was heated at about 95° C. for about 10 minutes with agitation. After cooling down the plates to room temperature, trypsin digest buffer was added and the plate was incubated at about 37° C. for about 3 hours with shaking. The digestion process was stopped with a stop buffer. The supernatant was separated from the particles by a magnetic collector and further cleaned up by a peptide cleanup cartridge included in the kit. The peptide was eluted with about 75 μL of elution buffer twice and combined. Peptide concentration was measured by a quantitative colorimetric peptide assay kit from Pierce.
The peptide eluates were lyophilized and reconstituted in about 0.1% TFA. An about 2 μg aliquot (based on submitted protein quant values) was analyzed by nano LC/MS/MS with a Waters NanoAcquity HPLC system interfaced to a ThermoFisher Fusion Lumos. Peptides were loaded on a trapping column and eluted over a 75 μm analytical column at 350 nL/min; both columns were packed with Luna C18 resin (Phenomenex). A 2 hour gradient was employed in all cases except for sample 33295 that was also acquired with a 1 hour gradient. The mass spectrometer was operated in data-dependent mode, with MS and MS/MS performed in the Orbitrap at 60,000 FWHM resolution and 15,000 FWHM resolution, respectively. APD was turned on. The instrument was run with a 3 second cycle for MS and MS/MS. The mass spectrometry data were processed through the MaxQuant software v1.6.0.16. Swissprot was used to search for protein identifications with 1% protein and peptide false discovery rate (FDR). Peak areas were calculated for detected peptides. The MaxQuant results were parsed into the Scaffold software for visualization.
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This example describes the identification of proteins in urine protein corona.
To produce protein coronas from a urine sample, about 100 μL of P39 particles were mixed with 100 μL of neat urine samples in microtiter plates. The plates were sealed and incubated at 37° C. for 1 hour with shaking at 300 rpm. The rest of the assay was performed the same way as CSF protein corona, as described in EXAMPLE 1.
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This example describes sample preparation for identification of peptide corona.
To generate proteomic data from a peptide corona, plasma samples were first denatured and reduced before digestion with trypsin. The resulting peptides were incubated with about 100 μL of paramagnetic particles in microtiter plates. The plates were sealed and incubated at about 37° C. for about 1 hour with shaking at 300 rpm. The peptide corona was washed 3 times with a TE buffer with magnetic separation. Bound peptides were eluted with 1% TFA in 50% of acetonitrile. The peptide eluates were lyophilized and reconstituted in 0.1% TFA before submitting for mass spectrometry analysis.
Example 4 Multiplexing Measurement of Protein CoronaThis example describes multiplexing measurement of protein corona.
Protein corona can be multiplexed in two different ways: particle mixing and post-digestion mixing.
With particle mixing, the particles were prepared at about equal concentrations and pre-mixed before being plated to the microtiter plate at about 100 μL. Biological samples were prepared as usual and mixed with the particles completely by pipetting the mixture up and down for at least about 10 times. The plates were sealed and incubated at about 37° C. for about 1 hour with shaking at 300 rpm. The rest of the assay was performed the same way as CSF protein corona, as described in EXAMPLE 1.
With post-digestion mixing, the protein corona assay was performed the same way as CSF protein corona, as described above. After digested peptides were eluted out, peptides derived from different particles were combined and mixed before lyophilization. The peptide elutes were lyophilized and reconstituted in 0.1% TFA before submitting for mass spectrometry analysis.
This example describes the identification of a variety of proteins in particle protein corona.
Proteins identified in the corona of 23 different particle types were compared to the cellular concentration of the identified protein.
This example describes a procedure for particle-based serial interrogation.
Plasma was interrogated with various particles at the first step, and serially interrogated with a new or same particle to further look at subtle changes of proteins-particle and/or protein-protein interactions. An example of a workflow for such serial interrogation is provided in TABLE 2. Particle types can be changed depending on experimental design.
As shown in
This example describes a depletion assay followed by serial incubation and assaying with particles.
For depletion, the PureProteome™ Human Albumin/Immunoglobulin depletion kit from EMD Millipore Sigma was used. The original buffer of the beads was removed, the beads were washed twice with TE, and 4× diluted plasma was added and vortexed. Then, the beads and plasma were incubated at about room temperature with rotation for about 1 hour. The supernatant was removed.
