Abstract:
The invention provides a method for screening for and detection of solid organ graft rejection in a subject that comprises assaying a patient sample of plasma, serum or blood from the subject for a protein marker identified herein. An elevated or reduced amount of marker present in the patient sample compared to a control sample is indicative of rejection, and identifies subjects in need of biopsy or modified treatment. The method can be used to screen for patients in danger of transplant rejection without having to undergo more costly, risky and invasive biopsy procedures.

Description:
[0001]    This application claims the benefit of U.S. provisional patent application No. 61/977,567, filed Apr. 9, 2014, the entire contents of which are incorporated herein by reference. 
     
    
     TECHNICAL FIELD OF THE INVENTION 
       [0002]    The present invention relates generally to detection, prediction, and monitoring of transplant rejection, including renal allograft rejection. The invention more specifically pertains to use of protein markers that can be detected in serum for early detection of allograft rejection. 
       BACKGROUND OF THE INVENTION 
       [0003]    A transplant to replace damaged tissues with healthy ones from either living or decreased individuals of the same species is called an allograft. Tissues and cells from another individual are usually recognized as foreign by the mammalian immune system. This stimulates a response of the host defenses to reject the foreign tissue. The immune system can occasionally recognize very small differences in molecular structure and develop an alloimmune response. Some cell types are very similar among individuals such as blood cells. It is possible to administer blood products such red blood cells, and plasma without an immune response if the blood type is compatible. Virtually all mammalian cells, except red blood cells, express major histocompatibility molecules on their cell surface. These molecules are a critical mechanism by which the immune system can distinguish self from foreign cells. 
         [0004]    Organ transplantation is the definitive therapy for many forms of end-stage disease of the kidney, liver, heart, lung, pancreas and intestine. Transplantation of specialized cells such as islets of Langerhans and nerve cells are becoming more common, as well as complex tissue transplantation such as a limb or face. However, the long-term success of these procedures is limited by the immune response. Unless the donor is an identical twin, most recipients must take immunosuppressive medications. Current immunosuppressive therapies are not capable of preventing rejection in all cases, and have multiple significant side effects. These drugs may lead to life threatening infection, cardiovascular disease, diabetes, and cancer. 
         [0005]    A number of methods are currently used to monitor the function of transplanted organs and tissue: serum creatinine for kidney, serum transaminases for liver, ejection fraction for heart, oxygen saturation for lung, and serum glucose for pancreas transplant. Unfortunately, these tests have poor sensitivity or specificity for rejection. In many cases the definitive test for organ rejection is an invasive and expensive biopsy. 
         [0006]    The histologic patterns of rejection are different for each organ and distinct patterns of tissue injury can be identified for “cellular” versus “humoral” rejection. This distinction is important since the best treatment for “cellular” rejection may be administration of immunosuppressive medications targeted to prevent further proliferation of T lymphocytes, while “humoral” rejection is treated by medications that suppress B lymphocytes and clear the plasma of the antibodies which recognize the graft as foreign. In general, a mild cellular rejection can frequently be reversed and may not cause long-term injury. Humoral rejection is more difficult to reverse and has a higher risk of leading to poor graft function. In many cases of transplant rejection there are components of both a cellular and humoral immune response combined. The gold standard for classification of transplant rejection is allograft biopsy. 
         [0007]    Despite significant improvements in one-year allograft function with current immunosuppressive strategies, there has been less progress in the long term maintenance of graft function. It is hypothesized that both immunologic and non-immunologic factors such as drug toxicity or hypertension contribute to this disease. Chronic transplant dysfunction is a phenomenon in solid organ transplants with a gradual deterioration of function accompanied by characteristic histological features on graft biopsy. In kidney transplantation, this is known as chronic rejection, chronic allograft nephropathy (CAN), or interstitial fibrosis with tubular atrophy (IFTA). In heart transplantation there is accelerated atherosclerosis and in liver transplantation the bile ducts atrophy. Chronic transplant injury is characterized by fibrosis of the internal blood vessels of the transplant and may be related to sub-clinical AMR. Detecting this problem at an early stage is difficult even with protocol biopsy. 
         [0008]    Current diagnostic methods of renal allograft rejection are neither sensitive nor specific. Needle biopsies are invasive and associated with patient morbidity. Thus, it is desirable to develop noninvasive tests to predict and diagnose rejection. 
       SUMMARY OF THE INVENTION 
       [0009]    The invention provides a set of protein markers and methods of using these markers for assessment of a patient&#39;s immune status and for predicting rejection of an organ transplant. The markers include complement C4 anaphylatoxin (C4A), Apolipoprotein A1 (ApoA1), α-1 anti-chymotrypsin C terminal fragment (AACT), C1 protease inhibitor (C-inh), Serum Amyloid A (SAA), C-reactive Protein (CRP), Apolipoprotein E (ApoE), alpha-1-antitrypsin (A1AT), Post-translational modified ApoA1, Inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), and Alpha-2-macroglobulin (A2M), as well fragments of these proteins (see Tables 1 and 4, and SEQ ID NOs: 1-18). 
         [0010]    The invention provides a method for detecting susceptibility in a patient to solid organ graft rejection, which can be achieved with a high degree of sensitivity and specificity. In one embodiment, the method detects rejection with at least 90% sensitivity and at least 90% specificity. In one embodiment, the method comprises the steps of: (a) measuring the amount of a 5 kiloDalton (kDa) fragment of complement C4 anaphylatoxin (C4A) in a sample obtained from the patient; (b) comparing the amount of the 5 kDa fragment of C4A in the patient sample with the amount in a control sample; and (c) detecting susceptibility to graft rejection when the comparing shows an increase in the 5 kDa fragment of C4A in the patient sample relative to the control sample. In another embodiment, the method comprises the steps of: (a) contacting a sample obtained from the patient with a reagent that specifically binds a 5 kiloDalton (kDa) fragment of complement C4 anaphylatoxin (C4A); (b) measuring the amount of specific binding between the reagent and the patient sample; (c) comparing the amount of specific binding in (b) with the amount of specific binding of reagent to a control sample; and (d) detecting susceptibility to graft rejection when the comparing in (c) shows an increase in specific binding to the 5 kDa fragment of C4A in the patient sample relative to the control sample. In one embodiment, the contacting further comprises contacting the patient sample with a reagent that binds Apolipoprotein A1 (ApoA1) and/or α-1 anti-chymotrypsin C terminal fragment (AACT), and the detecting further comprises detecting susceptibility to graft rejection when the comparing shows a decrease in the amount of ApoAl and/or AACT in the patient sample relative to the control sample. In one embodiment, the contacting and comparing of (b) and (c) comprise contacting the patient sample with reagents that bind ApoA1 and AACT. 
         [0011]    In another embodiment, the invention provides a method for detecting susceptibility in a patient to solid organ graft rejection. In one embodiment, the method comprises the steps of: (a) contacting a sample obtained from the patient with a reagent that specifically binds a set of biomarkers comprising two or more markers listed in Table 1; (b) measuring the amount of specific binding between the reagents and the patient sample; (c) comparing the amount of specific binding in (b) with the amount of specific binding of the reagents to a control sample; and (d) detecting susceptibility to graft rejection when the comparing in (c) shows a significant increase or decrease in specific binding to the biomarkers in the patient sample relative to the control sample. In some embodiments, steps (a)-(c) are performed for 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, up to 19 of the markers listed in Table 1. In one embodiment, the set of markers consists of 8 or fewer markers listed in Table 1. In another embodiment, the set of markers consists of 6 or fewer markers listed in Table 1. In yet another embodiment, the set of markers consists of 4 or fewer markers listed in Table 1. 
         [0012]    With respect to the following markers, susceptibility to graft rejection is detected when the specific binding of reagent to marker is increased in the patient sample relative to the control: C1 protease inhibitor (C1-inh), Serum Amyloid A (SAA), C-reactive Protein (CRP), Apolipoprotein E (ApoE), alpha-1-antitrypsin (A1AT), and/or specific binding of reagent to the following markers is decreased relative to control: AACT, ApoA1, Post-translational modified ApoA1, Inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), Alpha-2-macroglobulin (A2M). In a typical embodiment, the difference is a decrease or increase of at least 10% relative to the control. 
         [0013]    In another embodiment, the invention provides a method for detecting susceptibility in a patient to solid organ graft rejection, the method comprising the steps of: (a) contacting a sample obtained from the patient with reagents that specifically bind a set of markers consisting of: a 5191 Dalton fragment of complement C4 anaphylatoxin (C4A), α-1 anti-chymotrypsin C terminal fragment (AACT), and Apo A1; and optionally further consisting of: complement C1 inhibitor, and/or a marker listed in Table 1; (b) measuring the amount of specific binding between the reagent and the sample; (c) comparing the amount of specific binding in (b) with a control sample; and (d) detecting susceptibility to graft rejection when the comparing in (c) shows an increase in the 5191 Dalton fragment of C4A or a decrease AACT and/or ApoAl relative to the control sample. 
         [0014]    In some embodiments, the measuring comprises an immunoassay. In other embodiments, the measuring comprises mass spectrometry. Representative examples of reagents include, but are not limited to, an antibody, a nucleic acid probe, or a synthetic probe. The probe or antibody may optionally be labeled with a detectable marker. 
         [0015]    Examples of solid organ grafts include, but are not limited to, kidney, liver, heart, pancreas, lung, intestine and thymus. In one embodiment, the solid organ graft rejection is acute cellular renal allograft rejection. Other types of solid organ graft rejection include chronic rejection, such as chronic allograft nephropathy, or interstitial fibrosis with tubular atrophy. 
         [0016]    The invention additionally provides a kit comprising antibodies that specifically bind the 5 kDa fragment of C4A, ApoA1, AACT, and, optionally, one or more additional markers listed in Table 1. In one embodiment, the kit comprises reagents that bind C4A (or a 5 kDa fragment thereof) and ApoA1 (or the fragment thereof at amino acids 148-183) and/or AACT (or the fragment thereof at amino acids 385-422), In one embodiment, the kit comprises reagents that specifically bind the 5191 Da fragment of AACT and ApoA1. In one embodiment, the kit further comprises a solid support onto which the antibodies are immobilized. Examples of a solid support include, but are not limited to, a microtiter plate, beads, a membrane or other support known to those skilled in the art. In one embodiment, the antibodies are immobilized via binding to antigen that is immobilized to the solid support. In one embodiment, the antibodies are immobilized via binding to a bead or particle such as luminex. In one embodiment, the kit further comprises a chromogenic substrate. 
         [0017]    Additionally provided is a method for detecting susceptibility in a patient to solid organ graft rejection, the method comprising the steps of: (a) contacting a sample obtained from the patient with a reagent that specifically binds complement C4 anaphylatoxin (C4A); (b) measuring the amount of specific binding between the reagent and the sample; (c) comparing the amount of specific binding in (b) with a control sample; wherein a greater amount of binding in (b) relative to the control is indicative of susceptibility to solid organ graft rejection. 
         [0018]    Another illustrative embodiment of the invention is a mass spectrometry assay to identify the peptide and/or protein profile in a patient that is associated with solid organ allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor and/or one of the other 16 proteins in Table 1 in plasma or serum or other body fluid, the assay comprising the steps of: (a) measuring the specific amount of specific peptide by mass spectrometry in plasma, serum or other body fluid; (b) comparing the specific quantity of protein/peptide in (a) with a control sample; wherein a greater or lesser amount of specific peptide relative to the control is indicative of susceptibility to solid organ graft rejection. 
         [0019]    Another illustrative embodiment of the invention is an ELISA kit to screen for a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor in plasma or serum, the kit comprising: (a) a microtiter plate coated with polyclonal or monoclonal antibodies specific to α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor; (b) polyclonal or monoclonal antibody-alkaline phosphatase conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor; (c) p-nitrophenyl-phosphate; and (d) α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor as an antigen standard. 
         [0020]    Also provided is a method for detecting susceptibility in a patient to acute cellular renal allograft rejection, the method comprising the steps of: (a) providing polyclonal or monoclonal antibodies against α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor; (b) providing a microtiter plate coated with the antibodies; (c) adding the serum or plasma to the microtiter plate; (d) providing alkaline phosphatase-antibody conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor to the microtiter plate; (e) providing p-nitrophenyl-phosphate to the microtiter plate; and (f) comparing the reaction which occurs as a result of steps (a) to (e) with a standard curve to determine the levels of α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor compared to a normal individual. 
         [0021]    Another illustrative embodiment of the invention is an ELISA kit to screen for a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor in plasma or serum, the kit comprising: (a) a microtiter plate coated with polyclonal or monoclonal antibodies specific to α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor; (b) polyclonal or monoclonal antibody-alkaline phosphatase conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor; (c) p-nitrophenyl-phosphate; and (d) α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor as an antigen standard. 
         [0022]    Another illustrative embodiment of the invention is a Luminex kit to screen in plasma, serum and\or biological fluid for a molecular profile in a patient that is associated with solid organ allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor and/or proteins described in Table 1, the kit comprising: (a) a microbead array coated with polyclonal or monoclonal antibodies specific to α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor and/or other proteins listed in Table 1; (b) polyclonal or monoclonal antibody fluorescent dye conjugates reactive with α- 1  anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor and/or other proteins listed in Table 1; (c) and α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor or other protein in Table 1 as an antigen standard. 
         [0023]    Embodiments of the invention provide assays and methods for the detection and/or quantitation in a sample of: AACT and/or Apo A1 and/or C4A and/or SAA and/or CRP and/or A2M and/or ApoE and/or ITIH4 and/or A1AT and/or C-inh and/or fragments of these polypeptides. Typical embodiments of the invention utilize ELISA-type assays of the type that are suitable for use with biological fluid samples such as blood, plasma, serum, or other bodily fluids of a mammal, particularly a human. Methodological embodiments include testing for the amounts of AACT and/or C4A and/or Apo A1 polypeptides, fragments of these markers, and/or a combination of the markers described herein in biological fluid samples. Certain embodiments examine together α-1 antichymotrypsin, Apo A1, complement C1 inhibitor and the 5191 Da peptide of C4A in order to, for example, identify a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection. Certain embodiments examine 1 (e.g. the 5191 Da C4A peptide) or 2 (e.g. C4A peptide plus α-1 antichymotrypsin or Apo A1) or 3 (e.g. α-1 antichymotrypsin, Apo A1 and the 5191 Da C4A peptide) or all 4 of these biomarkers. 
         [0024]    In certain embodiments of the invention, the 5191 Da C4A peptide is purified and this purified peptide is then injected into animals such as a rabbits to generate polyclonal antibodies specific to the 5191 Da peptide that can be used in ELISA tests or the like. Similarly, monoclonal antibody preparations to the protein may be prepared by injecting the purified 5191 Da peptide into mice, harvesting the spleen and lymph node cells, fusing these cells with mouse myeloma cells and using the resultant hybridoma cells to produce the monoclonal antibody. 
         [0025]    One illustrative embodiment of the invention is a method for detecting α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor in plasma to screen for a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection comprising the steps of: (a) providing polyclonal or monoclonal antibodies against α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor; (b) providing a microtiter plate coated with the antibodies; (c) adding the serum or plasma to the microtiter plate; (d) providing alkaline phosphatase-antibody conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor to the microtiter plate; (e) providing p-nitrophenyl-phosphate to the microtiter plate; and (f) comparing the reaction which occurs as a result of steps (a) to (e) with a standard curve to determine the levels of α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor compared to a normal individual. 
         [0026]    Another illustrative embodiment of the invention is an ELISA kit to screen for a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor in plasma or serum, the kit comprising: (a) a microtiter plate coated with polyclonal or monoclonal antibodies specific to α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor; (b) polyclonal or monoclonal antibody-alkaline phosphatase conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor; (c) p-nitrophenyl-phosphate; and (d) α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor as an antigen standard. 
     
