Compositions, methods and systems for protein corona analysis from biofluids and uses thereof

Abstract

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.

What is claimed is: 
     
         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 K 2 C 2 O 4 . 
     
     
         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.