# Patent

## Title
Method for replacing biomarkers of protein kinetics from tissue samples by biomarkers of protein kinetics from body fluids after isotopic labeling in vivo

## Abstract

Provided herein are method for measuring the rate of synthesis, breakdown, transport, or other kinetic parameters of a protein in a tissue of medical interest, without requiring physical sampling of the tissue, by a measurement of the protein in a body fluid. Methods may include selecting one or more target proteins in a tissue; administering an isotope-labeled molecule to a subject for a period of time sufficient for said isotope-labeled molecule to enter into and label the one or more target proteins to produce one or more isotope-labeled target proteins; collecting a volume of a body fluid, wherein the volume comprises one or more isotope-labeled target proteins that escaped or were released from the tissue; enriching or isolating the one or more isotope-labeled target proteins from the volume; performing a mass spectrometric measurement of the isotopic content, rate of incorporation, and/or pattern or rate of change in isotopic content and/or pattern of isotope labeling of the one or more enriched or isolated isotope-labeled target proteins; and calculating at least one kinetic parameter of the one or more enriched or isolated isotope-labeled target proteins, where the kinetic parameter of the one or more isotope-labeled target proteins from the volume of a body fluid reflects the corresponding kinetic parameter of the one or more target proteins in the tissue; and inferring the at least one kinetic parameter of the one or more target proteins in the tissue based on the corresponding at least one kinetic parameter of the one or more target proteins in the body fluid.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Patent Application Ser. No. 61/801,815, filed Mar. 15, 2013, which is incorporated herein by reference in its entirety.


BACKGROUND
1. Field
The present disclosure relates generally to methods for measuring protein kinetics, and more specifically to methods for measuring the kinetics of tissue proteins using biomarkers in bodily fluids based on isotopic labeling.
2. Description of Related Art
Biopsy, the sampling of cells or tissues for investigation, plays a critical role in the diagnosis and treatment of a multitude of diseases (e.g., cancers). Often, biopsies are performed to garner information regarding specific proteins in a tissue of interest that are known to be significant in the pathogenesis of a disease. For example, collagen types I or VI, matrix proteins, and lumican (a matrix proteoglycan) are known to play roles in liver fibrosis. Traditionally, an invasive biopsy would be performed to allow for an investigation of collagen or lumican, including the kinetics of collagen or lumican, in a subject suffering from, or at risk for, liver fibrosis. Biopsies, like most invasive procedures, present an element of risk for the subject and are often costly.
Accordingly, a less-invasive, cost-effective alternative to biopsy that can provide information, particularly kinetics, about a tissue protein of interest would be useful.
BRIEF SUMMARY
Certain aspects of the present disclosure relate to a method for measuring the rate of synthesis, breakdown, transport, or other kinetic parameters of a protein in a tissue of medical interest, without requiring physical sampling of the tissue, by a measurement of the protein in a body fluid is provided. These methods take advantage of the discovery that target proteins in a tissue of medical interest may also be found in a body fluid (e.g., plasma) because they may escape or be released from the tissue of medical interest. Therefore, upon labeling a target protein with an isotope label (e.g., a radioactive or stable, non-radioactive isotope), the isotope-labeled protein may be collected, enriched, and/or isolating from the body fluid, which advantageously may be accessed in a less intrusive manner than the tissue of medical interest itself.
Accordingly, in some embodiments, the method includes selecting one or more target proteins in a tissue; administering an isotope-labeled molecule to a subject for a period of time sufficient for the isotope-labeled molecule to enter into and label the one or more target proteins to produce one or more isotope-labeled target proteins; collecting a volume of a body fluid, wherein the volume contains one or more isotope-labeled target proteins that escaped or were released from the tissue; enriching or isolating the one or more isotope-labeled target proteins from the volume; performing a mass spectrometric measurement of the isotopic content, rate of incorporation, and/or pattern or rate of change in isotopic content and/or pattern of isotope labeling of the one or more enriched or isolated isotope-labeled target proteins; and calculating at least one kinetic parameter of the one or more enriched or isolated isotope-labeled target proteins, wherein the kinetic parameter of the one or more isotope-labeled target proteins from the volume of a body fluid reflects the corresponding kinetic parameter of the one or more target proteins in the tissue; and inferring the at least one kinetic parameter of the one or more target proteins in the tissue based on the corresponding at least one kinetic parameter of the one or more target proteins in the body fluid.



DESCRIPTION OF THE FIGURES
FIG. 1 depicts an exemplary overview of a “virtual biopsy” method.
FIG. 2 illustrates an application of the “virtual biopsy” method to assess tissue fibrogenesis from measurements of isotope-labeled blood proteins.
FIG. 3 shows the variation in collagen synthesis rates between individuals. Synthesis rates derived from individual subjects are provided for Collagen I α1 and α2 (A), Collagen III α1 (B), and Collagen VI α3 (C) are shown. Synthesis rates are expressed as the percentage of new collagen synthesized as a fraction of total collagen per day.
FIG. 4 shows the correlation (r2 value) between different plasma proteins and liver collagen turnover. Plasma lumican demonstrates the highest correlation (labeled).
FIG. 5 shows the correlation between plasma lumican and liver collagen turnover. Comparisons are provided between liver collagen and plasma lumican turnover (A), plasma lumican and liver Collagen III α1 (B), plasma lumican and liver Collagen VI α3 (C), and plasma lumican and an average liver turnover derived from Collagens I α1, I α2, III α1, VI α1, and VI α3 (D).
FIG. 6 shows that the rates of plasma lumican synthesis and plasma TGFBI synthesis correlate with each other and with liver collagen synthesis (A) and liver fibrosis score (B) in the same patients.
FIG. 7 shows the correlations between liver Collagen I α1 synthesis rate and liver fibrosis score (A) and between liver Collagen III α1 synthesis rate and liver inflammation score (B) in the same patients.
FIG. 8 shows that the synthesis rates of other selected proteins (plasma hemopexin, A and serum albumin, B) do not correlate with liver fibrosis score in the same patients.
FIG. 9 illustrates an application of the “virtual biopsy” method to assess muscle protein synthesis from measurements of isotope-labeled muscle creatine kinase in the blood.
FIG. 10 shows the correlation between rates of plasma creatine kinase MM synthesis and muscle creatine kinase MM synthesis. r- and p-values are also provided.
FIG. 11 shows that the synthesis rates of several muscle proteins correlate with the synthesis rate of muscle creatine kinase MM. Shown are the correlations between muscle creatine kinase MM synthesis rate and the synthesis rates of Actin (A), Myosin-2 (B), Troponin-I (C), and Tropomyosin-alpha (D).
FIG. 12 shows that the synthesis rate of plasma creatine kinase MM correlates with creatine kinase MM isolated from different muscle types. Shown are the correlations between plasma creatine kinase MM synthesis rate and the synthesis rates of creatine kinase MM isolated from the gastrocnemius (A) and quadriceps (B) muscles.