In a second assay, plasma samples were depleted using magnetic beads against albumin and immunoglobulin (Ig). Depleted plasma was depleted using a series of two HPLC columns to (1) deplete most abundant proteins and (2) to deplete moderate abundance proteins. Depleted and undepleted samples were interrogated with particles to form protein corona.
This example describes a procedure for depletion with spin columns.
For depletion with spin columns, the depletion spin column is equilibrated to about room temperature, 100 μL of sample is directly added to the resin slurry in the column, the mixture is incubated in the column with gentle end-over-end mixing for about 10 minutes at about room temperature, and then the mixture is centrifuged at 1,000×g for about 2 minutes. Then, the flow through is collected.
Example 9 Protein Depletion and Corona Analysis of Synovial Fluid SamplesThis example describes protein depletion and coronal analysis of synovial fluid samples.
Synovial fluid (SF) samples were incubated with particles to form particle protein corona. 100 μL of sample was incubated with 100 μL of particles for 1 hour. Following incubation, particles were pelleted using a magnet. Supernatants were removed using a pipette. The pellet was washed with PBS and re-pelleted three times. Proteins bound to the particles were digested with a trypsin digestion kit (iST 96X, PreOmics, Germany) according to the protocols provided in the kit and summarized in EXAMPLE 1. Peptide concentrations were measured by a quantitative colorimetric peptide assay kit from Thermo Fisher Scientific. Mass spectrometry was performed on the eluted peptides following the method described in EXAMPLE 1.
As indicated by bar height, greater than 1000 identified proteins were detected for each particle-containing corona sample. In contrast, only 334 identified proteins were detected in the neat SF negative control. When the corona analysis results from each of the 9 particles were combined, over 3500 proteins were detected (“All NP”).
Example 10 Protein Depletion and Corona Analysis of Tissue and Fine Needle Aspiration SamplesThis example describes protein depletion and coronal analysis of tissue and fine needle aspiration samples. Protein corona were prepared and analyzed for tissue samples and fine needle aspiration (FNA) samples as described in EXAMPLE 9 with respect to synovial fluid samples.
This example describes protein corona analysis and protein depletion. Protein corona were prepared and analyzed for matched plasma samples and serum samples as described in EXAMPLE 9 with respect to synovial fluid samples. Depleted plasma was depleted using a series of two HPLC columns to (1) deplete most abundant proteins and (2) to deplete moderate abundance proteins.
The experiment demonstrated that the greatest number of proteins were identified in depleted plasma samples for most particle treatments.
Example 12 Protein Corona Analysis of Samples Collected in Blood Collection Tubes Comprising a Nucleic Acid Stabilizing AgentThis example describes protein corona analysis of samples collected in blood collection tubes comprising a nucleic acid stabilizing agent.
Blood samples from three patients (#1, #2, and #3) were collected in EDTA blood collection tubes (BCTs, BD Biosciences Product #366643) were centrifuged and frozen within one hour of sample collection. Blood samples from the same three patients were also collected in Streck BCTs were stored at room temperature overnight with gentle rocking, after which plasma was processed and frozen. Streck sample treatment was designed to simulate overnight shipping of a sample at ambient temperature.
The number of proteins, peptides, and features present in each of the samples collected in either an EDTA BCT or a Streck BCT was then determined using a protein coronal analysis assay.
These assays indicated that protein coverage was substantially similar in corona derived from plasma collected in blood collection tubes comprising a nucleic acid stabilizing agent and in plasma collected in EDTA blood collection tubes. Proteins from certain groups of proteins, such as glycoproteins, nuclear-related proteins, DNA-related proteins, and RNA-related proteins were more frequently identified in plasma collected in blood collection tubes comprising a nucleic acid stabilizing agent than in plasma collected in EDTA blood collection tubes. Together these resulted indicated that samples collected in tubes comprising a nucleic acid stabilizing agent (e.g., Streck tubes) are suitable for protein corona analysis.