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         [0027]      FIGS. 1A-1C : Candidate plasma proteins which detect renal allograft rejection. ( 1 A) Classification and Regression Tree (CART) analysis assessing the biomarker candidates for detecting rejection vs. postrejection samples. ( 1 B) Box plots of the adjusted intensities of the 4467 Da and 5191 Da biomarker candidates in rejection (group A, n=17), postrejection (group B, n=17), and nonrejection (group C, n=48) plasma samples. ( 1 C) Box plots of the serum creatinine levels measured at the time of biopsy for rejection patients at the time of rejection and postrejection (n=16) compared with biopsy-proven nonrejection patients (n=19). 
           [0028]      FIGS. 2A-2D : Identification of the C-terminal fragment of α-1 antichymotrypsin and apolipoprotein A1 (Apo A1). ( 2 A) High-resolution MALDI-TOF mass spectrum of C8 high-performance liquid chromatography (HPLC)-purified fraction containing the 4467 Da biomarker candidate peptide (average mass as measured by SELDI-TOF MS). Monoisotopic mass differences indicate a sequence ladder of SALV (S, serine; A, alanine; L, leucine; and V, valine). ( 2 B) Immunoprecipitation of plasma samples with monoclonal antibody against α-1-antichymotrypsin. Numbered peptides with average masses (Da) are presented. ( 2 C) Immunoprecipitation of plasma samples with a monoclonal antibody against human Apo A1. ( 2 D) Box plots of the SELDI adjusted peak intensities of Apo A1 in rejection (group A, n=17), postrejection (group B, n=17) and nonrejection (group C, n=48) plasma samples. 
           [0029]      FIGS. 3A-3D : Validation of apolipoprotein A1 (Apo A1) by enzyme-linked immunosorbent assay (ELISA) for association with acute cellular rejection. ( 3 A) Box plots of the ELISA results of plasma samples of a subset of the original cohort. ( 3 B) Box plots of the ELISA results of the plasma samples of the second independent cohort. ( 3 C) Box plots of Apo A1 levels in recipients that had a sample collected within −3 to 0 days before the renal biopsy. Twenty-five rejection and 22 nonrejection samples were compared. The mean Apo A1 levels in nonrejection was 0.22 SD±0.06 and 0.13 SD±0.04 in rejection. The levels of Apo A1 were significantly lower at the time of rejection (P value &lt;0.0001) compared with recipients with biopsy-proven nonrejection. ( 3 D) Line graph indicating the individual Apo A1 results for 14 patients who had plasma samples from all three time periods (prerejection, rejection, and postrejection). (E) ROC analysis comparing the rejection samples to the nonrejection samples from both the original cohort and the second cohort combined showing a cut point of 0.167 mg/dL and 76% sensitivity and 86% specificity. 
           [0030]      FIG. 4 : ApoA1 comparison between biopsy proven non-rejectors versus biopsy proven rejectors, showing that patients diagnosed with renal allograft rejection had significantly lower Apo A1 levels (mean 0.156+/−0.77) compared to non-rejection (mean 0.239+/−0.16) (P&lt;0.0024). 
           [0031]      FIG. 5 : Sensitivity and specificity of ApoA1 comparison between biopsy proven non-rejectors versus biopsy proven rejectors. Using a cutpoint of 0.195, Apo A1 levels correctly classified patients with rejection 79% of the time with a sensitivity of 75% and specificity of 82%. 
           [0032]      FIG. 6 : Validation of Alpha-2-macroglobulin using an antibody-based ELISA. 
       
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
       [0033]    The invention described herein is based on the discovery that specific protein markers present in human plasma can be used to detect, predict and monitor transplant rejection. Assessment of the change in the levels of these proteins identifies patients at risk of rejection. 
       DEFINITIONS 
       [0034]    All scientific and technical terms used in this application have meanings commonly used in the art unless otherwise specified. As used in this application, the following words or phrases have the meanings specified. 
         [0035]    As used herein, a “sample” from a subject means a specimen obtained from the subject that contains plasma, blood, serum, saliva, urine, or other bodily fluid. 
         [0036]    As used herein, the term “subject” includes any human or non-human animal. The term “non-human animal” includes all vertebrates, e.g., mammals and non-mammals, such as non-human primates, horses, sheep, dogs, cows, pigs, chickens, amphibians, reptiles, rodents etc. In a typical embodiment, the subject, or patient, is a human. 
         [0037]    As used herein, a “control” sample means a sample that is representative of normal measures of the respective marker, or a baseline amount of marker to be used for comparison. Typically, the baseline will be a measurement taken from the same subject or patient. The sample can be an actual sample used for testing, or a reference level or range, based on known normal measurements of the corresponding marker. 
         [0038]    As used herein, “5 kiloDalton (kDa) fragment of complement C4 anaphylatoxin (C4A)” refers to a fragment of C4A that is approximately 5 kDa in molecular weight, and includes a 5,051 Da C4A fragment that corresponds to SEQ ID NO: 3, and a 5,191 Da C4A fragment that corresponds to SEQ ID NO: 2. In some embodiments, the 5 kDa fragment of C4A is the 5,191 Da fragment. 
         [0039]    As used herein, “a” or “an” means at least one, unless clearly indicated otherwise. 
       Markers &amp; Methods 
       [0040]    The invention provides a set of protein markers and methods of using these markers for assessment of a patient&#39;s immune status and for predicting rejection of an organ transplant. The markers include complement C4 anaphylatoxin (C4A), Apolipoprotein A1 (ApoA1), α-1 anti-chymotrypsin C terminal fragment (AACT), C1 protease inhibitor (C-inh), Serum Amyloid A (SAA), C-reactive Protein (CRP), Apolipoprotein E (ApoE), alpha-1-antitrypsin (A1AT), Post-translational modified ApoA1, Inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), and Alpha-2-macroglobulin (A2M), as well fragments of these proteins (see Tables 1 and 4, and SEQ ID NOs: 1-18). Changes in the levels of these markers in a patient&#39;s plasma or other bodily fluid are predictive of allograft rejection. 
         [0000]    
       
         
               
             
               
               
               
             
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Markers of Allograft Rejection 
               
             
          
           
               
                 m/z (Da) 
                 SEQ ID NO: 
                 Identity 
               
               
                   
               
             
          
           
               
                 2,505 
                 11 
                 Alpha-1-antitrypsin C-Terminal fragment 
               
               
                   
                   
                 (A1AT; amino acids 397-418) 
               
               
                 4,125 
                 5 
                 Apolipoprotein A1 fragment (Apo A1; 
               
               
                   
                   
                 amino acids 148-183) 
               
               
                 4,187 
                 13 
                 Plasma protease C1 inhibitor fragment 
               
               
                   
                   
                 (C1 inh; amino acids 445-478) 
               
               
                 4,467 
                 8 
                 Alpha-1-antichymotrypsin C-terminal 
               
               
                   
                   
                 fragment (AACT; aa 385-422) 
               
               
                 5,051 
                 3 
                 Complement C4 Anaphylatoxin (C4A; amino 
               
               
                   
                   
                 acids 698-742) 
               
               
                 5,191 
                 2 
                 Complement C4 Anaphylatoxin (C4A; amino 
               
               
                   
                   
                 acids 702-746) 
               
               
                 11,694 
                 14 
                 Serum Amyloid A (SAA) 
               
               
                 19,409 
                 15 
                 C-reactive protein (CRP) 
               
               
                 28,077 
                 6 
                 Apolipoprotein A1 (Apo A1) 
               
               
                 28,186 
                 6 
                 Post-translational modified Apo A1 
               
               
                 28,336 
                 6 
                 Post-translational modified Apo A1 
               
               
                 28,574 
                 6 
                 Post-translational modified Apo A1 
               
               
                 29,134 
                 6 
                 Post-translational modified Apo A1 
               
               
                 36,747 
                 16 
                 Apolipoprotein E (Apo E) 
               
               
                 50,835 
                 10 
                 Alpha-1-antitrypsin (A1AT) 
               
               
                 64,932 
                 10 
                 Alpha-1-antitrypsin (A1AT) 
               
               
                 109,796 
                 17 
                 Inter-alpha-trypsin inhibitor heavy 
               
               
                   
                   
                 chain H4 (ITIH4) 
               
               
                 143,718 
                 18 
                 Alpha-2-macroglobulin (A2M or Alpha-2-M) 
               
               
                 188,758 
                 18 
                 Alpha-2-macroglobulin (A2M or Alpha-2-M) 
               
               
                   
               
             
          
         
       
     