DETAILED DESCRIPTION
The following description sets forth exemplary methods, parameters and the like. It should be recognized, however, that such description is not intended as a limitation on the scope of the present disclosure but is instead provided as a description of exemplary embodiments.
Described herein is a method for non-invasively measuring from a body fluid the rate of protein synthesis or protein breakdown in a tissue of medical interest as a diagnostic biomarker (e.g., protein kinetic biomarker), thereby avoiding the need for invasive sampling of the tissue of interest. Tissues of medical interest may include but are not limited to skeletal muscle, heart muscle, fibroblasts in liver or other tissues, pancreatic β-cells, or cancer tissues, and sampled body fluids may include but are not limited to blood, cerebrospinal fluid, saliva, or urine.
FIG. 1 provides an exemplary overview of an embodiment of the virtual biopsy process. The process includes a selection step of selecting a targeted protein or proteins whose kinetics in a tissue of medical interest reflect a disease process or therapeutic response in the tissue and provide information about the disease process in the tissue. The selection can be informed through experimental measurement of kinetics of the protein(s) in the tissue or through published information about kinetics of the protein(s) in the tissue, or by a combination thereof. Step 2 is a label administration step that may include administering a stable- or radio-isotopic tracer (including but not limited to 2H2O, 13C2-leucine, 3H-phenylalanine, 13C-glucose, 13C-acetate, 15N-glycine, 15N-labeled spirulina) that is metabolically incorporated into newly synthesized proteins to a subject with an established or suspected disease condition in the tissue of interest, or to a subject at risk for a disease condition in the tissue of interest, for a sufficient period of time to label the target protein(s) that are undergoing synthesis in the tissue of interest. Sampling of volume of a body fluid is then performed in the subject, the body fluid including but not limited to blood, urine, sputum, or cerebrospinal fluid. An enrichment or isolation step is then performed, wherein targeted proteins that are synthesized in the tissue, that derive solely or primarily from the tissue of origin, and that then escape into an accessible body fluid, are isolated, enriched, or purified from the volume of the body fluid. The pathway of escape from the tissue of origin into the body fluid can be via secretion, exocytosis, membrane leakage, targeted vesicular fusion, attachment on exosomes, death of the cell, or any other biologic or pathologic process of escape. The protein(s) or peptides from the protein(s) are then isolated from the body fluid by methods known in the art, including but not limited to immuno-isolation, physical separation on gels or columns, liquid chromatographic separation, partial enzymatic hydrolysis followed by anti-peptide immuno-isolation, physical separation, or tandem mass spectrometry. A measurement step is then performed, which may include measuring the isotopic content and/or pattern in the target proteins by, in a preferred embodiment, use of mass spectrometry of peptides from the targeted proteins. Finally, a calculation step is carried out to determine the kinetics of the targeted proteins isolated from the body fluid. In this manner, a “virtual biopsy” of the target protein(s) from the tissue of origin will have been carried out, without requiring a physical sample from the tissue of medical interest.
In a preferred embodiment disclosed here, creatine kinase MM was targeted as a protein kinetic biomarker of skeletal muscle protein synthesis and breakdown, for use in diagnosis and drug development for sarcopenia, cachexia, muscular dystrophies, exercise training, and other medical conditions. 2H2O was administered to humans or experimental animals, and plasma creatine kinase MM was isolated from plasma by immunoprecipitation, subjected to trypsin digestion, and analyzed by LC/MS/MS (liquid chromatography-tandem mass spectrometry) to determine alterations in mass isotopomer pattern, from which the synthesis rate of creatine kinase MM in blood plasma was calculated. The synthesis rate of plasma creatine kinase MM was verified to closely reflect the synthesis rate of creatine kinase MM isolated from muscle biopsies in the same subjects, and the synthesis rates of plasma creatine kinase MM or skeletal muscle creatine kinase MM closely correlated with the synthesis rates of several other muscle proteins. In contrast, creatine kinase MB (cardiac muscle-specific) that was isolated from plasma exhibited much higher synthesis rates than creatine kinase MM, indicating tissue-specific measurement of creatine kinase synthesis from blood measurements.
In another embodiment disclosed here, the collagen fibril-associated protein lumican was targeted in plasma as a biomarker of tissue fibrogenesis (e.g., accumulation of fibroblast-derived collagen in the extracellular matrix of tissues), for use in diagnosis and drug development in fibrosis of liver, lung, heart, skin, kidney or other tissues. 2H2O was administered to humans and experimental animals and lumican-derived peptides were isolated and identified by LC/MS/MS. Alterations in mass isotopomer pattern were measured, from which the synthesis rate of lumican in blood plasma was calculated. The synthesis rate of plasma lumican was verified to closely reflect the synthesis rate of collagen Types I, III, and VI in the liver of patients with hepatitis and suspected fibrosis, in the same subjects, indicating measurement of liver fibrogenesis rate from a blood measurement.
The “virtual biopsy” method disclosed here is generalizable to many tissues and disease processes and has utility as biomarkers that can be used in drug discovery and development, or to identify disease subsets in personalized medicine, or for clinical diagnosis and management of patients.
I. GENERAL TECHNIQUES
The practice of the present disclosure will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are within the skill of the art. Such techniques are explained fully in the literature, such as, Molecular Cloning: A Laboratory Manual, second edition (Sambrook et al., 1989) Cold Spring Harbor Press; Oligonucleotide Synthesis (M. J. Gait, ed., 1984); Methods in Molecular Biology, Humana Press; Cell Biology: A Laboratory Notebook (J. E. Cellis, ed., 1998) Academic Press; Animal Cell Culture (R. I. Freshney, ed., 1987); Introduction to Cell and Tissue Culture (J. P. Mather and P. E. Roberts, 1998) Plenum Press; Cell and Tissue Culture: Laboratory Procedures (A. Doyle, J. B. Griffiths, and D. G. Newell, eds., 1993-8) 3. Wiley and Sons; Methods in Enzymology (Academic Press, Inc.); Handbook of Experimental Immunology (D. M. Weir and C. C. Blackwell, eds.); Gene Transfer Vectors for Mammalian Cells (J. M. Miller and M. P. Cabs, eds., 1987); Current Protocols in Molecular Biology (F. M. Ausubel et al., eds., 1987); PCR: The Polymerase Chain Reaction, (Mullis et al., eds., 1994); Current Protocols in Immunology (J. E. Coligan et al., eds., 1991); Short Protocols in Molecular Biology (Wiley and Sons, 1999); and Mass isotopomer distribution analysis at eight years: theoretical, analytic and experimental considerations by Hellerstein and Neese (Am J Physiol 276 (Endocrinol Metab. 39) E1146-E1162, 1999). Furthermore, procedures employing commercially available assay kits and reagents will typically be used according to manufacturer-defined protocols unless otherwise noted.
U.S. Pat. No. 8,129,335, which is incorporated by reference in its entirety, provides methods and disclosures that may be useful for practice of methods described herein.
II. DEFINITIONS
Unless otherwise defined, all terms of art, notations and other scientific terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this disclosure pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. The techniques and procedures described or referenced herein are generally well understood and commonly employed using conventional methodology by those skilled in the art, such as, for example, Mass isotopomer distribution analysis at eight years: theoretical, analytic and experimental considerations by Hellerstein and Neese (Am J Physiol 276 (Endocrinol Metab. 39) E1146-E1162, 1999). As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted.
“Kinetic parameters” and “molecular flux rates” may be used interchangeably herein and may refer to the rate of synthesis, breakdown, and/or transport of a protein. “Kinetic parameters” or “molecular flux rates” also refer to a protein's input into or removal from a pool of molecules, and are therefore synonymous with the flow into and out of the pool of molecules.
“Isotopologues” refer to isotopic homologues or molecular species that have identical elemental and chemical compositions but differ in isotopic content (e.g., CH3NH2 vs. CH3NHD in the example above). Isotopologues are defined by their isotopic composition; therefore, each isotopologue has a unique exact mass but may not have a unique structure. An isotopologue usually includes of a family of isotopic isomers (isotopomers) which differ by the location of the isotopes on the molecule (e.g., CH3NHD and CH2DNH2 are the same isotopologue but are different isotopomers).
“Isotope-labeled water” includes water labeled with one or more specific heavy isotopes of either hydrogen or oxygen. Specific examples of isotope-labeled water include 2H2O, 3H2O, and H218O.
“Protein precursor” refers to any organic or inorganic molecule or component thereof, wherein one or more atoms of which are capable of being incorporated into protein molecules in cell, tissue, organism, or other biological system, through the biochemical processes of the cell, tissue, or organism. Examples of protein precursors include, but are not limited to, amino acids, 2H2O, CO2, NH3, and HCO3.
“Isotope-labeled protein precursor” refers to a protein precursor that contains an isotope of an element that differs from the most abundant isotope of the element present in nature, cells, tissue, or organisms. The isotope label may include specific heavy isotopes of elements present in biomolecules, such as 2H, 13C, 15N, 18O, 33S, 34, or may contain other isotopes of elements present in biomolecules such as 3H, 14C, 35S, 125I, 131I. Isotope labeled protein precursors include; but are not limited to 2H2O, 15NH3, 13CO2, H113CO3, 2H-labeled amino acids, 13C labeled amino acids, 15N labeled amino acids, 18O labeled amino acids, 34S or 33S labeled amino acids, 3H2O, 3H-labeled amino acids, and 14C labeled amino acids.
“Isotope-labeled organic metabolite precursors” refer to an organic metabolite precursor that contains an isotope of an element that differs from the most abundant isotope of the element present in nature or cells, tissues, or organisms. Isotopic labels include specific heavy isotopes of elements, present in biomolecules, such as 2H, 13C, 15N, 18O, 35S, 34, or may contain other isotopes of elements present in biomolecules, such as 3H, 14C, 35S, 125I, 131I. Isotope labeled organic metabolite precursors include but are not limited to 2H2O, 15NH3, 13CO2, H13CO3, 2H-labeled amino acids, 13C-labeled amino acids, 15N-labeled amino acids, 18O-labeled amino acids, 33S or 34S-labeled amino acids, 3H2O, 3H-labeled amino acids, 14C-labeled amino acids, 14CO2, and H14CO2.
“Partially purifying” refers to methods of removing one or more components of a mixture of other similar compounds. For example, “partially purifying a protein” refers to removing one or more proteins from a mixture of one or more proteins. As used herein, the term “enriching” may be used interchangeably.
“Isolating” refers to separating one compound from a mixture of compounds. For example, “isolating a protein” refers to separating one specific protein from all other proteins in a mixture of one or more proteins.
A “biological sample” encompasses any sample obtained from a cell, tissue, or organism. The definition encompasses blood and other liquid samples of biological origin, that are accessible from an organism through sampling by minimally invasive or non-invasive approaches (e.g., urine collection, blood drawing, needle aspiration, and other procedures involving minimal risk, discomfort or effort). The definition also includes samples that have been manipulated in any way after their procurement, such as by treatment with reagents, solubilization, or enrichment for certain components, such as proteins or organic metabolites. The term “biological sample” also encompasses a clinical sample such as serum, plasma, other biological fluid, or tissue samples, and also includes cells in culture, cell supenatants and cell lysates. A volume of a body fluid may be used to refer to a liquid biological sample.
“Body fluid” refers to, but is not limited to, urine, blood, interstitial fluid, edema fluid, saliva, lacrimal fluid, inflammatory exudates, synovial fluid, abscess, empyema or other infected fluid, cerebrospinal fluid, sweat, pulmonary secretions (sputum), seminal fluid, feces, bile, intestinal secretions, or other biological fluid.
“Exact mass” refers to mass calculated by summing the exact masses of all the isotopes in the formula of a molecule (e.g., 32.04847 for CH3NHD).
“Nominal mass” refers to the integer mass obtained by rounding the exact mass of a molecule.