Example 13 Protein Corona Analysis of Lung Cancer Samples Collected in Tubes Comprising a Nucleic Acid Stabilizing AgentThis example describes protein corona analysis of lung cancer samples collected in tubes comprising a nucleic acid stabilizing agent.
Samples were collected from subjects participating in a lung cancer study. Samples from each subject were collected in EDTA plasma collection tubes and Streck plasma collection tubes. Collected samples were processed for protein corona analysis. Samples collected in EDTA sample collection tubes were analyzed on site. Samples collected in Streck sample collection tubes were shipped overnight and analyzed at a remote facility. Samples from 20 subjects were analyzed with a single particle type. Each sample was assayed in triplicate. MS analysis was performed on each sample and replicates using a TF Lumos with 1 hour data-dependent acquisition (DDA) runs.
This example describes corona analysis via serial interrogation of a cerebrospinal fluid sample. A cerebrospinal fluid sample is collected from a subject. A first particle type selected from the particles provided in TABLE 1 is added to 100 μL of the cerebrospinal fluid sample and incubated to form protein corona. The first particle type is separated from the cerebrospinal fluid sample by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A second particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the second particle type is the same as the first particle type. The second particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A third particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the third particle type is the same as the first particle type. The third particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. The supernatant is re-interrogated with up to ten particle types selected from the particles provided in TABLE 1, and the protein corona formed on each particle type are analyzed by mass spectrometry. Proteins are identified from the mass spectrometry analysis of the protein corona formed on each of the up to ten particle types.
Example 15 Corona Analysis Via Serial Interrogation of a Synovial Fluid SampleThis example describes corona analysis via serial interrogation of a synovial fluid sample. A synovial fluid sample is collected from a subject. A first particle type selected from the particles provided in TABLE 1 is added to 100 μL of the synovial fluid sample and incubated to form protein corona. The first particle type is separated from the synovial fluid sample by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A second particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the second particle type is the same as the first particle type. The second particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A third particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the third particle type is the same as the first particle type. The third particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. The supernatant is re-interrogated with up to ten particle types selected from the particles provided in TABLE 1, and the protein corona formed on each particle type are analyzed by mass spectrometry. Proteins are identified from the mass spectrometry analysis of the protein corona formed on each of the up to ten particle types.
Example 16 Corona Analysis Via Serial Interrogation of a Homogenized Tissue SampleThis example describes corona analysis via serial interrogation of a homogenized tissue sample. A homogenized tissue sample is collected from a subject. A first particle type selected from the particles provided in TABLE 1 is added to 100 μL of the homogenized tissue sample and incubated to form protein corona. The first particle type is separated from the homogenized tissue sample by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A second particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the second particle type is the same as the first particle type. The second particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A third particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the third particle type is the same as the first particle type. The third particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. The supernatant is re-interrogated with up to ten particle types selected from the particles provided in TABLE 1, and the protein corona formed on each particle type are analyzed by mass spectrometry. Proteins are identified from the mass spectrometry analysis of the protein corona formed on each of the up to ten particle types.
Example 17 Corona Analysis Via Serial Interrogation of a Plasma SampleThis example describes corona analysis via serial interrogation of a plasma sample. A plasma sample is collected from a subject. A first particle type selected from the particles provided in TABLE 1 is added to 100 μL of the plasma sample and incubated to form protein corona. The first particle type is separated from the plasma sample by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A second particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the second particle type is the same as the first particle type. The second particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A third particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the third particle type is the same as the first particle type. The third particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. The supernatant is re-interrogated with up to ten particle types selected from the particles provided in TABLE 1, and the protein corona formed on each particle type are analyzed by mass spectrometry. Proteins are identified from the mass spectrometry analysis of the protein corona formed on each of the up to ten particle types.