         [0041]    The invention provides a method for detecting susceptibility in a patient to solid organ graft rejection. In one embodiment, the method detects susceptibility to rejection with greater than 80% sensitivity and specificity, and in a typical embodiment, with at least 90% sensitivity and at least 90% specificity. In one embodiment, the method comprises the steps of: (a) measuring the amount of a 5 kiloDalton (kDa) fragment of complement C4 anaphylatoxin (C4A) in a sample obtained from the patient; (b) comparing the amount of the 5 kDa fragment of C4A in the patient sample with the amount in a control sample; and (c) detecting susceptibility to graft rejection when the comparing shows an increase in the 5 kDa fragment of C4A in the patient sample relative to the control sample. In another embodiment, the method comprises the steps of: (a) contacting a sample obtained from the patient with a reagent that specifically binds a 5 kiloDalton (kDa) fragment of complement C4 anaphylatoxin (C4A); (b) measuring the amount of specific binding between the reagent and the patient sample; (c) comparing the amount of specific binding in (b) with the amount of specific binding of the reagent in a control sample; and (d) detecting susceptibility to graft rejection when the comparing in (c) shows an increase in specific binding to the 5 kDa fragment of C4A in the patient sample relative to the control sample. In one embodiment, the contacting further comprises contacting the patient sample with a reagent that binds Apolipoprotein A1 (ApoA1) and/or α-1 anti-chymotrypsin C terminal fragment (AACT), and the detecting further comprises detecting susceptibility to graft rejection when the comparing shows a decrease in the amount of ApoA1 and/or AACT in the patient sample relative to the control sample. In one embodiment, the contacting and comparing comprise contacting the patient sample with reagents that bind ApoA1 and AACT. 
         [0042]    In another embodiment, the invention provides a method for detecting susceptibility in a patient to solid organ graft rejection. In one embodiment, the method comprises the steps of: (a) contacting a sample obtained from the patient with a reagent that specifically binds a set of biomarkers comprising two or more markers listed in Table 1; (b) measuring the amount of specific binding between the reagents and the patient sample; (c) comparing the amount of specific binding in (b) with the amount of specific binding of the reagents in a control sample; and (d) detecting susceptibility to graft rejection when the comparing in (c) shows a significant increase or decrease in specific binding to the biomarkers in the patient sample relative to the control sample. In some embodiments, steps (a)-(c) are performed for 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, up to 19 of the markers listed in Table 1. In one embodiment, the set of markers consists of 8 or fewer markers listed in Table 1. In another embodiment, the set of markers consists of 6 or fewer markers listed in Table 1. In yet another embodiment, the set of markers consists of 4 or fewer markers listed in Table 1. 
         [0043]    With respect to the following markers, susceptibility to graft rejection is detected when the specific binding of reagent to marker is increased relative to the control: C4A, C1 protease inhibitor (C1-inh), Serum Amyloid A (SAA), C-reactive Protein (CRP), Apolipoprotein E (ApoE), alpha-1-antitrypsin (A1AT), including fragments thereof, and/or specific binding of reagent to the following markers is decreased relative to control: AACT, ApoA1, Post-translational modified ApoA1, Inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), Alpha-2-macroglobulin (A2M), including fragments thereof. In a typical embodiment, the difference is a decrease or increase of at least 10% relative to the control. 
         [0044]    In another embodiment, the invention provides a method for detecting susceptibility in a patient to solid organ graft rejection, the method comprising the steps of: (a) contacting a sample obtained from the patient with reagents that specifically bind a set of markers consisting of: a 5191 Dalton fragment of complement C4 anaphylatoxin (C4A), α-1 anti-chymotrypsin C terminal fragment (AACT), and Apo A1; and optionally further consisting of: complement C1 inhibitor, and/or a marker listed in Table 1; (b) measuring the amount of specific binding between the reagent and the sample; (c) comparing the amount of specific binding in (b) with the amount of specific binding of the reagent to a control sample; and (d) detecting susceptibility to graft rejection when the comparing in (c) shows an increase in the 5191 Dalton fragment of C4A or a decrease AACT and/or ApoA1 relative to the control sample. 
         [0045]    In some embodiments, the measuring comprises an immunoassay. In other embodiments, the measuring comprises mass spectrometry. Other assay methods include fluorescence activated cell sorting (FACS), western blotting, and amplification of a surrogate DNA template. Representative examples of reagents include, but are not limited to, an antibody, a nucleic acid probe, or a synthetic probe. The probe or antibody may optionally be labeled with a detectable marker. In some embodiments, the reagents are labeled with a detectable marker and/or observed using a chromogenic or fluorogenic substrate. 
         [0046]    Examples of solid organ grafts include, but are not limited to, kidney, liver, heart, pancreas, lung, intestine and thymus. In one embodiment, the solid organ graft rejection is acute cellular renal allograft rejection. Other types of solid organ graft rejection include chronic rejection, such as chronic allograft nephropathy, or interstitial fibrosis with tubular atrophy. 
         [0047]    Additionally provided is a method for detecting susceptibility in a patient to solid organ graft rejection, the method comprising the steps of: (a) contacting a sample obtained from the patient with a reagent that specifically binds complement C4 anaphylatoxin (C4A); (b) measuring the amount of specific binding between the reagent and the sample; (c) comparing the amount of specific binding in (b) with a control sample; wherein a greater amount of binding in (b) relative to the control is indicative of susceptibility to solid organ graft rejection. 
         [0048]    Another illustrative embodiment of the invention is a mass spectrometry assay to identify the peptide and/or protein profile in a patient that is associated with solid organ allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor and/or one of the other 16 proteins in Table 1 in plasma or serum or other body fluid, the assay comprising the steps of: (a) measuring the specific amount of specific peptide by mass spectrometry in plasma, serum or other body fluid; (b) comparing the specific quantity of protein/peptide in (a) with a control sample; wherein a greater or lesser amount of specific peptide relative to the control is indicative of susceptibility to solid organ graft rejection. 
         [0049]    Also provided is a method for detecting susceptibility in a patient to acute cellular renal allograft rejection, the method comprising the steps of: (a) providing polyclonal or monoclonal antibodies against α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor; (b) providing a microtiter plate coated with the antibodies; (c) adding the serum or plasma to the microtiter plate; (d) providing alkaline phosphatase-antibody conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor to the microtiter plate; (e) providing p-nitrophenyl-phosphate to the microtiter plate; and (f) comparing the reaction which occurs as a result of steps (a) to (e) with a standard curve to determine the levels of α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor compared to a normal individual. 
         [0050]    Embodiments of the invention provide assays and methods for the detection and/or quantitation in a sample of: AACT and/or Apo A1 and/or C4A and/or SAA and/or CRP and/or A2M and/or ApoE and/or ITIH4 and/or A1AT and/or C-inh and/or fragments of these polypeptides. Typical embodiments of the invention utilize ELISA-type assays of the type that are suitable for use with biological fluid samples such as blood, plasma, serum, or other bodily fluids of a mammal, particularly a human. Methodological embodiments include testing for the amounts of AACT and/or C4A and/or Apo A1 polypeptides, fragments of these markers, and/or a combination of the markers described herein in biological fluid samples. Certain embodiments examine together: α-1 antichymotrypsin, Apo A1, complement C1 inhibitor and the 5191 Da peptide of C4A in order to, for example, identify a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection. Certain embodiments examine 1 (e.g. the 5191 Da C4A peptide) or 2 (e.g. C4A peptide plus α-1 antichymotrypsin or Apo A1) or 3 (e.g. α-1 antichymotrypsin, Apo A1 and the 5191 Da C4A peptide) or all 4 of these biomarkers. 
         [0051]    In certain embodiments of the invention, the 5191 Da C4A peptide is purified and this purified peptide is then injected into animals such as a rabbits to generate polyclonal antibodies specific to the 5191 Da peptide that can be used in ELISA tests or the like. Similarly, monoclonal antibody preparations to the protein may be prepared by injecting the purified 5191 Da peptide into mice, harvesting the spleen and lymph node cells, fusing these cells with mouse myeloma cells and using the resultant hybridoma cells to produce the monoclonal antibody. 
         [0052]    One illustrative embodiment of the invention is a method for detecting α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor in plasma to screen for a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection comprising the steps of: (a) providing polyclonal or monoclonal antibodies against α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor; (b) providing a microtiter plate coated with the antibodies; (c) adding the serum or plasma to the microtiter plate; (d) providing alkaline phosphatase-antibody conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor to the microtiter plate; (e) providing p-nitrophenyl-phosphate to the microtiter plate; and (f) comparing the reaction which occurs as a result of steps (a) to (e) with a standard curve to determine the levels of α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor compared to a normal individual. 
         [0053]    An amount of marker is considered increased or decreased if it differs by a statistically significant amount from the amount present in the control. In some embodiments, the difference is an increase or decrease of at least 10%; in other embodiments, the difference is at least 20%, 30%, 40%, 50% or more. In other embodiments, a reference range has been identified for the amount of the marker present in a normal, control sample, and a test sample having an amount of the marker that is outside the reference range for that marker is susceptible to rejection. In a typical embodiment, the sample is a plasma sample. Other bodily fluids can be used for the sample, including serum, urine and saliva. 
         [0054]    The following combinations of markers are contemplated for use with the methods of the invention: C4A, ApoA1; C4A, AACT; C4A, A1AT; C4A, C1-inh; C4A, SAA; C4A, CRP; C4A, ApoE; C4A, ITIH4; C4A, A2M; ApoA1, A1AT; ApoA1, C1-inh; ApoA1, SAA; ApoA1, CRP; ApoA1, ApoE; ApoA1, ITIH4; ApoA1, A2M; AACT, A1AT; AACT, C1-inh; AACT, SAA; AACT, CRP; AACT, ApoE; AACT, ITIH4; AACT, A2M; A1AT, C1-inh; A1AT, SAA; A1AT, CRP; A1AT, ApoE; A1AT, ITIH4; A1AT, A2M; C1-inh, SAA; C1-inh, CRP; C1-inh, ApoE; C1-inh, ITIH4; C1-inh, A2M; SAA, CRP; SAA, ApoE; SAA, ITIH4; SAA, A2M; CRP, ApoE; CRP, ITIH4; CRP, A2M; ApoE, ITIH4; ApoE, A2M; ITIH4, A2M; C4A, ApoA1, AACT; C4A, ApoA1, A1AT; C4A, ApoA1, C1-inh; C4A, ApoA1, SAA; C4A, ApoA1, CRP; C4A, ApoA1, ApoE; C4A, ApoA1, ITIH4; C4A, ApoA1, A2M; C4A, AACT, A1AT; C4A, AACT, C1-inh; C4A, AACT, SAA; C4A, AACT, CRP; C4A, AACT, ApoE; C4A, AACT, ITIH4; C4A, AACT, A2M; C4A, A1AT, C1-inh; C4A, A1AT, SAA; C4A, A1AT, CRP; C4A, A1AT, ApoE; C4A, A1AT, ITIH4; C4A, A1AT, A2M; C4A, C1-inh, SAA; C4A, C1-inh, CRP; C4A, C1-inh, ApoE; C4A, C1-inh, ITIH4; C4A, C1-inh, A2M; C4A, SAA, CRP; C4A, SAA, ApoE; C4A, SAA, ITIH4; C4A, SAA, A2M; C4A, CRP, ApoE; C4A, CRP, ITIH4; C4A, CRP, A2M; C4A, ApoE, ITIH4; C4A, ApoE, A2M; C4A, ITIH4, A2M; ApoA1, AACT, A1AT; ApoA1, AACT, C1-inh; ApoA1, AACT, ApoE; ApoA1, AACT, ITIH4; ApoA1, AACT, A2M; ApoA1, A1AT, C1-inh; ApoA1, A1AT, SAA; ApoA1, A1AT, CRP; ApoA1, A1AT, ApoE; ApoA1, A1AT, ITIH4; ApoA1, A1AT, A2M; ApoA1, C1-inh, SAA; ApoA1, C1-inh, CRP; ApoA1, C1-inh, ApoE; ApoA1, C1-inh, ITIH4; ApoA1, C1-inh, A2M; ApoA1, SAA, CRP; ApoA1, SAA, ApoE; ApoA1, SAA, ITIH4; ApoA1, SAA, A2M; ApoA1, CRP, ApoE; ApoA1, CRP, ITIH4; ApoA1, CRP, A2M; ApoA1, ApoE, ITIH4; ApoA1, ApoE, A2M; ApoA1, ITIH4, A2M; AACT, A1AT, C1-inh; AACT, A1AT, ApoE; AACT, A1AT, ITIH4; AACT, C1-inh, SAA; AACT, C1-inh, CRP; AACT, C1-inh, ApoE; AACT, C1-inh, ITIH4; AACT, C1-inh, A2M; AACT, SAA, CRP; AACT, SAA, ApoE; AACT, SAA, ITIH4; AACT, SAA, A2M; AACT, CRP, ApoE; AACT, CRP, ITIH4; AACT, CRP, A2M; AACT, ApoE, ITIH4; AACT, ApoE, A2M; AACT, ITIH4, A2M; A1AT, C1-inh, SAA; A1AT, C1-inh, CRP; A1AT, C1-inh, ApoE; A1AT, C1-inh, ITIH4; A1AT, C1-inh, A2M; A1AT, SAA, CRP; A1AT, SAA, ApoE; A1AT, SAA, ITIH4; A1AT, SAA, A2M; A1AT, CRP, ApoE; A1AT, CRP, ITIH4; A1AT, CRP, A2M; A1AT, ApoE, ITIH4; A1AT, ApoE, A2M; A1AT, ITIH4, A2M; C1-inh, SAA, CRP; C1-inh, SAA, ApoE; C1-inh, SAA, ITIH4; C1-inh, SAA, A2M; C1-inh, CRP, ApoE; C1-inh, CRP, ITIH4; C1-inh, CRP, A2M; C1-inh, ApoE, ITIH4; C1-inh, ApoE, A2M; C1-inh, ITIH4, A2M; SAA, CRP, ApoE; SAA, CRP, ITIH4; SAA, CRP, A2M; SAA, ApoE, ITIH4; SAA, ApoE, A2M; SAA, ITIH4, A2M; CRP, ApoE, ITIH4; CRP, ApoE, A2M; CRP, ITIH4, A2M; ApoE, ITIH4, A2M; C4A, ApoA1, AACT, A1AT; C4A, ApoA1, AACT, C1-inh; C4A, ApoA1, AACT, SAA; C4A, ApoA1, AACT, CRP; C4A, ApoA1, AACT, ApoE; C4A, ApoA1, AACT, ITIH4; C4A, ApoA1, AACT, A2M; C4A, ApoA1, A1AT, C1-inh; C4A, ApoA1, A1AT, SAA; C4A, ApoA1, A1AT, CRP; C4A, ApoA1, A1AT, ApoE; C4A, ApoA1, A1AT, ITIH4; C4A, ApoA1, A1AT, A2M; C4A, ApoA1, C1-inh, SAA; C4A, ApoA1, C1-inh, CRP; C4A, ApoA1, C1-inh, ApoE; C4A, ApoA1, C1-inh, ITIH4; C4A, ApoA1, C1-inh, A2M; C4A, ApoA1, SAA, CRP; C4A, ApoA1, SAA, ApoE; C4A, ApoA1, SAA, ITIH4; C4A, ApoA1, SAA, A2M; C4A, ApoA1, CRP, ApoE; C4A, ApoA1, CRP, ITIH4; C4A, ApoA1, CRP, A2M; C4A, ApoA1, ApoE, ITIH4; C4A, ApoA1, ApoE, A2M; C4A, ApoA1, ITIH4, A2M; C4A, AACT, A1AT, C1-inh; C4A, AACT, A1AT, SAA; C4A, AACT, A1AT, CRP; C4A, AACT, A1AT, ApoE; C4A, AACT, A1AT, ITIH4; C4A, AACT, A1AT, A2M; C4A, AACT, C1-inh, SAA; C4A, AACT, C1-inh, CRP; C4A, AACT, C1-inh, ApoE; C4A, AACT, C1-inh, ITIH4; C4A, AACT, C1-inh, A2M; C4A, AACT, SAA, CRP; C4A, AACT, SAA, ApoE; C4A, AACT, SAA, ITIH4; C4A, AACT, SAA, A2M; C4A, AACT, CRP, ApoE; C4A, AACT, CRP, ITIH4; C4A, AACT, CRP, A2M; C4A, AACT, ApoE, ITIH4; C4A, AACT, ApoE, A2M; C4A, AACT, ITIH4, A2M; C4A, A1AT, C1-inh, SAA; C4A, A1AT, C1-inh, CRP; C4A, A1AT, C1-inh, ApoE; C4A, A1AT, C1-inh, ITIH4; C4A, A1AT, C1-inh, A2M; C4A, A1AT, SAA, CRP; C4A, A1AT, SAA, ApoE; C4A, A1AT, SAA, ITIH4; C4A, A1AT, SAA, A2M; C4A, A1AT, CRP, ApoE; C4A, A1AT, CRP, ITIH4; C4A, A1AT, CRP, A2M; C4A, A1AT, ApoE, ITIH4; C4A, A1AT, ApoE, A2M; C4A, A1AT, ITIH4, A2M; C4A, C1-inh, SAA, CRP; C4A, C1-inh, SAA, ApoE; C4A, C1-inh, SAA, ITIH4; C4A, C1-inh, SAA, A2M; C4A, C1-inh, CRP, ApoE; C4A, C1-inh, CRP, ITIH4; C4A, C1-inh, CRP, A2M; C4A, C1-inh, ApoE, ITIH4; C4A, C1-inh, ApoE, A2M; C4A, C1-inh, ITIH4, A2M; C4A, SAA, CRP, ApoE; C4A, SAA, CRP, ITIH4; C4A, SAA, CRP, A2M; C4A, SAA, ApoE, ITIH4; C4A, SAA, ApoE, A2M; C4A, SAA, ITIH4, A2M; C4A, CRP, ApoE, ITIH4; C4A, CRP, ApoE, A2M; C4A, CRP, ITIH4, A2M; C4A, ApoE, ITIH4, A2M; ApoA1, AACT, A1AT, C1-inh; ApoA1, AACT, A1AT, SAA; ApoA1, AACT, A1AT, CRP; ApoA1, AACT, A1AT, ApoE; ApoA1, AACT, A1AT, ITIH4; ApoA1, AACT, A1AT, A2M; ApoA1, AACT, C1-inh, SAA; ApoA1, AACT, C1-inh, CRP; ApoA1, AACT, C1-inh, ApoE; ApoA1, AACT, C1-inh, ITIH4; ApoA1, AACT, C1-inh, A2M; ApoA1, AACT, SAA, ApoE; ApoA1, AACT, SAA, ITIH4; ApoA1, AACT, SAA, A2M; ApoA1, AACT, CRP, ApoE; ApoA1, AACT, CRP, ITIH4; ApoA1, AACT, CRP, A2M; ApoA1, AACT, ApoE, ITIH4; ApoA1, AACT, ApoE, A2M; ApoA1, AACT, ITIH4, A2M; ApoA1, A1AT, C1-inh, SAA; ApoA1, A1AT, C1-inh, CRP; ApoA1, A1AT, C1-inh, ApoE; ApoA1, A1AT, C1-inh, ITIH4; ApoA1, A1AT, C1-inh, A2M; ApoA1, A1AT, SAA, CRP; ApoA1, A1AT, SAA, ApoE; ApoA1, A1AT, SAA, ITIH4; ApoA1, A1AT, SAA, A2M; ApoA1, A1AT, CRP, ApoE; ApoA1, A1AT, CRP, ITIH4; ApoA1, A1AT, CRP, A2M; ApoA1, A1AT, ApoE, ITIH4; ApoA1, A1AT, ApoE, A2M; ApoA1, A1AT, ITIH4, A2M; ApoA1, C1-inh, SAA, CRP; ApoA1, C1-inh, SAA, ApoE; ApoA1, C1-inh, SAA, ITIH4; ApoA1, C1-inh, SAA, A2M; ApoA1, C1-inh, CRP, ApoE; ApoA1, C1-inh, CRP, ITIH4; ApoA1, C1-inh, CRP, A2M; ApoA1, C1-inh, ApoE, ITIH4; ApoA1, C1-inh, ApoE, A2M; ApoA1, C1-inh, ITIH4, A2M; ApoA1, SAA, CRP, ApoE; ApoA1, SAA, CRP, ITIH4; ApoA1, SAA, CRP, A2M; ApoA1, SAA, ApoE, ITIH4; ApoA1, SAA, ApoE, A2M; ApoA1, SAA, ITIH4, A2M; ApoA1, CRP, ApoE, ITIH4; ApoA1, CRP, ApoE, A2M; ApoA1, CRP, ITIH4, A2M; ApoA1, ApoE, ITIH4, A2M; AACT, A1AT, C1-inh, SAA; AACT, A1AT, C1-inh, CRP; AACT, A1AT, C1-inh, ApoE; AACT, A1AT, C1-inh, ITIH4; AACT, A1AT, C1-inh, A2M; AACT, A1AT, SAA, ApoE; AACT, A1AT, SAA, ITIH4; AACT, A1AT, CRP, ApoE; AACT, A1AT, CRP, ITIH4; AACT, A1AT, ApoE, ITIH4; AACT, A1AT, ApoE, A2M; AACT, A1AT, ITIH4, A2M; AACT, C1-inh, SAA, CRP; AACT, C1-inh, SAA, ApoE; AACT, C1-inh, SAA, ITIH4; AACT, C1-inh, SAA, A2M; AACT, C1-inh, CRP, ApoE; AACT, C1-inh, CRP, ITIH4; AACT, C1-inh, CRP, A2M; AACT, C1-inh, ApoE, ITIH4; AACT, C1-inh, ApoE, A2M; AACT, C1-inh, ITIH4, A2M; AACT, SAA, CRP, ApoE; AACT, SAA, CRP, ITIH4; AACT, SAA, CRP, A2M; AACT, SAA, ApoE, ITIH4; AACT, SAA, ApoE, A2M; AACT, SAA, ITIH4, A2M; AACT, CRP, ApoE, ITIH4; AACT, CRP, ApoE, A2M; AACT, CRP, ITIH4, A2M; AACT, ApoE, ITIH4, A2M; A1AT, C1-inh, SAA, CRP; A1AT, C1-inh, SAA, ApoE; A1AT, C1-inh, SAA, ITIH4; A1AT, C1-inh, SAA, A2M; A1AT, C1-inh, CRP, ApoE; A1AT, C1-inh, CRP, ITIH4; A1AT, C1-inh, CRP, A2M; A1AT, C1-inh, ApoE, ITIH4; A1AT, C1-inh, ApoE, A2M; A1AT, C1-inh, ITIH4, A2M; A1AT, SAA, CRP, ApoE; A1AT, SAA, CRP, ITIH4; A1AT, SAA, CRP, A2M; A1AT, SAA, ApoE, ITIH4; A1AT, SAA, ApoE, A2M; A1AT, SAA, ITIH4, A2M; A1AT, CRP, ApoE, ITIH4; A1AT, CRP, ApoE, A2M; A1AT, CRP, ITIH4, A2M; A1AT, ApoE, ITIH4, A2M; C1-inh, SAA, CRP, ApoE; C1-inh, SAA, CRP, ITIH4; C1-inh, SAA, CRP, A2M; C1-inh, SAA, ApoE, ITIH4; C1-inh, SAA, ApoE, A2M; C1-inh, SAA, ITIH4, A2M; C1-inh, CRP, ApoE, ITIH4; C1-inh, CRP, ApoE, A2M; C1-inh, CRP, ITIH4, A2M; C1-inh, ApoE, ITIH4, A2M; SAA, CRP, ApoE, ITIH4; SAA, CRP, ApoE, A2M; SAA, CRP, ITIH4, A2M; SAA, ApoE, ITIH4, A2M; CRP, ApoE, ITIH4, A2M; C4A, ApoA1, AACT, A1AT, C1-inh; C4A, ApoA1, AACT, A1AT, SAA; C4A, ApoA1, AACT, A1AT, CRP; C4A, ApoA1, AACT, A1AT, ApoE; C4A, ApoA1, AACT, A1AT, ITIH4; C4A, ApoA1, AACT, A1AT, A2M; C4A, ApoA1, AACT, C1-inh, SAA; C4A, ApoA1, AACT, C1-inh, CRP; C4A, ApoA1, AACT, C1-inh, ApoE; C4A, ApoA1, AACT, C1-inh, ITIH4; C4A, ApoA1, AACT, C1-inh, A2M; C4A, ApoA1, AACT, SAA, CRP; C4A, ApoA1, AACT, SAA, ApoE; C4A, ApoA1, AACT, SAA, ITIH4; C4A, ApoA1, AACT, SAA, A2M; C4A, ApoA1, AACT, CRP, ApoE; C4A, ApoA1, AACT, CRP, ITIH4; C4A, ApoA1, AACT, CRP, A2M; C4A, ApoA1, AACT, ApoE, ITIH4; C4A, ApoA1, AACT, ApoE, A2M; C4A, ApoA1, AACT, ITIH4, A2M; C4A, ApoA1, A1AT, C1-inh, SAA; C4A, ApoA1, A1AT, C1-inh, CRP; C4A, ApoA1, A1AT, C1-inh, ApoE; C4A, ApoA1, A1AT, C1-inh, ITIH4; C4A, ApoA1, A1AT, C1-inh, A2M; C4A, ApoA1, A1AT, SAA, CRP; C4A, ApoA1, A1AT, SAA, ApoE; C4A, ApoA1, A1AT, SAA, ITIH4; C4A, ApoA1, A1AT, SAA, A2M; C4A, ApoA1, A1AT, CRP, ApoE; C4A, ApoA1, A1AT, CRP, ITIH4; C4A, ApoA1, A1AT, CRP, A2M; C4A, ApoA1, A1AT, ApoE, ITIH4; C4A, ApoA1, A1AT, ApoE, A2M; C4A, ApoA1, A1AT, ITIH4, A2M; C4A, ApoA1, C1-inh, SAA, CRP; C4A, ApoA1, C1-inh, SAA, ApoE; C4A, ApoA1, C1-inh, SAA, ITIH4; C4A, ApoA1, C1-inh, SAA, A2M; C4A, ApoA1, C1-inh, CRP, ApoE; C4A, ApoA1, C1-inh, CRP, ITIH4; C4A, ApoA1, C1-inh, CRP, A2M; C4A, ApoA1, C1-inh, ApoE, ITIH4; C4A, ApoA1, C1-inh, ApoE, A2M; C4A, ApoA1, C1-inh, ITIH4, A2M; C4A, ApoA1, SAA, CRP, ApoE; C4A, ApoA1, SAA, CRP, ITIH4; C4A, ApoA1, SAA, CRP, A2M; C4A, ApoA1, SAA, ApoE, ITIH4; C4A, ApoA1, SAA, ApoE, A2M; C4A, ApoA1, SAA, ITIH4, A2M; C4A, ApoA1, CRP, ApoE, ITIH4; C4A, ApoA1, CRP, ApoE, A2M; C4A, ApoA1, CRP, ITIH4, A2M; C4A, ApoA1, ApoE, ITIH4, A2M; C4A, AACT, A1AT, C1-inh, SAA; C4A, AACT, A1AT, C1-inh, CRP; C4A, AACT, A1AT, C1-inh, ApoE; C4A, AACT, A1AT, C1-inh, ITIH4; C4A, AACT, A1AT, C1-inh, A2M; C4A, AACT, A1AT, SAA, CRP; C4A, AACT, A1AT, SAA, ApoE; C4A, AACT, A1AT, SAA, ITIH4; C4A, AACT, A1AT, SAA, A2M; C4A, AACT, A1AT, CRP, ApoE; C4A, AACT, A1AT, CRP, ITIH4; C4A, AACT, A1AT, CRP, A2M; C4A, AACT, A1AT, ApoE, ITIH4; C4A, AACT, A1AT, ApoE, A2M; C4A, AACT, A1AT, ITIH4, A2M; C4A, AACT, C1-inh, SAA, CRP; C4A, AACT, C1-inh, SAA, ApoE; C4A, AACT, C1-inh, SAA, ITIH4; C4A, AACT, C1-inh, SAA, A2M; C4A, AACT, C1-inh, CRP, ApoE; C4A, AACT, C1-inh, CRP, ITIH4; C4A, AACT, C1-inh, CRP, A2M; C4A, AACT, C1-inh, ApoE, ITIH4; C4A, AACT, C1-inh, ApoE, A2M; C4A, AACT, C1-inh, ITIH4, A2M; C4A, AACT, SAA, CRP, ApoE; C4A, AACT, SAA, CRP, ITIH4; C4A, AACT, SAA, CRP, A2M; C4A, AACT, SAA, ApoE, ITIH4; C4A, AACT, SAA, ApoE, A2M; C4A, AACT, SAA, ITIH4, A2M; C4A, AACT, CRP, ApoE, ITIH4; C4A, AACT, CRP, ApoE, A2M; C4A, AACT, CRP, ITIH4, A2M; C4A, AACT, ApoE, ITIH4, A2M; C4A, A1AT, C1-inh, SAA, CRP; C4A, A1AT, C1-inh, SAA, ApoE; C4A, A1AT, C1-inh, SAA, ITIH4; C4A, A1AT, C1-inh, SAA, A2M; C4A, A1AT, C1-inh, CRP, ApoE; C4A, A1AT, C1-inh, CRP, ITIH4; C4A, A1AT, C1-inh, CRP, A2M; C4A, A1AT, C1-inh, ApoE, ITIH4; C4A, A1AT, C1-inh, ApoE, A2M; C4A, A1AT, C1-inh, ITIH4, A2M; C4A, A1AT, SAA, CRP, ApoE; C4A, A1AT, SAA, CRP, ITIH4; C4A, A1AT, SAA, CRP, A2M; C4A, A1AT, SAA, ApoE, ITIH4; C4A, A1AT, SAA, ApoE, A2M; C4A, A1AT, SAA, ITIH4, A2M; C4A, A1AT, CRP, ApoE, ITIH4; C4A, A1AT, CRP, ApoE, A2M; C4A, A1AT, CRP, ITIH4, A2M; C4A, A1AT, ApoE, ITIH4, A2M; C4A, C1-inh, SAA, CRP, ApoE; C4A, C1-inh, SAA, CRP, ITIH4; C4A, C1-inh, SAA, CRP, A2M; C4A, C1-inh, SAA, ApoE, ITIH4; C4A, C1-inh, SAA, ApoE, A2M; C4A, C1-inh, SAA, ITIH4, A2M; C4A, C1-inh, CRP, ApoE, ITIH4; C4A, C1-inh, CRP, ApoE, A2M; C4A, C1-inh, CRP, ITIH4, A2M; C4A, C1-inh, ApoE, ITIH4, A2M; C4A, SAA, CRP, ApoE, ITIH4; C4A, SAA, CRP, ApoE, A2M; C4A, SAA, CRP, ITIH4, A2M; C4A, SAA, ApoE, ITIH4, A2M; C4A, CRP, ApoE, ITIH4, A2M; ApoA1, AACT, A1AT, C1-inh, SAA; ApoA1, AACT, A1AT, C1-inh, CRP; ApoA1, AACT, A1AT, C1-inh, ApoE; ApoA1, AACT, A1AT, C1-inh, ITIH4; ApoA1, AACT, A1AT, C1-inh, A2M; ApoA1, AACT, A1AT, SAA, CRP; ApoA1, AACT, A1AT, SAA, ApoE; ApoA1, AACT, A1AT, SAA, ITIH4; ApoA1, AACT, A1AT, SAA, A2M; ApoA1, AACT, A1AT, CRP, ApoE; ApoA1, AACT, A1AT, CRP, ITIH4; ApoA1, AACT, A1AT, CRP, A2M; ApoA1, AACT, A1AT, ApoE, ITIH4; ApoA1, AACT, A1AT, ApoE, A2M; ApoA1, AACT, A1AT, ITIH4, A2M; ApoA1, AACT, C1-inh, SAA, CRP; ApoA1, AACT, C1-inh, SAA, ApoE; ApoA1, AACT, C1-inh, SAA, ITIH4; ApoA1, AACT, C1-inh, SAA, A2M; ApoA1, AACT, C1-inh, CRP, ApoE; ApoA1, AACT, C1-inh, CRP, ITIH4; ApoA1, AACT, C1-inh, CRP, A2M; ApoA1, AACT, C1-inh, ApoE, ITIH4; ApoA1, AACT, C1-inh, ApoE, A2M; ApoA1, AACT, C1-inh, ITIH4, A2M; ApoA1, AACT, SAA, CRP, ApoE; ApoA1, AACT, SAA, CRP, ITIH4; ApoA1, AACT, SAA, CRP, A2M; ApoA1, AACT, SAA, ApoE, ITIH4; ApoA1, AACT, SAA, ApoE, A2M; ApoA1, AACT, SAA, ITIH4, A2M; ApoA1, AACT, CRP, ApoE, ITIH4; ApoA1, AACT, CRP, ApoE, A2M; ApoA1, AACT, CRP, ITIH4, A2M; ApoA1, AACT, ApoE, ITIH4, A2M; ApoA1, A1AT, C1-inh, SAA, CRP; ApoA1, A1AT, C1-inh, SAA, ApoE; ApoA1, A1AT, C1-inh, SAA, ITIH4; ApoA1, A1AT, C1-inh, SAA, A2M; ApoA1, A1AT, C1-inh, CRP, ApoE; ApoA1, A1AT, C1-inh, CRP, ITIH4; ApoA1, A1AT, C1-inh, CRP, A2M; ApoA1, A1AT, C1-inh, ApoE, ITIH4; ApoA1, A1AT, C1-inh, ApoE, A2M; ApoA1, A1AT, C1-inh, ITIH4, A2M; ApoA1, A1AT, SAA, CRP, ApoE; ApoA1, A1AT, SAA, CRP, ITIH4; ApoA1, A1AT, SAA, CRP, A2M; ApoA1, A1AT, SAA, ApoE, ITIH4; ApoA1, A1AT, SAA, ApoE, A2M; ApoA1, A1AT, SAA, ITIH4, A2M; ApoA1, A1AT, CRP, ApoE, ITIH4; ApoA1, A1AT, CRP, ApoE, A2M; ApoA1, A1AT, CRP, ITIH4, A2M; ApoA1, A1AT, ApoE, ITIH4, A2M; ApoA1, C1-inh, SAA, CRP, ApoE; ApoA1, C1-inh, SAA, CRP, ITIH4; ApoA1, C1-inh, SAA, CRP, A2M; ApoA1, C1-inh, SAA, ApoE, ITIH4; ApoA1, C1-inh, SAA, ApoE, A2M; ApoA1, C1-inh, SAA, ITIH4, A2M; ApoA1, C1-inh, CRP, ApoE, ITIH4; ApoA1, C1-inh, CRP, ApoE, A2M; ApoA1, C1-inh, CRP, ITIH4, A2M; ApoA1, C1-inh, ApoE, ITIH4, A2M; ApoA1, SAA, CRP, ApoE, ITIH4; ApoA1, SAA, CRP, ApoE, A2M; ApoA1, SAA, CRP, ITIH4, A2M; ApoA1, SAA, ApoE, ITIH4, A2M; ApoA1, CRP, ApoE, ITIH4, A2M; AACT, A1AT, C1-inh, SAA, CRP; AACT, A1AT, C1-inh, SAA, ApoE; AACT, A1AT, C1-inh, SAA, ITIH4; AACT, A1AT, C1-inh, SAA, A2M; AACT, A1AT, C1-inh, CRP, ApoE; AACT, A1AT, C1-inh, CRP, ITIH4; AACT, A1AT, C1-inh, CRP, A2M; AACT, A1AT, C1-inh, ApoE, ITIH4; AACT, A1AT, C1-inh, ApoE, A2M; AACT, A1AT, C1-inh, ITIH4, A2M; AACT, A1AT, SAA, CRP, ApoE; AACT, A1AT, SAA, CRP, ITIH4; AACT, A1AT, SAA, CRP, A2M; AACT, A1AT, SAA, ApoE, ITIH4; AACT, A1AT, SAA, ApoE, A2M; AACT, A1AT, SAA, ITIH4, A2M; AACT, A1AT, CRP, ApoE, ITIH4; AACT, A1AT, CRP, ApoE, A2M; AACT, A1AT, CRP, ITIH4, A2M; AACT, A1AT, ApoE, ITIH4, A2M; AACT, C1-inh, SAA, CRP, ApoE; AACT, C1-inh, SAA, CRP, ITIH4; AACT, C1-inh, SAA, CRP, A2M; AACT, C1-inh, SAA, ApoE, ITIH4; AACT, C1-inh, SAA, ApoE, A2M; AACT, C1-inh, SAA, ITIH4, A2M; AACT, C1-inh, CRP, ApoE, ITIH4; AACT, C1-inh, CRP, ApoE, A2M; AACT, C1-inh, CRP, ITIH4, A2M; AACT, C1-inh, ApoE, ITIH4, A2M; AACT, SAA, CRP, ApoE, ITIH4; AACT, SAA, CRP, ApoE, A2M; AACT, SAA, CRP, ITIH4, A2M; AACT, SAA, ApoE, ITIH4, A2M; AACT, CRP, ApoE, ITIH4, A2M; A1AT, C1-inh, SAA, CRP, ApoE; A1AT, C1-inh, SAA, CRP, ITIH4; A1AT, C1-inh, SAA, CRP, A2M; A1AT, C1-inh, SAA, ApoE, ITIH4; A1AT, C1-inh, SAA, ApoE, A2M; A1AT, C1-inh, SAA, ITIH4, A2M; A1AT, C1-inh, CRP, ApoE, ITIH4; A1AT, C1-inh, CRP, ApoE, A2M; A1AT, C1-inh, CRP, ITIH4, A2M; A1AT, C1-inh, ApoE, ITIH4, A2M; A1AT, SAA, CRP, ApoE, ITIH4; A1AT, SAA, CRP, ApoE, A2M; A1AT, SAA, CRP, ITIH4, A2M; A1AT, SAA, ApoE, ITIH4, A2M; A1AT, CRP, ApoE, ITIH4, A2M; C1-inh, SAA, CRP, ApoE, ITIH4; C1-inh, SAA, CRP, ApoE, A2M; C1-inh, SAA, CRP, ITIH4, A2M; C1-inh, SAA, ApoE, ITIH4, A2M; C1-inh, CRP, ApoE, ITIH4, A2M; SAA, CRP, ApoE, ITIH4, A2M; ; ; 1 st  3 plus:; A1AT, C1-inh; A1AT, SAA; A1AT, CRP; A1AT, ApoE; A1AT, ITIH4; A1AT, A2M; C1-inh, SAA; C1-inh, CRP; C1-inh, ApoE; C1-inh, ITIH4; C1-inh, A2M; SAA, CRP; SAA, ApoE; SAA, ITIH4; SAA, A2M; CRP, ApoE; CRP, ITIH4; CRP, A2M; ApoE, ITIH4; ApoE, A2M; ITIH4, A2M; A1AT, C1-inh, SAA; A1AT, C1-inh, CRP; A1AT, C1-inh, ApoE; A1AT, C1-inh, ITIH4; A1AT, C1-inh, A2M; A1AT, SAA, CRP; A1AT, SAA, ApoE; A1AT, SAA, ITIH4; A1AT, SAA, A2M; A1AT, CRP, ApoE; A1AT, CRP, ITIH4; A1AT, CRP, A2M; A1AT, ApoE, ITIH4; A1AT, ApoE, A2M; A1AT, ITIH4, A2M; C1-inh, SAA, CRP; C1-inh, SAA, ApoE; C1-inh, SAA, ITIH4; C1-inh, SAA, A2M; C1-inh, CRP, ApoE; C1-inh, CRP, ITIH4; C1-inh, CRP, A2M; C1-inh, ApoE, ITIH4; C1-inh, ApoE, A2M; C1-inh, ITIH4, A2M; SAA, CRP, ApoE; SAA, CRP, ITIH4; SAA, CRP, A2M; SAA, ApoE, ITIH4; SAA, ApoE, A2M; SAA, ITIH4, A2M; CRP, ApoE, ITIH4; CRP, ApoE, A2M; CRP, ITIH4, A2M; ApoE, ITIH4, A2M; A1AT, C1-inh, SAA, CRP; A1AT, C1-inh, SAA, ApoE; A1AT, C1-inh, SAA, ITIH4; A1AT, C1-inh, SAA, A2M; A1AT, C1-inh, CRP, ApoE; A1AT, C1-inh, CRP, ITIH4; A1AT, C1-inh, CRP, A2M; A1AT, C1-inh, ApoE, ITIH4; A1AT, C1-inh, ApoE, A2M; A1AT, C1-inh, ITIH4, A2M; A1AT, SAA, CRP, ApoE; A1AT, SAA, CRP, ITIH4; A1AT, SAA, CRP, A2M; A1AT, SAA, ApoE, ITIH4; A1AT, SAA, ApoE, A2M; A1AT, SAA, ITIH4, A2M; A1AT, CRP, ApoE, ITIH4; A1AT, CRP, ApoE, A2M; A1AT, CRP, ITIH4, A2M; A1AT, ApoE, ITIH4, A2M; C1-inh, SAA, CRP, ApoE; C1-inh, SAA, CRP, ITIH4; C1-inh, SAA, CRP, A2M; C1-inh, SAA, ApoE, ITIH4; C1-inh, SAA, ApoE, A2M; C1-inh, SAA, ITIH4, A2M; C1-inh, CRP, ApoE, ITIH4; C1-inh, CRP, ApoE, A2M; C1-inh, CRP, ITIH4, A2M; C1-inh, ApoE, ITIH4, A2M; SAA, CRP, ApoE, ITIH4; SAA, CRP, ApoE, A2M; SAA, CRP, ITIH4, A2M; SAA, ApoE, ITIH4, A2M; CRP, ApoE, ITIH4, A2M; A1AT, C1-inh, SAA, CRP, ApoE; A1AT, C1-inh, SAA, CRP, ITIH4; A1AT, C1-inh, SAA, CRP, A2M; A1AT, C1-inh, SAA, ApoE, ITIH4; A1AT, C1-inh, SAA, ApoE, A2M; A1AT, C1-inh, SAA, ITIH4, A2M; A1AT, C1-inh, CRP, ApoE, ITIH4; A1AT, C1-inh, CRP, ApoE, A2M; A1AT, C1-inh, CRP, ITIH4, A2M; A1AT, C1-inh, ApoE, ITIH4, A2M; A1AT, SAA, CRP, ApoE, ITIH4; A1AT, SAA, CRP, ApoE, A2M; A1AT, SAA, CRP, ITIH4, A2M; A1AT, SAA, ApoE, ITIH4, A2M; A1AT, CRP, ApoE, ITIH4, A2M; C1-inh, SAA, CRP, ApoE, ITIH4; C1-inh, SAA, CRP, ApoE, A2M; C1-inh, SAA, CRP, ITIH4, A2M; C1-inh, SAA, ApoE, ITIH4, A2M; C1-inh, CRP, ApoE, ITIH4, A2M; SAA, CRP, ApoE, ITIH4, A2M. 