“Mass isotopomer” refers to family of isotopic isomers that is grouped on the basis of nominal mass rather than isotopic composition. A mass isotopomer may comprise molecules of different isotopic compositions, unlike an isotopologue (e.g., CH3NHD, 13CH3NH2, CH315NH2 are part of the same mass isotopomer but are different isotopologues). In operational terms, a mass isotopomer is a family of isotopologues that are not resolved by a mass spectrometer. For quadrupole mass spectrometers, this typically means that mass isotopomers are families of isotopologues that share a nominal mass. Thus, the isotopologues CH3NH2 and CH3NHD differ in nominal mass and are distinguished as being different mass isotopomers, but the isotopologues CH3NHD, CH2DNH2, 13CH3NH2, and CH315NH2 are all of the same nominal mass and hence are the same mass isotopomers. Each mass isotopomer is therefore typically composed of more than one isotopologue and has more than one exact mass. The distinction between isotopologues and mass isotopomers is useful in practice because all individual isotopologues are not resolved using quadrupole mass spectrometers and may not be resolved even using mass spectrometers that produce higher mass resolution, so that calculations from mass spectrometric data must be performed on the abundances of mass isotopomers rather than isotopologues. The mass isotopomer lowest in mass is represented as Mo; for most organic molecules, this is the species containing all 12C, 1H, 16O, 14N, etc. Other mass isotopomers are distinguished by their mass differences from M.sub.0 (M1, M2, etc.). For a given mass isotopomer, the location or position of isotopes within the molecule is not specified and may vary (i.e., “positional isotopomers” are not distinguished).
“Mass isotopomer envelope” refers to the set of mass isotopomers associated with a molecule or ion fragment.
“Mass isotopomer pattern” refers to a histogram of the abundances of the mass isotopomers of a molecule. Traditionally, the pattern is presented as percent relative abundances where all of the abundances are normalized to that of the most abundant mass isotopomer; the most abundant isotopomer is said to be 100%. The preferred form for applications involving probability analysis, such as mass isotopomer distribution analysis (MIDA), however, is proportion or fractional abundance, where the fraction that each species contributes to the total abundance is used. The term “isotope pattern” may be used synonymously with the term “mass isotopomer pattern.”
“Monoisotopic mass” refers to the exact mass of the molecular species that contains all 1H, 12C, 14N, 16O, 32S, s etc. For isotopologues composed of C, H, N, O, P, S, F, Cl, Br, and I, the isotopic composition of the isotopologue with the lowest mass is unique and unambiguous because the most abundant isotopes of these elements are also the lowest in mass. The monoisotopic mass is abbreviated as m.sub.0, and the masses of other mass isotopomers are identified by their mass differences from m.sub.0 (m1, m2, etc.).
“Isotopically perturbed” refers to the state of an element or molecule that results from the explicit incorporation of an element or molecule with a distribution of isotopes that differs from the distribution found in nature, whether a naturally less abundant isotope is present in excess (enriched) or in deficit (depleted).
“Monomer” refers to a chemical unit that combines during the synthesis of a polymer and which is present two or more times in the polymer.
“Polymer” refers to a molecule synthesized from and containing two or more repeats of a monomer.
“Protein” refers to a polymer of amino acids. As used herein, a “protein” may refer to long amino acid polymers as well as short polymers such as peptides.
III. METHODS OF THE DISCLOSURE
The present disclosure is directed to methods measuring the kinetic parameters of a protein in a tissue of medical interest, without requiring physical sampling of the tissue, by a measurement of the protein in a body fluid. The methods may include selecting one or more target proteins in a tissue; administering an isotope-labeled molecule to a subject for a period of time sufficient for the isotope-labeled molecule to enter into and label the one or more target proteins to produce one or more isotope-labeled target proteins; collecting a volume of a body fluid, where the volume contains one or more isotope-labeled target proteins that escaped or were released from the tissue; enriching or isolating the one or more isotope-labeled target proteins from the volume; performing a mass spectrometric measurement of the isotopic content, rate of incorporation, and/or pattern or rate of change in isotopic content and/or pattern of isotope labeling of the one or more enriched or isolated isotope-labeled target proteins; calculating at least one kinetic parameter of the one or more enriched or isolated isotope-labeled target proteins, where the kinetic parameter of the one or more isotope-labeled target proteins from the volume of a body fluid reflects the corresponding kinetic parameter of the one or more target proteins in the tissue; and inferring the at least one kinetic parameter of the one or more target proteins in the tissue based on the corresponding at least one kinetic parameter of the one or more target proteins in the body fluid. The relative and absolute mass isotopomer abundances of the ions within the isotopomeric envelope corresponding to each identified target protein or peptide are quantified by mass spectrometry, and the molecular flux rates of each identified target protein or peptide are calculated to determine the kinetic parameters of the target protein(s).
A. Selecting a Target Protein
Suitable target proteins may include any protein detectable in a body fluid. In some embodiments, a target protein is related to tissue collagen deposition or fibril formation. In some embodiments, a target protein may be derived from collagen-synthesizing fibroblasts. In some embodiments, target proteins may include lumican, perlecan, fibronectin, procollagen, and collagen. In some embodiments, a target protein may include any creatine kinase protein (e.g., any protein known or predicted to have the enzymatic activity of EC 2.7.3.2). A creatine kinase protein may consist of two subunits that are either brain type (B) or muscle type (M). As such, a creatine kinase protein may be a combination of subunits, including MM, MB, and BB. Different tissues are known to express different proportions of these proteins. For example, creatine kinase MM is known to be highly specific for skeletal muscle, and cardiac tissue (e.g., myocardium) is known to express a higher proportion of creatine kinase MB than other tissues. In some embodiments a target protein may include a blood protein derived from pancreatic β-cell secretory granules, e.g., insulin.
B. Administering an Isotope-Labeled Molecule
1. Labeled Precursor Molecules
a. Isotope Labels
The first step in measuring molecular flux rates involves administering an isotope-labeled precursor molecule to a cell, tissue, or organism. The isotope labeled precursor molecule may be a stable isotope or radioisotope. Isotope labels that can be used include, but are not limited to, 2H, 13C, 15N, 18O, 3H, 14C, 35S, 32P, 125I, 131I, or other isotopes of elements present in organic systems. In one embodiment, the isotope label is 2H.
b. Precursor Molecules
The precursor molecule may be any molecule having an isotope label that is incorporated into a protein or organic metabolite. Isotope labels may be used to modify all precursor molecules disclosed herein to form isotope-labeled precursor molecules.
The entire precursor molecule may be incorporated into one or more proteins and/or organic metabolites. Alternatively, a portion of the precursor molecule may be incorporated into one or more proteins and/or organic metabolite.
Precursor molecules may include, but not limited to, CO2, NH3, glucose, lactate, 2H2O, acetate, and fatty acids.
i. Protein Precursors
A protein precursor molecule may be any protein precursor molecule known in the art. These precursor molecules may be CO2, NH3, glucose, lactate, H2O, acetate, and fatty acids.
Precursor molecules of proteins may also include one or more amino acids. The precursor may be any amino acid. The precursor molecule may be a singly or multiply deuterated amino acid. For example, the precursor molecule may be one or more of 13C-lysine, 15N-histidine, 13C-serine, 13C-glycine, 2H-leucine, 15N-glycine, 13C-leucine, 2H5-histidine, and any deuterated amino acid. Labeled amino acids may be administered, for example, undiluted or diluted with non-labeled amino acids. All isotope labeled precursors may be purchased commercially, for example, from Cambridge Isotope Labs (Andover, Mass.).
Protein precursor molecules may also include any precursor for post-translational or pre-translationally modified amino acids. These precursors include but are not limited to precursors of methylation such as glycine, serine or H2O; precursors of hydroxylation, such as H.sub.2O or O.sub.2; precursors of phosphorylation, such as phosphate, H2O or O2; precursors of prenylation, such as fatty acids, acetate, H2O, ethanol, ketone bodies, glucose, or fructose; precursors of carboxylation, such as CO2, O2, H2O, or glucose; precursors of acetylation, such as acetate, ethanol, glucose, fructose, lactate, alanine, H2O, CO2, or O2; and other post-translational modifications known in the art.
The degree of labeling present in free amino acids may be determined experimentally, or may be assumed based on the number of labeling sites in an amino acid. For example, when using hydrogen isotopes as a label, the labeling present in C—H bonds of free amino acid or, more specifically, in tRNA-amino acids, during exposure to 2H2O in body water may be identified. The total number of C—H bonds in each non-essential amino acid is known—e.g., 4 in alanine, 2 in glycine, etc.
The precursor molecule for proteins may be water. The hydrogen atoms on C—H bonds are the hydrogen atoms on amino acids that are useful for measuring protein synthesis from 2H2O since the O—H and N—H bonds of proteins are labile in aqueous solution. As such, the exchange of 2H-label from 2H2O into O—H or N—H bonds occurs without the synthesis of proteins from free amino acids as described above. C—H bonds undergo incorporation from H2O into free amino acids during specific enzyme-catalyzed intermediary metabolic reactions. The presence of 2H-label in C—H bonds of protein-bound amino acids after 2H2O administration therefore means that the protein was assembled from amino acids that were in the free form during the period of 2H2O exposure—i.e., that the protein is newly synthesized. Analytically, the amino add derivative used must contain all the C—H bonds but must remove all potentially contaminating N—H and O—H bonds.
Hydrogen atoms from body water may be incorporated into free amino acids. 2H or 3H from labeled water can enter into free amino adds in the cell through the reactions of intermediary metabolism, but .sup.2H or .sup.3H cannot enter into amino acids that are present in peptide bonds or that are bound to transfer RNA. Free essential amino acids may incorporate a single hydrogen atom from body water into the .alpha.-carbon C—H bond, through rapidly reversible transamination reactions. Free non-essential amino adds contain a larger number of metabolically exchangeable C—H bonds, of course, and are therefore expected to exhibit higher isotopic enrichment values per molecule from 2H2O in newly synthesized proteins.
One of skill in the art will recognize that labeled hydrogen atoms from body water may be incorporated into other amino acids via other biochemical pathways. For example, it is known in the art that hydrogen atoms from water may be incorporated into glutamate via synthesis of the precursor α-ketoglutrate in the citric acid cycle. Glutamate, in turn, is known to be the biochemical precursor for glutamine, proline, and arginine. By way of another example, hydrogen atoms from body water may be incorporated into post-translationally modified amino acids, such as the methyl group in 3-methyl-histine, the hydroxyl group in hydroxyproline or hydroxylysine, and others. Other amino adds synthesis pathways are known to those of skill in the art.
Oxygen atoms (H218O) may also be incorporated into amino acids through enzyme-catalyzed reactions. For example, oxygen exchange into the carboxylic acid moiety of amino acids may occur during enzyme catalyzed reactions. Incorporation of labeled oxygen into amino acids is known to one of skill in the art. Oxygen atoms may also be incorporated into amino acids from 18O2 through enzyme catalyzed reactions (including hydroxyproline, hydroxylysine or other post-translationally modified amino acids).
Hydrogen and oxygen labels from labeled water may also be incorporated into amino acids through post-translational modifications. In one embodiment, the post-translational modification may already include labeled hydrogen or oxygen through biosynthetic pathways prior to post-translational modification. In another embodiment, the post-translational modification may incorporate labeled hydrogen, oxygen, carbon, or nitrogen from metabolic derivatives involved in the free exchange labeled hydrogens from body water, either before or after post-translational modification step (e.g. methylation, hydroxylation, phosphorylation, prenylation, sulfation, carboxylation, acetylation or other known post-translational modifications).
Protein precursors for that are suitable for administration into a subject include, but are not limited to H2O, CO2, NH3 and HCO3, in addition to the standard amino acids found in proteins.
ii. Modes of Administering Precursors of Proteins