Example 18 Corona Analysis Via Serial Interrogation of a Urine SampleThis example describes corona analysis via serial interrogation of a urine sample. A urine sample is collected from a subject. A first particle type selected from the particles provided in TABLE 1 is added to 100 μL of the urine sample and incubated to form protein corona. The first particle type is separated from the urine sample by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A second particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the second particle type is the same as the first particle type. The second particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. A third particle type selected from the particles provided in TABLE 1 is added to the supernatant and incubated to form protein corona. Optionally, the third particle type is the same as the first particle type. The third particle type is separated from the supernatant by centrifugation or magnetic pulldown. The supernatant is collected. The pellet containing the particles is washed and resuspended, and the corona are analyzed by mass spectrometry. The supernatant is re-interrogated with up to ten particle types selected from the particles provided in TABLE 1, and the protein corona formed on each particle type are analyzed by mass spectrometry. Proteins are identified from the mass spectrometry analysis of the protein corona formed on each of the up to ten particle types.
Example 19 Protein Detection by ELISA in Plasma Samples Collected in EDTA or Blood Collection Tubes Comprising a Nucleic Acid Stabilizing AgentThis example describes protein detection by ELISA in plasma samples collected in EDTA or blood collection tubes comprising a nucleic acid stabilizing agent. Plasma samples were collected from human subjects into either EDTA blood collection tubes or Streck blood collection tubes. Paired EDTA and Streck samples were collected from each of 20 patients for comparison. Concentrations of three high importance proteins, C-reactive protein (CRP), Calgranulin A and B (“S100”), and MUC16/CA125 (“CA125”), were measured in each sample by enzyme-linked immunosorbent assay (ELISA). CRP is a pentameric protein found in blood plasma, whose circulating concentrations rise in response to inflammation. Elevated levels of CRP are associated with increased future risk of cancer of any type, lung cancer, and possibly colorectal cancer. Calgranulin A and B are calcium-binding proteins that are secreted in a heterodimeric form by activated immune cells, such as monocytes, granulocytes, and neutrophils and are expressed in larger amounts in inflammatory diseases such as rheumatoid arthritis, and in some types of cancer. CA125 is a component of the ocular surface, the respiratory tract and the female reproductive tract and has been shown to play a role in advancing tumorigenesis and tumor proliferation by several different mechanisms.
Protein concentrations were measured using commercially available kits specific for each protein. CRP was detected using the Human C-Reactive Protein/CRP Kit (R&D Systems, Inc.), S100 was detected using the Human S100A8/S100A9 Heterodimer Kit (R&D Systems, Inc.), and CA125 was detected using the Human CA125/MUC16 Kit (R&D Systems, Inc.).
This example describes dynamic range compression of plasma using protein corona analysis.
In order to evaluate the ability of particles to compress the measured dynamic range, measured and identified protein feature intensities were compared to the published values for the concentration of the same protein. First, the resulting peptide features for each protein was selected with the maximum MS-determined intensity of all possible features for a protein (using the OpenMS MS data processing tools to extract monoisotopic peak values), and then the intensities were modeled against the published abundance levels for those same proteins.
By comparing the regression model slopes and the intensity span of the measured data, the particle coronas contain more proteins at lower abundances (measured or reported) than does plasma. The dynamic range of those measured values was compressed (the slope of the regression model is reduced) for particle measurements as compared to plasma measurements. This was consistent with previous observations that particle can effectively compress the measured dynamic range for abundances in the resulting corona as compared to the original dynamic range in plasma, which could be attributable to the combination of absolute concentration of a protein, its binding affinity to particles, and its interactions with neighboring proteins. The results indicated that the protein corona strategy facilitated the identification of a broad spectrum of plasma proteins, particularly those in the low abundance that are challenging for rapid detection by conventional proteomic techniques.
Example 21 Serial Interrogation as Compared to Parallel Interrogation of a SampleThis example describes serial interrogation of a sample with particles as compared to parallel interrogation of a sample with particles.
A first sample having a low sample volume of 10 μL is serially interrogated with two or more particle types. A first particle type is contacted to the first sample, the first sample and the first particle type are incubated to allow formation of a first biomolecule corona on the first particle type, and the first particle type is separated from the first sample. The remainder of the first sample is contacted to a second particle type, the remainder of the first sample and the second particle type are incubated to allow formation of a second biomolecule corona on the first particle type, and the second particle type is separated from the remainder of the first sample. The contacting, incubating, and separating are optionally repeated with additional particle types. The biomolecule corona on the first particle type, the second particle type, and any additional particle types are analyzed by assaying for proteins in the corona, for example, by mass spectrometry.