         [0055]    Examples of markers for which an increase relative to control is indicative of rejection include C4A, CRP, SAA, C1-inh, A1AT, and ApoE. Markers for which a decrease relative to control is indicative of rejection include AACT, ApoA1, ITIH4, and A2M. 
         [0056]    In one embodiment, the measuring comprises chromatography or spectrometry. The chromatography can be gas or liquid chromatography. The spectrometry can be mass spectrometry. Other known methods of marker detection are also contemplated, and may be selected based on the characteristics of the individual marker of interest. Examples of other assays that can be employed include immunoassay and electrochemical detection. Measures of test samples can be compared directly to controls, such as comparing the amount of the marker present in the test sample to the amount of the marker in a control sample or to a known normal level of the marker. Alternatively, in some embodiments, the marker amount is compared to a baseline amount for the same subject. 
         [0057]    The following patent documents pertain to the molecular diagnosis of transplant rejection: U.S. Pat. No. 7,666,596, US 2009/0304705; U.S. Pat. No. 7,691,569; U.S. Pat. No. 7,645,575; WO 2009/101083; WO 2009/045104; US 2009/0022730; WO 2007/104537; WO 2008/027428; US 2008/0038746; WO 2007/138011; WO 2007/121922; US 2007/0202085; U.S. Pat. No. 7,235,358; US 2007/0037166; US 2006/0088836; U.S. Pat. No. 7,026,121; WO 2004/042346; U.S. Pat. No. 7,192,716; US 2003/0104371; and WO 01/81916. The following patent publications relate to genotypic and phenotypic tests for transplant rejection: US20077235358; WO2006029184; US20070082356; EP000253514; EP000953220; US2004000584728; WO2005077980; US2004000557234; WO02075306; US2006000641625; and US20050152893. 
       Kits 
       [0058]    For use in the methods described herein, kits are also within the scope of the invention. Such kits can comprise a carrier, package or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in the method. The probes, antibodies and other reagents of the kit may be provided in any suitable form, including frozen, lyophilized, or in a pharmaceutically acceptable buffer such as TBS or PBS. The kit may also include other reagents required for utilization of the reagents in vitro or in vivo such as buffers (i.e., TBS, PBS), blocking agents (solutions including nonfat dry milk, normal sera, Tween-20 Detergent, BSA, or casein), and/or detection reagents (i.e., goat anti-mouse IgG biotin, streptavidin-HRP conjugates, allophycocyanin, B-phycoerythrin, R-phycoerythrin, peroxidase, fluors (i.e., DyLight, Cy3, Cy5, FITC, HiLyte Fluor 555, HiLyte Fluor 647), and/or staining kits (i.e., ABC Staining Kit, Pierce)). The kits may also include other reagents and/or instructions for using antibodies, probes, and other reagents in commonly utilized assays described above such as, for example, liquid or gas chromatography, spectrometry, electrochemical assay, flow cytometric analysis, ELISA, immunoblotting (i.e., western blot), immunocytochemistry, immunohistochemistry. 
         [0059]    In one embodiment, the kit provides the reagent in purified form. In another embodiment, the reagents are immunoreagents that are provided in biotinylated form either alone or along with an avidin-conjugated detection reagent (i.e., antibody). In another embodiment, the kit includes a fluorescently labeled immunoreagent which may be used to directly detect antigen. Buffers and the like required for using any of these systems are well-known in the art and may be prepared by the end-user or provided as a component of the kit. The kit may also include a solid support containing positive- and negative-control protein and/or tissue samples. For example, kits for performing spotting or western blot-type assays may include control cell or tissue lysates for use in SDS-PAGE or nylon or other membranes containing pre-fixed control samples with additional space for experimental samples. 
         [0060]    The kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes, and package inserts with instructions for use. In addition, a label can be provided on the container to indicate that the composition is used for a specific application, and can also indicate directions for use, such as those described above. Directions and or other information can also be included on an insert which is included with the kit. 
         [0061]    The invention additionally provides a kit comprising antibodies that specifically bind the 5 kDa fragment of C4A, ApoA1, AACT, and, optionally, one or more additional markers listed in Table 1. In one embodiment, the kit comprises reagents that bind C4A (or a 5 kDa fragment thereof) and ApoA1 (or the fragment thereof at amino acids 148-183) and/or AACT (or the fragment thereof at amino acids 385-422), In one embodiment, the kit comprises reagents that specifically bind the 5191 Da fragment of AACT and ApoA1. In one embodiment, the kit further comprises a solid support onto which the antibodies are immobilized. Examples of a solid support include, but are not limited to, a microtiter plate, beads, a membrane or other support known to those skilled in the art. In one embodiment, the antibodies are immobilized via binding to antigen that is immobilized to the solid support. In one embodiment, the antibodies are immobilized via binding to a bead or particle such as luminex. In one embodiment, the kit further comprises a chromogenic substrate. 
         [0062]    Another illustrative embodiment of the invention is an ELISA kit to screen for a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor in plasma or serum, the kit comprising: (a) a microtiter plate coated with polyclonal or monoclonal antibodies specific to α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor; (b) polyclonal or monoclonal antibody-alkaline phosphatase conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor; (c) p-nitrophenyl-phosphate; and (d) α-1 anti-chymotrypsin and/or Apo A1 and/or the 5191 peptide disclosed herein and/or complement C1 inhibitor as an antigen standard. 
         [0063]    Another illustrative embodiment of the invention is an ELISA kit to screen for a plasma molecular profile in a patient that is associated with acute cellular renal allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor in plasma or serum, the kit comprising: (a) a microtiter plate coated with polyclonal or monoclonal antibodies specific to α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor; (b) polyclonal or monoclonal antibody-alkaline phosphatase conjugates reactive with α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor; (c) p-nitrophenyl-phosphate; and (d) α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor as an antigen standard. 
         [0064]    Another illustrative embodiment of the invention is a Luminex kit to screen in plasma, serum and\or biological fluid for a molecular profile in a patient that is associated with solid organ allograft rejection by detecting α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor and/or proteins described in Table 1, the kit comprising: (a) a microbead array coated with polyclonal or monoclonal antibodies specific to α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor and/or other proteins listed in Table 1; (b) polyclonal or monoclonal antibody fluorescent dye conjugates reactive with α- 1  anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor and/or other proteins listed in Table 1; (c) and α-1 anti-chymotrypsin and/or Apo A1 and/or C4A and/or complement C1 inhibitor or other protein in Table 1 as an antigen standard. 
       EXAMPLES 
       [0065]    The following examples are presented to illustrate the present invention and to assist one of ordinary skill in making and using the same. The examples are not intended in any way to otherwise limit the scope of the invention. 
       Example 1 
     Apolipoprotein A1 and C-Terminal Fragment of α-1 Antichymotrypsin are Plasma Biomarkers Associated with Acute Renal Allograft Rejection 
       [0066]    This example demonstrates, using a case-control approach and SELDI-TOF-MS, the identification of plasma proteins associated with renal allograft rejection. From each rejection patient, two plasma samples (one near the biopsy date and the other at a time post-biopsy) were compared. Biopsy confirmed non-rejection patients were further analyzed as controls. Antibody-based quantitative ELISA was performed to validate candidate biomarker apolipoprotein A1 (Apo A1) in a subset of the original and a second cohort of biopsy confirmed rejection (n=40) and non-rejection (n=70) patients. Twenty-two proteins/peptides showed significant differences between rejection and post-rejection samples. Peptides 5191 Da and 4467 Da detected rejection with 100% sensitivity and 94% specificity. The 4467 Da peptide was identified as the C-terminal fragment of α-1 anti-chymotrypsin and a 28 kDa protein was determined as Apo A1. Both protein levels were significantly lower at rejection compared to post-rejection. Protein levels of non-rejection patients were similar to the post-rejection samples. Apo A1 ELISA results showed significantly lower Apo A1 levels (p=0.001 for the original and p=4.14E-11 for the second cohort) at the time of rejection compared to non-rejection which coincides with the SELDI findings. Together α-1 antichymotrypsin, Apo A1, and the 5191 Da peptide (a fragment of C4A) provide a plasma molecular profile, and this is associated with acute cellular renal allograft rejection. 
       Methods 
       [0067]    Study Design and Patient Population. 
         [0068]    Renal transplant patients were enrolled in the University of California Los Angeles Institutional Review Board-approved immune monitoring study by written consent. Sixteen renal transplant recipients contributed 34 blood specimens associated with 17 “independent” episodes of biopsy-confirmed ACR. One recipient had two rejection episodes far enough apart (4 months), and the intermediate serum creatinine was normal, so we considered the second rejection an independent event. Patients with biopsy-proven nonrejection were also selected (n=48). All biopsies were performed for cause and taken after a serum creatinine rise or delayed graft function. Rejection biopsies occurred within the first 100 days posttransplant with the exception of one which occurred at 656 days (median=27 days posttransplant). Banff classification was used to score acute rejection (35, 36). Two biopsies with ACR also showed evidence of AMR and were C4d positive. The rejection patients were studied at two time points: rejection specimen (group A) were selected at a time point closest to the positive biopsy date (median=−1 day, range: −16 to +8 days); and postrejection samples (group B) were selected closest to 14 days after biopsy date (median=28 days, range: 14-180 days). Twelve of 17 rejection samples (group A) were collected within 8 days before biopsy, and 5 of 17 were obtained within 8 days after the biopsy. For the postrejection samples (group B), 16 of 17 were collected within 60 days after the biopsy, and 1 of 17 was collected at 180 days after the biopsy. The nonrejection plasma samples (defined as controls, group C) were selected at one time point closest to the negative biopsy (median=1 day, range: −35 to +44 days). Table 2 illustrates the demographics of the study population and shows no significant differences with respect to age, gender, race, transplant number, or degree of human leukocyte antigen mismatch. The percentage of deceased and living donors was similar to U.S. Organ Procurement Transplant Network national data. 
         [0000]    
       