Modes of administering the one or more isotope-labeled precursors may vary, depending upon the absorptive properties of the isotope-labeled precursor and the specific biosynthetic pool into which each compound is targeted. Precursors may be administered to organisms, plants and animals including humans directly for in vivo analysis. In addition, precursors may be administered in vitro to living cells. Specific types of living cells include hepatocytes, adipocytes, myocytes, fibroblasts, neurons, pancreatic β-cells, intestinal epithelial cells, leukocytes, lymphocytes, erythrocytes, microbial cells and any other cell-type that can be maintained alive and functional in vitro.
Generally, an appropriate mode of administration is one that produces a steady state level of precursor within the biosynthetic pool and/or in a reservoir supplying such a pool for at least a transient period of time. Intravenous or oral routes of administration are commonly used to administer such precursors to organisms, including humans. Other routes of administration, such as subcutaneous or intra-muscular administration, optionally when used in conjunction with slow release precursor compositions, are also appropriate. Compositions for injection are generally prepared in sterile pharmaceutical excipients. Modes of administration may comprise continuous administration or discontinuous administration (e.g., a pulse chase).
B. Collecting a Volume of a Body Fluid Containing Isotope-Labeled Proteins
In practicing the method of the invention, in one aspect, proteins and organic metabolites are obtained from a cell, tissue, or organism according to the methods known in the art. The methods may be specific to the proteins or organic metabolites of interest. Proteins and organic metabolites of interest may be isolated from a biological sample.
A plurality of proteins or a plurality of organic metabolites may be acquired from the cell, tissue, or organism. The one or more biological samples may be obtained, for example, by blood draw, urine collection, biopsy, or other methods known in the art. The one or more biological sample may be a volume of one or more biological fluids. The protein or organic metabolite may also be obtained from specific organs or tissues, such as muscle, liver, adrenal tissue, prostate tissue, endometrial tissue, blood, skin, and breast tissue. Proteins or organic metabolites may be obtained from a specific group of cells, such as tumor cells or fibroblast cells.
The frequency of biological sampling can vary depending on different factors. Such factors include, but are not limited to, the nature of the proteins or organic metabolites, ease and safety of sampling, synthesis and breakdown/removal rates of the proteins or organic metabolites from which it was derived, and the half-life of a therapeutic agent or biological agent.
The proteins or organic metabolites may also be purified partially, or optionally, isolated, by conventional purification methods including high pressure liquid chromatography (HPLC), fast performance liquid chromatography (FPLC), chemical extraction, thin layer chromatography, gas chromatography, gel electrophoresis, and/or other separation methods known to those skilled in the art.
In another embodiment, the proteins or organic metabolites may be hydrolyzed or otherwise degraded to form smaller molecules. Hydrolysis methods include any method known in the art, including, but not limited to, chemical hydrolysis (such as acid hydrolysis) and biochemical hydrolysis (such as peptidase degradation). Hydrolysis or degradation may be conducted either before or after purification and/or isolation of the proteins or organic metabolites. The proteins or organic metabolites also may be partially purified, or optionally, isolated, by conventional purification methods including high performance liquid chromatography (HPLC), fast performance liquid chromatography (FPLC), gas chromatography, gel electrophoresis, and/or any other methods of separating chemical and/or biochemical compounds known to those skilled in the art.
C. Enriching or Isolating an Isotope-Labeled Protein
In some embodiments, an isotope-labeled target protein is enriched or isolated from a volume of body fluid. Proteins or organic metabolites may be partially purified, enriched, or isolated, from a biological sample (e.g., a volume of body fluid) using standard biochemical methods known in the art. For example, suitable methods of enriching or isolating a protein may include, but are not limited to, immunoprecipitation, chromatography (e.g., by size exclusion, hydrophobic interaction, affinity, metal binding, immunoaffinity, or HPLC), centrifugation through a density gradient, etc. Suitable methods for enrichment and isolation may depend upon, for example, protein abundance, biochemical properties of the protein, the type of sample (e.g., body fluid), and the relative degree of enrichment or purity required.
D. Performing a Mass Spectrometric Measurement
Isotopic enrichment in proteins and organic metabolites can be determined by various methods such as mass spectrometry, including but not limited to liquid chromatography-tandem mass spectrometry (LC/MS/MS), gas chromatography-mass spectrometry (GC-MS), isotope-ratio mass spectrometry, GC-isotope ratio-combustion-MS, GC-isotope ratio-pyrrolysis-MS, liquid chromatography-MS, electrospray ionization-MS, matrix assisted laser desorption-time of flight-MS, Fourier-transform-ion-cyclotron-resonance-MS, and cycloidal-MS.
Mass spectrometers convert molecules such as proteins and organic metabolites into rapidly moving gaseous ions and separate them on the basis of their mass-to-charge ratios. The distributions of isotopes or isotopologues of ions, or ion fragments, may thus be used to measure the isotopic enrichment in a plurality of proteins or organic metabolites.
Generally, mass spectrometers include an ionization means and a mass analyzer. A number of different types of mass analyzers are known in the art. These include, but are not limited to, magnetic sector analyzers, electrospray ionization, quadrupoles, ion traps, time of flight mass analyzers, and Fourier transform analyzers.
Mass spectrometers may also include a number of different ionization methods. These include, but are not limited to, gas phase ionization sources such as electron impact, chemical ionization, and field ionization, as well as desorption sources, such as field desorption, fast atom bombardment, matrix assisted laser desorption/ionization, and surface enhanced laser desorption/ionization.
In addition, two or more mass analyzers may be coupled (MS/MS) first to separate precursor ions, then to separate and measure gas phase fragment ions. These instruments generate an initial series of ionic fragments of a protein, and then generate secondary fragments of the initial ions. The resulting overlapping sequences allows complete sequencing of the protein, by piecing together overlaying “pieces of the puzzle” based on a single mass spectrometric analysis within a few minutes (plus computer analysis time).
The MS/MS peptide fragmentation patterns and peptide exact molecular mass determinations generated by protein mass spectrometry provide unique information regarding the amino acid sequence of proteins and find use in the present invention. An unknown protein can be sequenced and identified in minutes, by a single mass spectrometric analytic run. The library of peptide sequences and protein fragmentation patterns that is now available provides the opportunity to identify components of complex proteome mixtures with near certainty.
Different ionization methods are also known in the art. One key advance has been the development of techniques for ionization of large, non-volatile macromolecules including proteins and polynucleotides. Techniques of this type have included electrospray ionization (ESI) and matrix assisted laser desorption (MALDI). These have allowed MS to be applied in combination with powerful sample separation introduction techniques, such as liquid chromatography and capillary zone electrophoresis.
In addition, mass spectrometers may be coupled to separation means such as gas chromatography (GC) and high performance liquid chromatography (HPLC). In gas-chromatography mass-spectrometry (GC/MS), capillary columns from a gas chromatograph are coupled directly to the mass spectrometer, optionally using a jet separator. In such an application, the gas chromatography (GC) column separates sample components from the sample gas mixture and the separated components are ionized and chemically analyzed in the mass spectrometer.
When GC/MS (or other mass spectrometric modalities that analyze ions of proteins and organic metabolites, rather than small inorganic gases) is used to measure mass isotopomer abundances of organic molecules, hydrogen-labeled isotope incorporation from isotope-labeled water is amplified 3 to 7-fold, depending on the number of hydrogen atoms incorporated into the organic molecule from isotope-labeled water in vivo.
In general, in order to determine a baseline mass isotopomer frequency distribution for the protein, such a sample is taken before infusion of an isotopically labeled precursor. Such a measurement is one means of establishing in the cell, tissue or organism, the naturally occurring frequency of mass isotopomers of the protein. When a cell, tissue or organism is part of a population of subjects having similar environmental histories, a population isotopomer frequency distribution may be used for such a background measurement. Additionally, such a baseline isotopomer frequency distribution may be estimated, using known average natural abundances of isotopes. For example, in nature, the natural abundance of .sup.13C present in organic carbon in 1.11%. Methods of determining such isotopomer frequency distributions are discussed below. Typically, samples of the protein are taken prior to and following administration of an isotopically labeled precursor to the subject and analyzed for isotopomer frequency as described below. Similar considerations apply to the isolation of organic molecules for Dynamic Organeomics.
Thus, a single analysis of even an enormously complex mixture of proteins (that has been subjected to proteolytic cleavage or analyzed directly) can uniquely identify peptides representing thousands of expressed proteins.
Proteins may also be detected using protein chips. Several commercial “protein chip” equivalents are now marketed, using mass spectrometry (e.g. Ciphergen Biosystems). The efficiency of peptide sequence determination by mass analysis, combined with powerful ion fragmentation technology (MS/MS instruments) and/or peptide generating biochemical methods (e.g. proteolysis), improvements in sample introduction methods (HPLC, surface desorption, etc.), improved capacity for ionization of even the largest macromolecules (ESI, MALDI/SELDI) and rapid computerized handling of large data sets and comparison to peptide/protein reference libraries, have made mass spectrometry a general and powerful tool for automated, large-scale, high-throughput static proteomics.
Measuring Relative and Absolute Mass Isotopomer Abundances
Measured mass spectral peak heights, or alternatively, the areas under the peaks, may be expressed as ratios toward the parent (zero mass isotope) isotopomer. It is appreciated that any calculation means which provides relative and absolute values for the abundances of isotopomers in a sample may be used in describing such data, for the purposes of the invention.
Calculating Labeled: Unlabeled Proportion of Proteins
The proportion of labeled and unlabeled proteins is then calculated. The practitioner first determines measured excess molar ratios for isolated isotopomer species of a molecule. The practitioner then compares measured internal pattern of excess ratios to the theoretical patterns. Such theoretical patterns can be calculated using the binomial or multinomial distribution relationships as described in U.S. Pat. Nos. 5,338,686; 5,910,403; and 6,010,846 which are hereby incorporated by reference in their entirety. The calculations may include Mass Isotopomer Distribution Analysis (MIDA). Variations of Mass Isotopomer Distribution Analysis (MIDA) combinatorial algorithm are discussed in a number of different sources known to one skilled in the art. The method is further discussed by Hellerstein and Neese (1999), as well as Chinkes, et al. (1996), and Kelleher and Masterson (1992), and U.S. patent application Ser. No. 10/279,399, all of which are hereby incorporated by reference in their entirety. In addition to the above-cited references, calculation software implementing the method is publicly available from Professor Marc Hellerstein, University of California, Berkeley.
The comparison of excess molar ratios to the theoretical patterns can be carried out using a table generated for a protein of interest, or graphically, using determined relationships. From these comparisons, a value, such as the value p, which describes the probability of mass isotopic enrichment of a subunit in a precursor subunit pool, is determined. This enrichment is then used to determine a value, such as the value A.sub.X*, which describes the enrichment of newly synthesized proteins for each mass isotopomer, to reveal the isotopomer excess ratio which would be expected to be present, if all isotopomers were newly synthesized.
Fractional abundances are then calculated. Fractional abundances of individual isotopes (for elements) or mass isotopomers (for molecules) are the fraction of the total abundance represented by that particular isotope or mass isotopomer. This is distinguished from relative abundance, wherein the most abundant species is given the value 100 and all other species are normalized relative to 100 and expressed as percent relative abundance. For a mass isotopomer MX,
Fractional abundance of Mx=Ax=Abundance Mxi=0 n Abundance Mi,