A second sample, from the same source as the first sample, is split into 10 μL multiple aliquots for parallel interrogation with two or more particle types. The sample is split into a number of aliquots greater than or equal to the number of particle types to be used in the method of assaying for proteins. A first particle type is contacted to a first aliquot, the first aliquot and the first particle type are incubated to allow formation of a first biomolecule corona on the first particle type, and the first particle type is separated from the first aliquot. In parallel, a second particle type is contacted to a second aliquot, the second aliquot and the second particle type are incubated to allow formation of a second biomolecule corona on the second particle type, and the second particle type is separated from the second aliquot. The contacting, incubating, and separating are performed with additional particle types in additional aliquots. The biomolecule corona on the first particle type, the second particle type, and any additional particle types are analyzed by assaying for proteins in the corona, for example, by mass spectrometry.
Serial interrogation with two or more particle types of the first sample uses a smaller sample volume (10 μL total) for protein corona analysis than parallel interrogation of the second sample, which uses 10 μL of sample per particle type to be assayed. Even while using less total sample, serial interrogation of the first sample enables detection of a range of proteins that is comparable to or broader than the range detected by parallel interrogation. As shown in
While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. It is intended that the following claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby.
Claims
1. A method of analyzing a biofluid, the method comprising:
- a) contacting the biofluid in a biofluid collection tube with a particle type, the biofluid comprising cell-free nucleic acid molecules stabilized with a stabilization reagent in the biofluid collection tube; and
- b) incubating the biofluid and the particle type in the biofluid collection tube to permit binding of proteins of the biofluid to the particle type, thereby forming a biomolecule corona comprising proteins bound to the particle type,
- wherein the proteins bound to the particle type comprises a population of proteins that is detectable when the particle type is incubated in the biofluid when stored in EDTA and permitted to form a control biomolecule corona; and
- wherein, when the biofluid and the particle type are incubated in the biofluid collection tube at from about 20° C. to about 35° C., 50% or more of the population of proteins of the biomolecule corona is also detectable in the control biomolecule corona.
2. The method of claim 1, wherein at least a subset of the population of proteins is detectable at a higher abundance than when the particle type is incubated in the biofluid when stored in EDTA.
3. The method of claim 1, wherein at least 5% of the population of proteins is detectable at a higher abundance than when the particle type is incubated in the biofluid when stored in EDTA.
4. The method of claim 1, further comprising assaying the proteins in the biomolecule corona at a lower limit of detection than when the particle type is incubated in the biofluid when stored in EDTA.
5. The method of claim 1, wherein the incubating in the biofluid collection tube comprises incubating for up to 14 days.
6. The method of claim 1, wherein the biomolecule corona comprises a protein that is absent from the control biomolecule corona.
7. The method of claim 1, wherein the biomolecule corona comprises at least 100 distinct proteins.
8. The method of claim 1, wherein the biofluid is selected from the group consisting of: plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, fluidized solids, fine needle aspiration samples, tissue homogenates, cell culture samples, and any combination thereof.
9. The method of claim 1, further comprising determining a composition and concentration of the proteins in the biomolecule corona.
10. The method of claim 9, wherein the determining the composition and concentration of the proteins comprises mass spectrometry, gel electrophoresis, liquid chromatography, or a combination thereof.
11. The method of claim 1, wherein the stabilization reagent comprises a metabolic inhibitor, a protease inhibitor, a phosphatase inhibitor, a nuclease inhibitor, a preservative agent, or a combination thereof.
12. The method of claim 11, wherein the metabolic inhibitor is selected from the group consisting of: glyceraldehyde, dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, 1,3-bisphosphoglycerate, 3-phosphoglycerate, 2-phosphoglycerate, phosphoenolpyruvate, pyruvate and glycerate dihydroxyacetate, sodium fluoride, and K2C2O4.