         
               
             
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 Demographic characteristics of patients 
               
             
          
           
               
                   
                 Rejection 
                 Non- 
                   
               
               
                   
                 patients 
                 rejectors 
               
               
                 Parameters 
                 (n = 16) 
                 (n = 48) 
                 P a   
               
               
                   
               
             
          
           
               
                 Age (yr: mean ± SD) 
                 48.7 ± 12.2 
                 49.5 ± 13.9 
                 0.84 
               
               
                 Gender (male/female) 
                 14/2 
                 32/16 
                 0.20 
               
               
                 Race 
                   
                   
                 0.74 b   
               
               
                 Asian 
                 19% 
                  5% 
               
               
                 Black 
                 25% 
                 20% 
               
               
                 White 
                 44% 
                 54% 
               
               
                 Other 
                 12% 
                 21% 
               
               
                 Regraft 
                   
                   
                 0.74 
               
               
                 First allograft 
                 81% 
                 76% 
               
               
                 Regraft 
                 19% 
                 24% 
               
               
                 Multiorgan transplants 
                   
                   
                 0.16 
               
               
                 +Pancreas 
                 11% 
                  2% 
               
               
                 +Liver 
                  0% 
                  2% 
               
               
                 HLA mismatch 
                 2.7 ± 0.7 
                 2.2 ± 1.3 
                 0.15 
               
               
                 (mean ± SD) 
               
               
                 Type of donor 
                   
                   
                 0.21 
               
               
                 Deceased 
                 56% 
                 74% 
               
               
                 Living 
                 44% 
                 26% 
               
               
                 Induction 
                   
                   
                 0.74 c   
               
               
                 Anti-IL2Rα 
                 74% 
                 72% 
               
               
                 ATG 
                 22% 
                 21% 
               
               
                 Combined 
                  4% 
                  7% 
               
               
                 Time of blood draw 
                   
                   
                 0.37 
               
               
                 relative to biopsy 
               
               
                 (days: median/range) 
               
               
                 Rejection sample 
                 −1/−16 to 8    
               
               
                 Postrejection sample 
                 28/14 to 147 
               
               
                 Nonrejection sample 
                   
                 1/−35 to 44 
               
               
                   
               
               
                   a P values for categorical variables from Fisher exact test, and P values for continuous variables from t test. 
               
               
                   b Race (black vs. other). 
               
               
                   c Induction (ATG vs. any anti-IL2Rα). 
               
               
                 ATG, antithymoglobulin; IL2Rα, interleukin-2 receptor alpha chain; SD, standard deviation; HLA, human leukocyte antigen. 
               
             
          
         
       