  
    
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where 0 to n is the range of nominal masses relative to the lowest mass (M0) mass isotopomer in which abundances occur.




  
    
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where subscript e refers to enriched and b refers to baseline or natural abundance.
In order to determine the fraction of polymers that were actually newly synthesized during a period of precursor administration, the measured excess molar ratio (EMX) is compared to the calculated enrichment value, AX*, which describes the enrichment of newly synthesized biopolymers for each mass isotopomer, to reveal the isotopomer excess ratio which would be expected to be present if all isotopomers were newly synthesized.
F. Calculating Kinetic Parameters
One skilled in the art may establish that a kinetic parameter of the one or more isotope-labeled target proteins from the volume of a body fluid reflects the corresponding kinetic parameter of the one or more target proteins in the tissue by any means known in the art, including, e.g., independently comparing measurements of the kinetic parameter of the one or more target proteins in individual subjects.
The method of determining rate of synthesis includes calculating the proportion of mass isotopically labeled subunit present in the protein precursor pool, and using this proportion to calculate an expected frequency of a protein containing at least one mass isotopically labeled subunit. This expected frequency is then compared to the actual, experimentally determined protein isotopomer frequency. From these values, the proportion of protein which is synthesized from added isotopically labeled precursors during a selected incorporation period can be determined. Thus, the rate of synthesis during such a time period is also determined.
A precursor-product relationship is then applied. For the continuous labeling method, the isotopic enrichment is compared to asymptotic (i.e., maximal possible) enrichment and kinetic parameters (e.g., synthesis rates) are calculated from precursor-product equations. The fractional synthesis rate (k.sub.s) may be determined by applying the continuous labeling, precursor-product formula:

ks[−ln(1−f)/t]

where f=fractional synthesis=product enrichment/asymptotic precursor/enrichment and t=time of label administration of contacting in the system studied.
For the discontinuous labeling method, the rate of decline in isotope enrichment is calculated and the kinetic parameters of proteins are calculated from exponential decay equations. In practicing the method, biopolymers are enriched in mass isotopomers, preferably containing multiple mass isotopically labeled precursors. These higher mass isotopomers of the proteins, e.g., proteins containing 3 or 4 mass isotopically labeled precursors, are formed in negligible amounts in the absence of exogenous precursor, due to the relatively low abundance of natural mass isotopically labeled precursor, but are formed in significant amounts during the period of protein precursor incorporation. The proteins taken from the cell, tissue, or organism at the sequential time points are analyzed by mass spectrometry, to determine the relative frequencies of a high mass protein isotopomer. Since the high mass isotopomer is synthesized almost exclusively before the first time point, its decay between the two time points provides a direct measure of the rate of decay of the protein.
Preferably, the first time point is at least 2-3 hours after administration of precursor has ceased, depending on mode of administration, to ensure that the proportion of mass isotopically labeled subunit has decayed substantially from its highest level following precursor administration. In one embodiment, the following time points are typically 1-4 hours after the first time point, but this timing will depend upon the replacement rate of the biopolymer pool.
The rate of decay of the protein is determined from the decay curve for the three-isotope protein. In the present case, where the decay curve is defined by several time points, the decay kinetics can be determined by fitting the curve to an exponential decay curve, and from this, determining a decay constant.
Breakdown rate constants (kd) may be calculated based on an exponential or other kinetic decay curve:

kd[−ln f]/t. 