13. The method of claim 11, wherein the protease inhibitor is selected from the group consisting of: antipain, aprotinin, chymostatin, elastatinal, phenylmethylsulfonyl fluoride (PMSF), APMSF, TLCK, TPCK, leupeptin, soybean trypsin inhibitor, indoleacetic acid (IAA), E-64, EDTA, pepstatin, VdLPFFVdL, 1,10-phenanthroline, phosphoramodon, amastatin, bestatin, diprotin A, diprotin B, alpha-2-macroglobulin, lima bean trypsin inhibitor, pancreatic protease inhibitor, egg white ovostatin, and egg white cystatin.
14. The method of claim 11, wherein the phosphatase inhibitor is selected from the group consisting of: calyculin A, nodularin, NIPP-1, microcystin LR, tautomycin, okadaic acid, cantharidin, microcystin LR, okadaic acid, fostriecin, tautomycin, cantharidin, endothall, nodularin, cyclosporin A, FK 506/immunophilin complexes, cypermethrin, deltamethrin, fenvalerate, bpV(phen), dephostatin, mpV(pic) DMHV, and sodium orthovanadate.
15. The method of claim 11, wherein the nuclease inhibitor is selected from the group consisting of: diethyl pyrocarbonate, ethanol, aurintricarboxylic acid (ATA), formamide, vanadyl-ribonucleoside complexes, macaloid, ethylenediamine tetraacetic acid (EDTA), proteinase K, heparin, hydroxylamine-oxygen-cupric ion, bentonite, ammonium sulfate, dithiothreitol (DTT), beta-mercaptoethanol, cysteine, dithioerythritol, tris(2-carboxyethyl) phosphene hydrochloride, and a divalent cation such as Mg+2, Mn+2, Zn+2, Fe+2, Ca+2, or Cu+2.
16. The method of claim 11, wherein the preservative agent is selected from the group consisting of: diazolidinyl urea, imidazolidinyl urea, dimethoylol-5,5-dimethylhydantoin, dimethylol urea, 2-bromo-2-nitropropane-1,3-diol, oxazolidines, sodium hydroxymethyl glycinate, 5-hydroxymethoxymethyl-1-1aza-3,7-dioxabicyclo[3.3.0]octane, 5-hydroxymethyl-1-1aza-3,7dioxabicyclo[3.3.0]octane, 5-hydroxypoly[methyleneoxy]methyl-1-1aza-3,7dioxabicyclo[3.3.0]octane, or quaternary adamantine.
17. The method of claim 1, wherein the biofluid collection tube is a blood collection tube.
18. The method of claim 1, wherein the particle type is a nanoparticle or a microparticle.
19. The method of claim 1, wherein the particle type is selected from the group consisting of: a nanoparticle, a microparticle, a micelle, a liposome, an iron oxide particle, a graphene particle, a silica particle, a protein-based particle, a polystyrene particle, a silver particle, a gold particle, a metal particle, a quantum dot, a superparamagnetic particle, and any combination thereof.
20. The method of claim 1, further comprising separating the particle type from the biofluid.
21. The method of claim 20, wherein the separating comprises magnetic separation, filtration, gravitational separation, or centrifugation.
22. The method of claim 20, further comprising contacting the biofluid with one or more additional particle types, incubating the biofluid with the one or more additional particle types to permit binding of proteins of the biofluid to the one or more additional particle type, thereby forming one or more additional biomolecule coronas comprising proteins bound to the one or more additional particle types.
23. The method of claim 22, further comprising repeating said separating and contacting multiple times.
24. The method of claim 22, wherein the one or more additional particle types binds a population of proteins that is distinct but overlapping with the population of proteins in the biomolecule proteins of the particle type.
25. The method of claim 22, wherein the one or more additional particle types is the same as or different from the particle type.
26. The method of claim 1, wherein the biofluid has a volume of less than or equal to about 1,000 picolitres (pL).
27. The method of claim 26, wherein the volume is less than or equal to about 100 pL.
Type: Application
Filed: Mar 29, 2021
Publication Date: Jul 15, 2021
Inventors: Xiaoyan Zhao (Foster City, CA), William Manning (Redwood City, CA), John Blume (Bellingham, WA), Lyndal Hesterberg (Loveland, CO), Gregory Troiano (Pembroke, MA), Michael Figa (San Mateo, CA), Hope Liou (Pleasanton, CA), Shadi Roshdiferdosi (Belmont, CA)
Application Number: 17/216,510