     
         [0069]    A second cohort of recipients with biopsy-proven renal allograft rejection (n=27) were selected, and again two plasma samples were studied (rejection and postrejection time points). All biopsies were performed for cause and taken after a serum creatinine rise or delayed graft function. Two of the ACR positive biopsies also had evidence of AMR, whereas four of the biopsies had evidence of only AMR. Rejection specimens (n=27) were selected at a time point within −7 days of the biopsy (median=−1 day, range=−7 to 0 days). The average rejection episode was 122 days after transplantation. Twenty of the 27 biopsies were within the first 3 months, 5 of 27 were within the first 9 months, and 2 of 27 were greater than 1 year. Postrejection samples were selected more than 8 days after the biopsy (median=32 days, range=8-573 days). For the postrejection samples, 20 of 27 were collected within 3 months after the biopsy, 3 of 27 were within 6 months, 1 of 27 was collected at 9 months, and 3 of 27 were collected 1 year after the biopsy. In addition, a cohort of 51 biopsy-proven nonrejection samples were selected at a time closest to the negative biopsy (median=8 days, range=−22 to 581 days). For the biopsy-proven nonrejection samples, 38 of 51 were collected within 3 months after the biopsy, 5 of 51 were within 6 months, 4 of 51 were collected within 9 months after the biopsy, and 4 of 51 were collected after 1 year. All biopsies from this group of nonrejectors were performed for cause and taken after a serum creatinine rise or delayed graft function. 
         [0070]    For both cohorts, maintenance immunosuppression included a calcineurin inhibitor (tacrolimus or cyclosporine), an antiproliferative agent (mycophenolate mofetil or sirolimus), and prednisone. In some cases without evidence of pretransplant sensitization, steroids were withdrawn. 
       Plasma Albumin and Immunoglobulin-G Depletion and Anion Exchange Fractionation 
       [0071]    Blood samples were collected in BD Vacutainer ACD solution A tubes (Becton, Dickinson and Company, Franklin Lakes, N.J.). Plasma was separated and stored. Antibody spin columns (Qproteome, Qiagen, Valencia, Calif.) were used to deplete human serum albumin and immunoglobulin-G. Complete Mini (ethylenediaminetetraacetic acid) Protease Inhibitor (Roche, Palo Alto, Calif.) was added. AcroPrep Mustang Q (hydrophilic polyethersulfone membrane) Anion Exchange Resin 96-well plates (Pall, East Hills, N.Y.) were used to separate the depleted plasma into the pH 9, pH 6, and pH 4 fractions. 
         [0000]    ProteinChip Array preparation 
         [0072]    ProteinChip arrays (CM10 and Q10) were preequilibrated for binding, pH fractions were bound to the arrays and analyzed in triplicate. Six pooled human serum (Sigma, St. Louis, Mo.) samples were used as internal controls on each array set. After sample array processing, matrix was applied: either saturated sinapinic acid (SPA, LaserBio Labs, Sophia-Antipolis, France) or 20% saturated alpha-cyano-4-hydroxy cinnamic acid (CHCA, LaserBio Labs). A Biomek 2000 liquid handling robot (Beckman, Fullerton, Calif.) was used for matrix spotting. 
       Mass Spectrum Data Analysis 
       [0073]    A ProteinChip Biology System (PBS IIc) mass spectrometer using Ciphergen ProteinChip Software 3.2 was calibrated in the high mass range before reading the SPA-spotted arrays (laser energies of 150 and 170). A peptide mixture was used for calibration of the CHCA-spotted arrays (laser energies of 120 and 135). Mass spectrum from each spot was an average of 240 laser shots. All spectra were preliminarily analyzed in CiphergenExpress Client Software 3.0 to create clusters by Expression Difference Mapping analysis. A cluster is a group of peaks with the same mass/charge (m/z) ratio and treated as the same protein or peptide across multiple spectra. Peak intensities from each spectrum were used to measure relative protein/peptide amounts. Total ion current was used to normalize the signals. The reproducibility of peak heights was similar to what was previously published (37), showing a CV of 15% to 30%. 
       Protein Identification 
       [0074]    MALDI-TOF-MS was performed with a prOTOF 2000 orthoganol-TOF mass spectrometer (Perkin Elmer, San Jose, Calif.). The high-performance liquid chromatography system was Prominence 2000 (Shimadzu Scientific Instruments, Columbia, Md.). All protocol and reagents were in accordance with manufacturer&#39;s suggestions. 
       4467 Da Peptide 
       [0075]    Q fractions with this peptide were loaded on a reverse phase C8 column (Axxiom, Moorpark, Calif.). The C8 fractions were subjected to collision-induced dissociation MS/MS fragmentation in a Thermo-Finnigan LTQ-FT electrospray mass spectrometer (Waltham, Mass.). The MS/MS data were searched by NCBI Blast. Immunoprecipitation was performed using a polyclonal antibody against α-1-antichymotrypsin (Lab Vision Corporation, Fremont, Calif.) followed by MALDI analysis. 
       28 kDa Protein 
       [0076]    Pooled samples fractions with high levels of the protein were separated by sodium dodecyl sulfate-PAGE. The gel was stained using the ProteoSilver Plus kit (Sigma). Bands near 28 kDa were excised, and in-gel tryptic digestion was performed. Peptides were analyzed by MALDI. Intact tryptic masses were searched in MASCOT with online protein fragment database searching. Immunoprecipitation was done using a monoclonal antibody against human Apo A1 (R&amp;D Systems, Minneapolis, Minn.) followed by MALDI analysis. 
       Statistical Analyses 
       [0077]    Nonparametric (binomial) and parametric (mixed effects and linear regression) models were used to identify significant peaks. Two-sided P values less than 0.05 were considered significant, and Bonferroni correction was used as needed. CART analysis was conducted to select a subset of candidate biomarkers and determine their ability to correctly classify rejection. Adjusted intensities of the selected protein/peptide peaks were used as the predictor variables in CART training. The R software package (version 3.1, at r-project.org) was used for statistical computations. Traditional logistic regression analysis was performed, and ROC plots were generated using STATA data analysis and statistical software. Cut points were selected by the maximum correctly classified. Details of the statistical analyses are presented in the Supplemental material (see Supplemental Digital Content 1, links.lww.com/TP/A465; published with the online version of this material as Ziegler, M. E., et al., 2011, Transplantation 92(4):10.1097). 
       ELISA for Quantitation of Plasma Apo A1 Levels 
       [0078]    Total Human Apolipoprotein A1 ELISA Assay (Alerchek, Portland, Me.) was used according to the manufacturer&#39;s protocol. Samples were run in duplicate along with a control plasma sample. Analysis was performed on the SpectraMax M2 plate reader with the SoftMax Pro 5.4 software (Molecular Devices, Sunnyvale, Calif.). 
       Results 
     Variations in Plasma Protein/Peptide Levels Between Rejection and Postrejection Samples 
       [0079]    The peak intensity differences across spectra between the rejection and postrejection groups were analyzed. In total, 653 peak clusters were detected, including 235 peaks in the pH 4 fraction, 186 peaks in the pH 6 fraction, and 232 peaks in the pH 9 fraction. 
         [0080]    The peak intensities of rejection and postrejection samples from the same patient were analyzed using a binomial model. Eighty-one peak intensities (see Table S1A, Supplemental Digital Content 1, links.lww.com/TP/A465) were significantly increased, whereas 63 peaks (see Table S1B, Supplemental Digital Content 1) were significantly decreased in the rejection samples. After Bonferroni correction for the total number of peaks in each condition, 24 peaks (Table S2, Supplemental Digital Content 1, at links.lww.com/TP/A465) were significantly different between rejection and postrejection samples by the linear mixed model. Twenty-two significant protein peaks were detected by both the binomial model and the linear mixed model (Table 3). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 Significant peaks found by both the 
               
               
                 linear mixed model and binomial model 
               
             
          
           
               
                   
                   
                 Protein 
                 P for 
                 P for 
                 Protein 
               
               
                   
                   
                 peak 
                 mixed 
                 binomial 
                 intensity 
               
               
                   
                 Condition a   
                 m/z (Da) 
                 model 
                 model 
                 ratio a  (&gt;1.5) 
               
               
                   
                   
               
             
          
           
               
                 1 
                 4CL 
                 4467 
                 3.06E−04 
                 0.004 
                 B/A 
               
               
                 2 
                   
                 4125 
                 1.35E−04 
                 0.011 
                 A/B 
               
               
                 3 
                   
                 5191 
                 1.15E−11 
                 0.000 
                 A/B 
               
               
                 4 
                 4SH 
                 50,835 
                 5.04E−06 
                 0.003 
                 A/B 
               
               
                 5 
                   
                 143,718 
                 3.62E−05 
                 0.001 
                 B/A 
               
               
                 6 
                 6CL 
                 4564 
                 4.41E−05 
                 0.030 
                 A/B 
               
               
                 7 
                   
                 4933 
                 1.80E−04 
                 0.030 
                 A/B 
               
               
                 8 
                   
                 5191 
                 1.10E−06 
                 0.002 
                 A/B 
               
               
                 9 
                 6SH 
                 59,256 
                 2.24E−04 
                 0.025 
                 B/A 
               
               
                 10 
                   
                 60,334 
                 3.72E−04 
                 0.025 
                 B/A 
               
               
                 11 
                   
                 63,615 
                 5.74E−04 
                 0.000 
                 B/A 
               
               
                 12 
                   
                 123,329 
                 2.10E−04 
                 0.025 
                 B/A 
               
               
                 13 
                 9CL 
                 5051 
                 3.29E−05 
                 0.001 
                 A/B 
               
               
                 14 
                   
                 5083 
                 6.40E−05 
                 0.020 
                 A/B 
               
               
                 15 
                   
                 5190 
                 8.58E−07 
                 0.020 
                 A/B 
               
               
                 16 
                   
                 5265 
                 1.21E−05 
                 0.001 
                 A/B 
               
               
                 17 
                 9SH 
                 28,186 
                 2.18E−04 
                 0.002 
                 B/A 
               
               
                 18 
                   
                 28,336 
                 1.42E−04 
                 0.007 
                 B/A 
               
               
                 19 
                   
                 28,574 
                 3.00E−04 
                 0.007 
                 B/A 
               
               
                 20 
                   
                 29,134 
                 1.40E−04 
                 0.026 
                 B/A 
               
               
                 21 
                   
                 109,796 
                 1.05E−04 
                 0.007 
                 B/A 
               
               
                 22 
                   
                 188,758 
                 2.59E−04 
                 0.026 
                 B/A 
               
               
                   
               
               
                   a Under “Condition,” the number refers to the pH fraction. The “Ratio” indicates whether the protein intensity is higher in rejection (A) or postrejection (B) patients. 
               
               
                 C, alpha-cyano-4-hydroxy cinnamic acid; S, sinapinic acid; L, low laser energy; H, high laser energy; m/z, mass to charge ratio. 
               
             
          
         
       