While the invention has been described with respect to specific mass isotopes and proteins, it will be appreciated how the method can be used to determine subunit pool composition, and rates of synthesis and decay for substantially any biopolymer which is formed from two or more identical subunits which can be mass isotopically labeled. Similar considerations apply for organic metabolites.
G. Inferring a Kinetic Parameter of a Protein in a Tissue
A kinetic parameter of an isotope-labeled target protein is calculated based upon measurements of the target protein enriched or isolated from a body fluid. In some embodiments, this kinetic parameter is then used to infer the corresponding kinetic parameter of the target protein in a tissue of medical interest. The kinetic parameters of the target protein in a tissue vs. body fluid may be related (i.e., the kinetic parameter of the target protein in the body fluid reflects the corresponding kinetic parameter in the tissue), but they are not required to be equivalent. The kinetic parameters in a tissue vs. in body fluid may be measured and compared by any means known in the art. The kinetic parameter of a protein in a tissue vs. that in a body fluid may be mathematically related by a known or unknown rate of protein escape or release from the tissue. Various means for determining a rate of protein escape or release from a tissue are known in the art.
Utility
Metabolic turnover kinetics of a protein of interest in a tissue of origin may be used as a diagnostic test, for the diagnosis, management or treatment selection of a human patient. By way of example, the measurement of skeletal muscle creatine kinase-MM (the terms “creatine-kinase M-type” and “CK-M” are used interchangeably herein), myoglobin, or troponin synthesis and/or breakdown rates from a body fluid can be used in the diagnosis, management or treatment selection of a patient with sarcopenia, cachexia, malnutrition, frailty, mobility disability, rehabilitation, muscular dystrophy or other disorder of skeletal muscle mass or function. The measurement of cardiac muscle creatine kinase-MB synthesis and/or breakdown rates from a body fluid in the diagnosis, management or treatment selection of a patient with heart failure, heart transplant, hypertension ischemic heart disease or other disorder of cardiac muscle mass or function. By way of another example, the rate of liver fibrogenesis can be determined from a blood measurement of lumican synthesis, for use in medical monitoring of patients with hepatitis C or B, alcoholic liver fibrosis, fatty liver disease or other fibrogenic disorders.
Example 1
Virtual Biopsy of Liver Fibrogenesis Through Measurements of Plasma Lumican from Blood Samples
This example demonstrates the use of a virtual biopsy to assess liver fibrogenesis by determining liver collagen synthesis rate through a body fluid biomarker. This example further illustrates an approach to discovering a virtual biopsy body fluid biomarker of tissue protein synthesis (and a corresponding rate thereof) when the biomarker in a body fluid is not identified in advance.
Tissue Collection
A total of 11 subjects were recruited at UCSF Liver Center who were imminently undergoing diagnostic biopsy. Subjects drank heavy water, a nonradioactive, stable isotopic tracer for 14 to 56 days in an outpatient setting for the period between referral and surgical biopsy date. Blood, urine, and an 18 gauge liver biopsy were collected. 50% of the biopsy material was used to generate histological tissue slides for pathological diagnosis of disease and fibrotic intensity. The remaining tissue was used for kinetic analysis as described below. Subjects had a range of diagnoses [Hep C Virus (HCV), Autoimmune Hepatitis (AIH), Hepatocellular carcinoma (HCC)] and a range of fibrotic scores (on a scale of 0-4). The study was approved by the Committee on Human Research at UCSF. All participants gave written informed consent, and Declaration of Helsinki protocols were followed.
Liver Tissue LCMS Prep
Liver biopsy tissue from 6 patients was weighed (3-13 mg) and subsequently homogenized with a Fast Prep-24TM (MP Biomedical) bead mill in pure, deionized water. Homogenized tissue was then subjected to acetone precipitation to purify total tissue protein. 9× volumes cold acetone was mixed with homogenate and incubated at −20° C. for 20 min followed by centrifugation at 1000×g for 5 min at 4 C. Pellets were resuspended in H2O and total protein quantification performed via BCA Protein Assay Kit (Thermo, Rockford Ill.). 80 μg of liver protein from each patient was isolated and denatured using ProteasMaxTM surfactant (0.1%; Promega, Madison Wis.) and urea (4M) in 25 mM ammonium bicarbonate (pH=8). The solution was reduced with TCEP (5 mM) for 20 minutes at RT with mixing, followed by incubation with iodoacetamide (10 mM) in the dark for 20 minutes to chemically modify reduced cysteines. Liver proteins were then digested with trypsin (Promega, Madison Wis.) at 37° C. overnight. The following day formic acid was added to a total volume of 5%, and peptides were concentrated and desalted prior to LC-MS/MS using a C18 spec tip (Varian, Palo Alto Calif.).
Plasma LCMS Prep
Plasma from 8 patients (10 μL) was depleted of high abundance proteins using a multi-affinity spin cartridge (Hu14, Agilent, Santa Clara, Calif.) according to the manufacturer's recommendations. Remaining protein components were quantified using a BCA Protein Assay Kit (Thermo, Rockford Ill.), and 50 μg of protein was isolated from each patient for trypsin digestion. Plasma proteins samples were denatured using ProteasMaxTM surfactant (0.1%; Promega, Madison Wis.) and urea (4M) in 25 mM ammonium bicarbonate (pH=8). The solution was reduced with TCEP (5 mM) for 20 minutes at RT with mixing, followed by incubation with Iodoacetamide (10 mM) in the dark for 20 minutes to chemically modify reduced cysteines. Plasma protein was then digested with trypsin (Promega, Madison Wis.) at 37° C. overnight. The following day formic acid was added to a total volume of 5%, and peptides were concentrated and desalted prior to LC-MS/MS using a C18 spec tip (Varian, Palo Alto Calif.).
Measurement of 2H Enrichment in Body Water
Aliquots of plasma were diluted 1:100, and placed into the caps of inverted sealed screw-capped vials for overnight distillation at 80° C. Body water 2H2O enrichments were determined by direct measurement of deuterium mole percent excess (MPE) in water distilled from the blood plasma. MPE was measured against a 2H2O standard curve using laser water isotope analyzer (LGR, Los Gatos Calif.) according to the published method (G. Lis, et al., Anal. Chem. 80 (2008) 287-293).
LCMS Data Acquisition and Isotopomer Extraction
Isotopic distributions of peptides were measured using an Agilent 6550 QToF with HPLC Chip-Cube Polaris Chip (Agilent, Santa Clara Calif.). Each sample was injected two times per analysis. During the first injection MSMS fragmentation spectra were collected for peptide identification. During the second injection no MSMS fragmentations were performed and a longer dwell time (1 spectrum per second) was used in the full scan acquisition. MSMS fragmentation data was analyzed using the Agilent software package Spectrum Mill and protein identifications were based on the Uniprot/Swissprot database where species=human, trypsin digest, and carbamidomethylation of cysteine were used as restrictions on the search. Pyroglutamate, oxidized methionine, and hydroxyproline were allowed as additional modifications. Isotopomer patterns were extracted from the MS scan data using the MassHunter software package from Agilent. The peptide list with calculated neutral mass, elemental formula, and retention time was used to filter the observed isotope clusters. A visual basic application was constructed to calculate peptide elemental composition from lists of peptide sequences and calculate isotopomer patterns over a range of precursor body 2H2O enrichments (p) for the number (n) of C—H positions actively incorporating H/D from body water. Theoretical peptide values for n were determined as previously described (J. C. Price et al., Anal. Biochem. 420 (2012) 73-83). Briefly, tryptic peptides exhibit a value of n that is the sum of the individual values of (nAA) the amino acids that make up the peptide. Subsequent data handling was performed using Microsoft Excel.
Calculation of Protein Fractional Synthesis (f) and Turnover Rate (k).
While mass spectrometry can quantify a shift to higher masses in a peptide with 2H-labeling, kinetic interpretation of the replacement rate of pre-existing protein molecules by newly synthesized ones requires understanding of the mass isotope pattern of newly-synthesized species as compared to unlabeled species. The mass isotopomer pattern of proteins synthesized in the presence of a stable-isotopically perturbed precursor pool can be calculated by combinatorial analysis (M. K. Hellerstein and R. A. Neese, Am. J. Physiol. 276 (1999) E1146-E1170). Fractional synthesis (f) is defined as the proportion of newly synthesized proteins in a population, expressed as a fraction of the total pool. We based our calculations off on the absolute value for change in intensity of the normalized monoisotopic peak (|EM0|). In principle, the shift in intensity of any isotopic peak in the envelope should reveal the same f. In practice, we find that the signal to noise is most favorable for |EM0|, because of the larger change in fractional abundance for this isotopomer (EM0 decreases while labeled species distribute among EM1-EM4). We normalized the fractional synthesis measurements for each subject to a time-independent turnover rate, k, using the equation: k=ln(1−f)/t, where t is the duration of exposure to heavy water prior to biopsy.
Criteria for Peptides Used in Calculation of Protein Turnover Rates
Peptides which met our criteria for inclusion had signal intensity >30,000 counts. Protein turnover rates were calculated as the mean of the peptide population that passed these criteria for each protein. A minimum of 2 peptides were required to determine a protein turnover rate for each sample.
Correlation of Collagen and Lumican Kinetics with Disease
Protein turnover rates (k) from liver (n=6) and plasma (n=8) sample proteins were correlated with one another, as well as with patient histological fibrotic score (0-4). Regression analysis was performed to determine statistically significant relationships (p<0.05) (e.g. liver type-1 collagen and plasma lumican vs. fibrotic score).
Results
As illustrated in FIG. 2, 2H2O was administered to humans and became incorporated into collagens and fibrogenesis-/collagen-related proteins during tissue fibrogenesis. Blood and urine were screened for then proteins whose synthesis rate correlated with liver collagen synthesis rate in order to identify potential body fluid diagnostic biomarkers of liver fibrosis. Protein turnover rates from liver and plasma sample proteins were correlated with each other, as well as with patient histological fibrotic score, as described above. Regression analysis was performed to determine statistically significant relationships as described above.
Alterations in mass isotopomer pattern in peptides derived from many proteins in plasma, including peptides derived from the protein lumican, were identified and measured by LC/MS/MS and compared to synthesis rates of liver tissue collagens. Collagen synthesis rates in liver varied among individual human subjects (FIG. 3). The synthesis rate of plasma lumican was verified to closely reflect the synthesis rate of collagen Types I, III, and VI in the liver of the same patients with hepatitis and suspected fibrosis, indicating measurement of liver fibrogenesis rate from a blood measurement (FIGS. 4-5).
Accordingly, the synthesis rate of lumican in blood plasma could be calculated from alterations in mass isotopomer pattern as represented by these data. Moreover, the synthesis rate of plasma transforming growth factor (TGF)-beta inducible protein was also shown to closely correlate with the synthesis rate of collagen type I α1 in the liver of patients with hepatitis (FIG. 6A) and suspected fibrosis in the same subjects (FIG. 6B). As illustrated in FIG. 7A, the synthesis rate of collagen type I in the liver of patients with hepatitis, and suspected fibrosis correlated with histologic fibrosis score in the same subjects. As illustrated in FIG. 7B, the synthesis rate of collagen type III in the liver of patients with hepatitis, and suspected fibrosis correlated with histologic inflammation score in the same subjects. In addition, the synthesis rates of most proteins in blood did not correlate with liver fibrosis scores (selected proteins as shown in FIG. 8), demonstrating that plasma protein synthesis rates are not a non-specific marker of an increase in general liver protein synthesis in these patients with hepatitis and suspected fibrosis.
Example 2
Virtual Biopsy of Creatine Kinase Using Blood Samples
Deuterated Water Labeling Protocol in Humans
All procedures and protocols were approved by the Institutional Review Board at Colorado State University. 17 subjects (7 males, 10 females) were included in the study, each volunteer was informed of the potential risks and benefits and provided written consent before participating. The study followed the guidelines set forth by the Declaration of Helsinki.
Deuterium labeling of newly synthesized proteins was achieved by oral consumption of 2H2O (70%; Cambridge Isotope Laboratories, Andover Mass., USA) for 4 weeks using protocols described previously (Robinson et al, 2011). A target of 1-2% enrichment was achieved during a 1-week priming stage, when subjects consumed 50 ml of 70% 2H2O 3 times a day for a total of 150 ml/day, which was maintained for 3 weeks with a dose of 50 ml of 70% 2H2O 2 times a day for a total of 100 ml/day.
Sample Collection
Saliva swabs were collected periodically during oral deuterated water consumption, Participants were instructed to not eat or drink anything for 30 min before saliva sampling. Saliva swabs were stored at −80° C. until analysis. Venous blood was collected and plasma separated by centrifugation (1200 g, 4° C., 15 min) and stored at −80° C. Muscle biopsy samples ( ̃100-150 mg) of the vastus lateralis were removed while the subjects were under local anesthesia (1% lidocaine) using a 5-mm Bergstrom needle with manual suction and then immediately frozen in liquid nitrogen and stored at −80° C.
Body Water Enrichment Analysis
Body water enrichment was determined from saliva swabs or plasma samples. Aliquots of plasma or saliva were diluted 1:200, and placed into the caps of inverted sealed screw-capped vials for overnight distillation at 80° C. Body water 2H2O enrichments were determined by direct measurement of deuterium mole percent excess (MPE) in water distilled from the blood plasma. MPE was measured against a 2H2O standard curve using laser water isotope analyzer (LGR, Los Gatos Calif.).
SDS-PAGE Fractionation, Coomassie Staining and In-Gel Trypsin Digestion of Muscle Proteins
10-30 mg muscle samples were homogenized in M-PER reagent (Thermo) at 100 mg/ml with 1× protease inhibitor cocktail (Thermo). The homogenate was centrifuged at 1000×g for 10 min at 4° C. to pellet insoluble material. 250 μg of protein from homogenate was prepared for SDS-PAGE and LC/MS. The samples were incubated at 95° C. for 5 min in 1×XT sample buffer (Bio-Rad) and 5 mM TCEP (Sigma). The samples were allowed to cool to room temperature and Iodoacetamide (Sigma) was added at a final concentration of 15 mM. The samples were incubated at room temperature in the dark for 20 min. The samples were loaded onto Criterion XT 12 well 4-12% Bis-Tris gels (Bio-Rad) with 1×XT MES running buffer (Bio-Rad) in the Bio-Rad Criterion Cell (165-6001). 10 μL of Kaliedoscope Pre-Stained Molecular Weight Standard (Bio-Rad) was loaded on flanking ends of the samples. The gels were run at 60V for 20 minutes to allow the samples to fully enter the gel and then run at 100V for 1 and a half hours. The gels were removed and washed 3 times with 200 ml of MilliQ H2O for 5 minutes with rotation. Coomassie (Bio-Rad) was added to barely cover the gels and incubated for 60 minutes with rotation. The gels were destained by washing 4 times with 200 ml of MilliQ H2O for 30 minutes with rotation; a Kimwipe was placed in the water to help absorb the stain. The gel-bands corresponding to 10-15, 15-20, 20-25, 25-37, 37-50, 50-75, 75-100, 100-150 and 150-250 kD were excised from the Coomassie-stained gels and subjected to overnight trypsin (Proteomics grade, Sigma) digestion at 37 C. The peptides were extracted from the gel, dried, reconstituted in 3% acetonitrile/0.1% formic acid for LC/MS analysis.
Immunoprecipitation of Creatine Kinase M-Type from Plasma, SDS-PAGE Fractionation and In-Gel Trypsin Digestion
Creatine-kinase M-type (CK-M) was immunoprecipitated from  ̃500 μl plasma using 20 μg of goat-anti-CK-M polyclonal antibody (CalBioreagents) conjugated to 1 mg epoxy Dynabeads (Invitrogen). Samples were incubated for 60 min at RT and the bound CK-M was eluted in sample buffer and prepared for SDS-PAGE fractionation and Coomassie staining as described above. The gel-band corresponding to 37-50 kD were excised from the Coomassie-stained gels and subjected to overnight trypsin (Proteomics grade, Sigma) digestion at 37° C. The peptides were extracted from the gel, dried, reconstituted in 3% acetonitrile/0.1% formic acid for LC/MS analysis.
LC/MS Analysis
The trypsin-digested peptides were analyzed on an Agilent 6520 or 6550 QToF with Chip Nano source and 1200 series nanoflow and capillary HPLC pumps (Agilent Technologies, Santa Clara, Calif.) as described previously (Price et al. 2011, 2012). Each sample was injected twice per analysis using a Polaris HR chip (Agilent #G4240-62030) consisting of a 360 nL enrichment column and a 0.075×150 mm analytical column, both packed with Polaris C18-A stationary phase (3 μm particle size). Mobile phase for the nano LC was 3% v/v acetonitrile, 0.1% formic acid, in 18MΩ water (Buffer A) and 95% acetonitrile, 0.1% formic acid in 18 MΩ water (Buffer B). Samples were eluted at a flow rate of 350 nL/min with an 18-27-min gradient. During the first injection, data dependent MSMS fragmentation spectra were collected with the instrument set to collect 6 MS scans per second, 4 MSMS spectra per second, and up to 12 precursors per cycle. During the second injection, no MSMS fragmentations were performed and a longer dwell time (1 spectrum per second) was used in the full scan acquisition. The longer dwell time increased the signal to noise ratio for the observed isotopomer patterns. MSMS fragmentation data were analyzed using Spectrum Mill MS Proteomics Workbench (version B.04.00, Agilent Technologies, Santa Clara, Calif.) using the Swiss-Prot mouse database (August 2010) with a global false discovery rate of 1%. Fixed modifications (carbamidomethylation of cysteine) and variable modifications (oxidized methionine, pyroglutamic acid) were enabled and up to two missed cleavages allowed. Results validated at the peptide and protein level were searched again allowing for non-specific cleavage of the protein. A list of peptides with scores greater than 6 and scored peak intensities greater than 50% was exported from Spectrum Mill and collapsed into a non-redundant peptide formula database using Excel. This database, containing peptide elemental composition, mass, and retention time, was used to extract peptide isotopomer abundances (containing kinetic information) of each peptide from corresponding MS-only acquisition files with the Find-by-Formula algorithm in Mass Hunter (version B.05.00, Agilent Technologies, Santa Clara, Calif.). A visual basic application was constructed to calculate peptide elemental composition from lists of peptide sequences and calculate isotopomer patterns over a range of precursor body 2H2O enrichments (p) for the number (n) of C—H positions actively incorporating hydrogen/deuterium (H/D) from body water. Subsequent data handling was performed using a series of Microsoft Excel templates, with input of body water enrichment for each subject to yield fractional synthesis data at the protein level. The kinetics data were filtered to include ≧2 peptides per protein.
Statistical Analysis
Pearson correlation analysis (GraphPad Prism) was performed to correlate the fractional synthesis of CK-M in the plasma to that measured in the muscle. In addition, correlation analysis was also performed with fractional synthesis of plasma CK-M and that of several myofibril and cytosolic proteins measured in the muscle. All correlations were considered significant at p<0.05.
Results
2H2O was administered to humans or experimental animals, and plasma creatine kinase MM was isolated from plasma by immunoprecipitation, subjected to trypsin digestion, and analyzed by LC/MS/MS (liquid chromatography-tandem mass spectrometry) to determine alterations in mass isotopomer pattern, from which the synthesis rate of creatine kinase MM in blood plasma was calculated (FIG. 9). The synthesis rate of plasma creatine kinase MM was verified to closely reflect the synthesis rate of creatine kinase MM isolated from muscle biopsies in the same subjects (FIG. 10). As illustrated in FIG. 11, the synthesis rates of skeletal muscle creatine kinase MM closely correlated with the synthesis rates of several other muscle proteins (Actin, FIG. 11A; Myosin-2, FIG. 11B; Troponin-I, FIG. 11C; Tropomyosin-alpha, FIG. 11D). In contrast, creatine kinase MB (cardiac muscle-specific) that was isolated from plasma exhibited much higher synthesis rates than creatine kinase MM, indicating tissue-specific measurement of creatine kinase synthesis from blood measurements.
In a parallel experiment in rats, 2H2O was administered to healthy rats, and plasma creatine kinase MM was isolated from plasma by immunoprecipitation, subjected to trypsin digestion, and analyzed by LC/MS/MS (liquid chromatography-tandem mass spectrometry) to determine alterations in mass isotopomer pattern, from which the synthesis rate of creatine kinase MM in blood plasma was calculated (as depicted in FIG. 9). The synthesis rates of plasma creatine kinase MM correlated extremely closely with the synthesis rate of gastrocnemius muscle creatine kinase MM (FIG. 12A) and the synthesis rate of quadriceps muscle creatine kinase MM (FIG. 12B).
REFERENCES


    1. G. L is, L. I. Wassenaar, M. J. Hendry, High-precision laser spectroscopy D/H and 18O/16O measurements of microliter natural water samples, Anal. Chem. 80 (2008) 287-293.
    2. M. K. Hellerstein, R. A. Neese, Mass isotopomer distribution analysis at eight years: theoretical, analytic, and experimental considerations, Am. J. Physiol. 276 (1999) E1146-E1170.
    3. J. C. Price, W. E. Holmes, K. W. Li, N. A. Floreani, R. A. Neese, S. M. Turner, M. K. Hellerstein, Measurement of human plasma proteome dynamics with 2H2O and liquid chromatography tandem mass spectrometry, Anal. Biochem. 420 (2012) 73-83.

## Claims

1. A method for measuring the rate of synthesis, breakdown, transport, or other kinetic parameters of a protein in a tissue of medical interest, without requiring physical sampling of said tissue, by a measurement of the protein in a body fluid, the method comprising:
a) selecting one or more target proteins in a tissue;
b) administering an isotope-labeled molecule to a subject for a period of time sufficient for said isotope-labeled molecule to enter into and label the one or more target proteins to produce one or more isotope-labeled target proteins;
c) collecting a volume of a body fluid, wherein said volume comprises one or more isotope-labeled target proteins that escaped or were released from the tissue;
d) enriching or isolating the one or more isotope-labeled target proteins from said volume;
e) performing a mass spectrometric measurement of the isotopic content, rate of incorporation, and/or pattern or rate of change in isotopic content and/or pattern of isotope labeling of the one or more enriched or isolated isotope-labeled target proteins;
f) calculating at least one kinetic parameter of the one or more enriched or isolated isotope-labeled target proteins, wherein the kinetic parameter of the one or more isotope-labeled target proteins from said volume of a body fluid reflects the corresponding kinetic parameter of the one or more target proteins in said tissue; and
g) inferring the at least one kinetic parameter of the one or more target proteins in the tissue based on the corresponding at least one kinetic parameter of the one or more target proteins in the body fluid.

2. The method of claim 1, wherein the isotope-labeled molecule is a general precursor that labels amino acids.

3. The method of claim 2, wherein the isotope-labeled molecule is selected from the group consisting of 2H2O, 13C2-leucine, 3H-phenylalanine, 15N-glycine, 15N-labeled spirulina, 13CO2, 2H3-leucine, and 13C-glucose.

4. The method of claim 1, wherein the isotope-labeled molecule is a stable, non-radioactive isotope-labeled molecule.

5. The method of claim 4, wherein the isotope-labeled molecule is 2H2O.

6. The method of claim 1, wherein the isotope-labeled molecule is a radioactive isotope-labeled molecule.

7. The method of claim 1, wherein the tissue is selected from the group consisting of skeletal muscle, heart muscle, brain, pancreatic β-cells or islets, and collagen-producing fibroblasts present in liver, lung, kidney, heart, or skin.

8. The method of claim 1, wherein the body fluid is selected from the group consisting of blood, urine, sputum, bile, cerebrospinal fluid, interstitial fluid of skin or adipose tissue, saliva, tears, bronchial-alveolar lavage, oropharyngeal secretions, intestinal fluids, cervico-vaginal or uterine secretions, and seminal fluid.

9. The method of claim 1, wherein the kinetic parameter of the one or more isotope-labeled target proteins from said volume of a body fluid has been established to reflect the corresponding kinetic parameter of the one or more target proteins in said tissue by independently comparing measurements of the kinetic parameter of the one or more target proteins in individual subjects.

10. The method of claim 1, wherein the isotope-labeled molecule is administered for a period of time sufficient to produce one or more isotope-labeled target proteins and then discontinued, and wherein enriching or isolating the one or more isotope-labeled target proteins from the volume of a body fluid takes place after the administration of the isotope-labeled molecule has been discontinued.

11. The method of claim 1, wherein the one or more target proteins are related to tissue collagen deposition or fibril formation and/or are derived from collagen-synthesizing fibroblasts.

12. The method of claim 1, wherein the one or more target proteins are selected from the group consisting of lumican, perlecan, fibronectin, procollagen, and collagen.

13. The method of claim 11, wherein the at least one kinetic parameter reveals a rate of a medically important process for the diagnosis, therapy, prognosis, management, stratification, or other characterization of a disease selected from the group consisting of hepatitis C or B; alcoholic liver fibrosis; fatty liver disease; fibrosis of liver, lung, heart, skin, or kidney; and other fibrogenic disorders.

14. The method of claim 12, wherein the at least one kinetic parameter reveals a rate of a medically important process for the diagnosis, therapy, prognosis, management, stratification, or other characterization of a disease selected from the group consisting of hepatitis C or B; alcoholic liver fibrosis; fatty liver disease; fibrosis of liver, lung, heart, skin, or kidney; and other fibrogenic disorders.

15. The method of claim 12, wherein the one or more target proteins are subjected to trypsin digestion between steps (d) and (e), and the one or more target proteins are analyzed as trypsin-digested peptides in step (e).

16. The method of claim 1, wherein the target protein is creatine kinase MM or creatine kinase MB.

17. The method of claim 16, wherein the body fluid is plasma; step (d) comprises immunoprecipitation; said creatine kinase MM or creatine kinase MB is subjected to trypsin digestion between steps (d) and (e); and said creatine kinase MM or creatine kinase MB is analyzed as a trypsin-digested peptide in step (e).

18. The method of claim 17, wherein step (e) comprises measuring mass isotopomer abundance by LC/MS/MS.

19. The method of claim 18, wherein creatine kinase MM-specific trypsin-digested peptides are analyzed by LC/MS/MS for alterations in mass isotopomer abundance, and wherein said alterations in mass isotopomer abundance are used to calculate a rate of synthesis and/or breakdown of creatine kinase in skeletal muscle tissue.

20. The method of claim 19, wherein the calculation of the rate of synthesis and/or breakdown of creatine kinase in skeletal muscle tissue is used in the diagnosis, management, rehabilitation, or treatment selection of a patient with sarcopenia, cachexia, malnutrition, frailty, mobility disability, muscular dystrophy, or another disorder of skeletal muscle mass or function.

21. The method of claim 18, wherein creatine kinase MB-specific trypsin-digested peptides are analyzed by LC/MS/MS for alterations in mass isotopomer abundance, and wherein said alterations in mass isotopomer abundance are used to calculate a rate of synthesis and/or breakdown of creatine kinase in cardiac tissue.

22. The method of claim 21, wherein the calculation of the rate of synthesis and/or breakdown of creatine kinase in cardiac tissue is used in the diagnosis, management, rehabilitation, or treatment selection of a patient with heart failure, heart transplant, hypertension ischemic heart disease, or another disorder of cardiac mass or function.

23. The method of claim 1, wherein the one or more target proteins are blood proteins derived from pancreatic β-cell secretory granules.

24. The method of claim 1, wherein the at least one kinetic parameter reveals a rate of a medically important process for the diagnosis, therapy, prognosis, management, stratification, or other characterization of a disease process in a tissue of medical interest.

25. The method of claim 1, wherein the calculation of the at least one kinetic parameter of the one or more target proteins is used as a diagnostic test.

26. The method of claim 25, wherein the diagnostic test is used in the diagnosis, management, or treatment selection of a human or veterinary patient.