     
         [0081]    The 17 independent rejection events were applied to a Classification and Regression Tree (CART) analysis and produced a combination of two peaks (4467 Da and 5191 Da) ( FIG. 1A ), which best differentiate rejection from postrejection samples. All the rejection samples were correctly detected, whereas only one postrejection sample was incorrectly detected; showing 100% sensitivity and 94% specificity. The intensity of the 5191 Da peak was significantly increased during rejection (P&lt;0.001), whereas the 4467 Da peak was significantly decreased during rejection (P&lt;0.004) ( FIG. 1B ). The ROC plots produced cut points, which were similar to those found by CART analysis. 
         [0082]    The peak intensities of these two proteins were compared with the nonrejection group (group C) ( FIG. 1B ). There was no significant difference in 5191 Da peak intensity between groups B and C (P=0.33). However, in rejection (group A), the 5191 Da peak was elevated over nonrejection (group C) (P&lt;0.001). The 4467 Da peak intensity was lower during rejection (group A) (P&lt;0.001) compared with nonrejection (group C), and nonrejection (group C) was only slightly higher than the postrejection samples (group B, P=0.04). 
         [0083]    Although the levels of the 5191 DA and 4467 DA protein peaks were significantly associated with diagnosis of rejection, their intensities did not appear to discriminate among Banff grades of rejection. Because of the limited numbers, rejections were classified as either mild (≦Banff 1A, n=10) or severe (≧Banff 1B, n=7). The two groups individually showed the same intensity patterns (versus nonrejection) as listed earlier for the combined cases of rejection (data not shown). 
         [0084]    Of the plasma samples used for protein profiling, blood sample serum creatinine levels were available in 16 of 17 rejection samples and 19 of 48 controls. There was no significant difference in serum creatinine levels between postrejection and samples collected during rejection. Although the creatinine levels in the postrejection samples (median=1.9) were in fact lower in all patients compared with the time of rejection (median=2.2), this difference was not statistically significant. Creatinine recovery can be slower due to a number of factors including type of rejection, the rejection therapy, and the donor condition. 
       Identification of Biomarker Candidates 
       [0085]    The 4467 Da peptide was detected in the pH 4 fraction, and further purification revealed a cluster of peaks ( FIG. 2A ) with mass differences matching the monoisotopic masses of valine, leucine, alanine, and serine giving a terminal sequence of SALV (S, serine; A, alanine; L, leucine; and V, valine), which corresponds to the C-terminal fragment of human α-1-antichymotrypsin (AACT). High-resolution MALDI analysis of immunoprecipitated plasma peptides confirmed the identity as AACT ( FIG. 2B ). 
         [0086]    To further develop a profile associated with renal allograft rejection, a cluster of peaks at −28 kDa found among the list of 22 significant proteins was analyzed (Table 3). Separation of the 28 kDa peaks by sodium dodecyl sulfate-PAGE followed by in-gel tryptic digestion produced peptides that were analyzed by MALDI-TOF-MS and searched on MASCOT to identify the protein as Apo A1. Immunoprecipitation using a monoclonal antibody confirmed the identity ( FIG. 2C ). The Apo A1 peak intensity was significantly higher in postrejection compared with the rejection and nonrejection patients and were more similar to the postrejection (P=0.035) than the rejection samples (P=0.001) ( FIG. 2D ). Although Apo A1 protein levels were significantly associated with diagnosis of acute rejection, they were not associated with an individual Banff grade of rejection. Logistic regression and CART analysis of the 4467 Da and the 28 kDa peaks showed that they differentiate rejection from postrejection with 59% sensitivity and 100% specificity. 
       Validation of Apo A1 
       [0087]    To validate the SELDI results, a quantitative Apo A1 ELISA was performed on a subset of the original rejection/postrejection samples (n=13) and the nonrejection samples (n=19). The pattern of Apo A1 levels measured by ELISA ( FIG. 3A ) is consistent with the SELDI intensity peak levels ( FIG. 2D ). To further substantiate these findings, the Apo A1 ELISA was performed on an independent cohort consisting of 27 plasma samples from patients with biopsy-confirmed acute cellular rejection (ACR) with a corresponding postrejection sample and 51 patients with biopsy-proven nonrejection. In the second cohort, Apo A1 levels by ELISA are significantly lower during rejection (mean=0.14±0.04), compared with postrejection (mean=0.22±0.09) and nonrejection samples (mean=0.23±0.07, P=4.14E-11) ( FIG. 3B ), a finding that is consistent with the original cohort. 
         [0088]    Among both cohorts, samples which were collected within −3 to 0 days before the renal biopsy were examined. Twenty-five rejection and 22 nonrejection samples were compared, and Apo A1 levels were significantly lower at the time of rejection (P value&lt;0.0001) compared with recipients with biopsy-proven nonrejection ( FIG. 3C ). 
         [0089]    A subset of the new cohort (n=14) also had available a plasma sample collected at a time point before the rejection episode (median=−50 days, range=−180 to −11 days). The prerejection samples demonstrated Apo A1 levels nearly identical to the average levels of the postrejection samples ( FIG. 3D ). 
         [0090]    An ROC analysis was performed using Apo A1 levels of the rejection and nonrejection samples from both the original and second cohort of patients ( FIG. 3E ). The results show a cut point of 0.167 g/dL provides a sensitivity of 76% and a specificity of 86% correctly detecting 80% of the patients. Twenty-six of the 27 rejection patients had Banff classification data as follows: borderline changes=2, Banff 1A=13, Banff 2A=6, Banff 3 vascular=1, and Banff antibody-mediated rejection (AMR)=4. The patients were grouped into categories based on mild ACR (borderline and Banff 1A=15), severe ACR (Banff 2A and Banff 3 vascular=7), or AMR with no ACR (n=4). The Apo A1 medial level was 0.14 for all three groups indicating that the severity of rejection was not distinguished by the Apo A1 level. 
       Discussion 
       [0091]    Twenty-two peptides/proteins discovered by surface-enhanced laser desorptionionization time-of-flight mass spectrometry were significantly associated with the diagnosis of acute allograft rejection. The identity of two of these proteins, AACT and Apo A1, was elucidated. The C-terminal fragment of AACT is significantly lower during rejection compared with postrejection and nonrejection. A different variation of the AACT fragment (4354 Da) is found at higher levels in urine of patients with acute rejection compared with those with stable transplants (14). Pimenta et al. (17) examined the hydrolysis of AACT by cathepsin D using high-performance liquid chromatography isolation and MADLI and found three peptides: 4354 Da, 4468 Da, and 4625 Da. These cleavage products are identical to the 4467 Da peak identified in plasma and the 4354 Da found in urine based on the sequence data, suggesting that both may be produced by cathepsin D. 
         [0092]    O&#39;Riordan et al. (14) examined the levels of total AACT in the kidney by immunohistochemistry and found no difference between rejection and controls and suggested that finding a peptide AACT whose level varied was the result of cleavage after target protease interaction, and therefore, the peptide level variation between patients is a reflection of the activity of the AACT target proteases. We hypothesize that variations in the peptide level may be a result of total AACT being blocked or bound to other substrates for cathepsin D such as cystatin C or kininogen (18). Alternatively, during rejection, total AACT may instead inhibit its primary target, cathepsin G (19), an inflammation-related neutrophil protease, which has been linked to allograft function (20, 21). 
         [0093]    The 28 kDa peak was identified as Apo A1. Apo A1 and synthetic peptides, which mimic Apo A1 activity, have strong antiinflammatory and antioxidant properties (22, 23). The Apo A1 mimetic peptide, D-4F, reduces intimal lesions caused by chronic rejection in a mouse model. The mechanism of this effect involves induction of the antioxidant gene heme oxygenase-1 in the graft and/or a direct effect on T-lymphocyte proliferation and effector cytokine production (24). 
         [0094]    Apo A1 was validated by ELISA in both the original and an independent cohort. Comparisons of the rejection, postrejection, and nonrejection samples in both cohorts were consistent with the SELDI findings indicating that lower levels of Apo A1 are associated with rejection. The prerejection time point in the independent cohort could not predict the onset of the rejection episode, indicating that the Apo A1 drop is closely associated with the time of rejection. In addition, the Apo A1 ROC analysis of all patients suggests that Apo A1 could potentially be part of a signature used to describe rejection. Apo A1 was also identified as a candidate biomarker in pulmonary arterial hypertension, colorectal cancer, and ovarian cancer (25-27) and more recently was associated with Chagas disease, polycystic ovarian syndrome, and chronic obstructive pulmonary disease (28-30). In all these studies, Apo A1 levels were lower in the disease state compared with nondisease. 
         [0095]    Infections can lead to changes in serum lipid profiles, and decreased Apo A1 has been postulated to link infection with chronic inflammation (31). The use of long-term immunosuppressive therapy leaves transplant patients susceptible to infection (32). We examined the 51 nonrejection patients from the second cohort and found five patients with evidence of bacterial infection at the time the plasma sample used for this study was collected. Apo A1 levels were not significantly different in nonrejection patients with infection compared with those without for this small subset of patients. This contributes to the hypothesis that for renal transplant patients, low levels of Apo A1 are associated with the rejection episode, but more studies are necessary to confirm this. 
         [0096]    Isolation and identification of the 5191 Da peptide have been hindered due to its low abundance in plasma, its copurification with other more abundant peptides, and the inability to directly fragment it. For unknown reasons, some peptides fragment poorly and yield MS/MS spectra that cannot be deciphered (33, 34). A combination of the 5191 and 4467 Da peaks robustly assessed rejection verses nonrejection, whereas the combination of the 4467 and 28 kDa peaks was not as valuable, thus identification of the 5191 Da peak is important. We are currently exploring alternative methods to better isolate and fragment this peptide for identification. 
         [0097]    A limitation of our study design is that the plasma was collected at routine patient visits, which was not always on the same day that the renal biopsy was performed. Also, the clinical parameters of our study population were not uniform with respect to immunosuppression. Furthermore, only two patients in the original cohort had AMR, and therefore, a signature for AMR could not be determined. A majority of patients rejected within the first 100 days, and thus, we were limited to only explore early rejection. In the future, it will be also valuable to explore these markers in patients undergoing late renal allograft rejection. Additionally, we did not find an association between severity of rejection based on Banff classification and Apo A1 levels. It would be of interest to attempt this comparison again in a larger cohort of subjects. Finally, we recognize that to better assess these markers, a prospective study is necessary to determine their true value in the clinical setting. To show the potential of a prospective study, we examined both cohorts of patients and found 25 rejection and 22 nonrejection samples collected −3 to 0 days before the renal biopsy. When we compared the Apo A1 levels between these groups, the rejection levels were significantly lower (P&lt;0.0001), suggesting that a prospective study would likely have differentiated these patients at the time of biopsy. 
         [0098]    This study demonstrates that searching for candidate biomarkers of renal allograft rejection in plasma has a promising clinical benefit. At the time point these plasma samples were collected, the candidate biomarkers showed variations that were more informative than serum creatinine level changes. Therefore, future studies should not only interrogate Apo A1 but also other markers for their ability to accurately detect renal allograft rejection. Finally, the two candidate markers identified are antiinflammatory proteins, and their functional characterization should be explored.
   1. Li B, et al. N Engl J Med. 2001; 344:947.   2. Clarke W. Ther Drug Monit. 2006; 28:19.   3. Beckingham I J, et al. Br J Urol. 1994; 73:13.   4. Rush D N, et al. Transplantation. 1994; 57:208.   5. Hu S. et al. Proteomics. 2006; 6:6326.   6. Lescuyer P, et al. J Proteome Res. 2007:6:3371.   7. Reddy G, Dalmasso E A. J Biomed Biotechnol. 2003; 2003:237.   8. Albitar M, et al. Cancer. 2006; 106:1587.   9. Clarke W, et al. Ann Surg. 2003; 237:660-4. discussion 664.   10. Schaub S, et al. Kidney Int. 2004; 65:323.   11. O&#39;Riordan E, et al. J Am Soc Nephrol. 2004; 15:3240.   12. Voshol H, et al. J Proteome Res. 2005; 4:1192.   13. Jahnukainen T, et al. J Am Soc Nephrol. 2006; 17:3248.   14. O&#39;Riordan E, et al. Am J Transplant. 2007; 7:930.   15. Ling X B, et al. J Am Soc Nephrol. 2010; 21:646.   16. Freue G V, et al. Mol Cell Proteomics. 2010; 9:1954.   17. Pimenta D C, et al. J Protein Chem. 2000; 19:411.   18. Lenarcic B, et al. FEBS Lett. 1991; 280:211.   19. Zhang S, Janciauskiene S. J Alzheimers Dis. 2002; 4:115.   20. Gibson T L, Cohen P. Growth Horm IGF Res. 1999; 9:241.   21. Koo D D, et al. Am J Pathol. 1998; 153:557.   22. Navab M, et al. Circulation. 2002; 105:290.   23. Navab M, et al. Arterioscler Thromb Vasc Biol. 2005; 25:1325.   24. Hsieh G R, et al. Transplantation. 2007; 84:238.   25. Yuditskaya S, et al. Blood. 2008; 113:1122.   26. Engwegen J Y, et al. World J Gastroenterol. 2006; 12:1536.   27. Kozak K R, et al. Proteomics. 2005; 5:4589.   28. Ndao M. et al. J Clin Microbiol. 2010; 48:1139.   29. Choi D H, et al. J Proteome Res. 2010; 9:4329.   30. Nicholas B L, et al. Am J Respir Crit Care Med. 2010; 181:1049.   31. Burger D, Dayer J M. Autoimmun Rev. 2002; 1:111.   32. Fishman J A, Rubin R H. N Engl J Med. 1998; 338:1741.   33. Shevchenko A. et al. Methods Mol Biol. 2000:146:1.   34. Shevchenko A, et al. Rapid Commun Mass Spectrom. 1997; 11:1015.   35. Racusen L C, et al. Am J Transplant. 2003; 3:708.   36. Racusen L C, et al. Kidney Int. 1999; 55:713.   37. Albrethsen J. Clin Chem. 2007; 53:852.   
 
       Example 2 
     Validation of Apoliprotein A1 (Apo A1) as a Plasma Biomarker Associated with Acute Renal Allograft Rejection 
       [0136]    The 28 kDa protein identified in Example 1 as Apo-A1 consistently showed lower levels in patients with biopsy proven renal allograft rejection. Using an enzyme-linked immunosorbent assay (ELISA) and an independent cohort of 27 plasma samples from patients with biopsy proven rejection and 51 patients without rejection, we confirmed the mass spectrometry studies and showed that lower levels are associated with diagnosis of renal allograft rejection. 
         [0137]    The aim of the current study was to validate the predictive value of the marker for renal allograft rejection using an independent cohort of 73 renal allograft recipients transplanted at UCLA between 2010 and 2013. 45/71 patients had rejection while 28 patients had biopsy proven non-rejection. 
         [0138]    Plasma samples from 73 renal recipients were assayed for Apo-A1 protein levels by ELISA. 45 of the patients experienced at least one biopsy proven rejection episode while 28 patients had biopsy proven no-rejection. Plasma samples obtained within 7 days prior or 2 days after diagnosis of rejection were quantitated by ELISA for Apo A1 levels. Renal allograft rejection was diagnosed using Banff criteria. As shown in Table 3 and  FIG. 4 , patients diagnosed with renal allograft rejection had significantly lower Apo A1 levels (mean 0.156+/−0.77) compared to non-rejection (mean 0.239+/−0.16) (P&lt;0.0024). Using a cutpoint of 0.195, Apo A1 levels correctly classified patients with rejection 79% of the time with a sensitivity of 75% and specificity of 82% ( FIG. 5 ). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
               
               
               
               
               
               
               
             
               
               
             
               
               
               
             
           
               
                 TABLE 3 
               
               
                   
               
               
                 T test for first biopsy per transplant 
               
               
                   
               
             
             
               
                 ttest maxb1 if brnk == 1, by (rej) 
               
               
                 Two-sample t test with equal variances 
               
             
          
           
               
                 Group 
                 Obs 
                 Mean 
                 Std. Err. 
                 Std. Dev. 
                 [95% Conf. Interval] 
               
               
                   
               
             
          
           
               
                 0 = no 
                 28 
                 .2399732 
                 .0312028 
                 .1651096 
                 .1759504 
                 .303996 
               
               
                 1 = yes 
                 45 
                 .1568389 
                 .0114993 
                 .0771399 
                 .1336635 
                 .1800143 
               
               
                 combined 
                 73 
                 .188726 
                 .0145791 
                 .1245642 
                 .1596631 
                 .217789 
               
               
                 diff 
                   
                 .0831343 
                 .0285355 
                   
                 .0262361 
                 .1400325 
               
               
                   
               
             
          
           
               
                 diff = mean(0 = no) − mean(1 = yes) 
                 t = 2.9134 
               
               
                 Ho: diff = 0 
                 degrees of freedom = 71 
               
             
          
           
               
                 Ha: diff &lt; 0 
                 Ha: diff != 0 
                 Ha: diff &gt; 0 
               
               
                 Pr(T &lt; t) = 0.9976 
                 Pr(|T| &gt; |t|) = 0.0048 
                 Pr(T &gt; t) = 0.0024 
               
               
                   
               
             
          
         
       
     
         [0139]    Conclusion: Significantly lower Apo A1 protein levels are found within a week of diagnosis of renal allograft rejection. This study further supports using Apo A1 as a biomarker of renal allograft rejection and can be used to not only aid in the diagnosis of renal allograft rejection but it may be used to monitor transplant recipients to determine risk of rejection. 
       Example 3 
     Validation of Alpha-2-Macroglobulin Using an Antibody-Based ELISA Assay 
       [0140]      FIG. 6  presents ELISA data showing the same patter of detection of Alpha-2-macroglobulin as was demonstrated using mass spectrometry. Paired plasma samples were collected at the time of rejection and post-rejection from 7 renal allograft recipients diagnosed with rejection. These are the same paired serum samples that were used in Example 1 above. The data show that the levels of Alpha-2-macroglobulin as detected by ELISA decrease at the time of diagnosis of rejection. 
       Example 4 
     Amino Acid Sequences of Biomarkers Identified by Mass Spectrometry 
       [0141]    Amino acid sequences of protein fragments identified in Example 1 above were determined as described in the following Table. 
         [0000]    
       
         
               
             
               
             
           
               
                 TABLE 4 
               
               
                   
               
               
                 Amino Acid Sequences of 
               
               
                 Biomarker Peptides and Proteins 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 Alpha-1-antitrypsin C-Terminal fragment 
               
               
                 (2505 Da, A1AT 397-418; SEQ ID NO: 11) 
               
               
                 LMIEQNTKSPLFMGKVVNPTQK 
               
               
                   
               
               
                 Apolipoprotein A1 fragment 
               
               
                 (4125 Da, Apo A1 148-183; SEQ ID NO: 5) 
               
               
                 AELQEGARQKLHELQEKLSPLGEEMRDRARAHVDAL 
               
               
                   
               
               
                 Plasma protease C1 inhibitor fragment 
               
               
                 (4187 Da, C1 inh 445-478; SEQ ID NO: 13) 
               
               
                 ARTLLVFEVQQPFLFVLWDQQHKFPVFMGRVYDPRA (+2 Ox) 
               
               
                   
               
               
                 Alpha-1-antichymotrypsin C-terminal fragment 
               
               
                 (4467 Da, AACT 385-422; SEQ ID NO: 8) 
               
               
                 ALVETRTIVRFNRPFLMIIVPTDTQNIFFMSKVTNPKQ 
               
               
                   
               
               
                 Complement C4 Anaphylatoxin 
               
               
                 (5051 Da, C4 alpha 698-742; SEQ ID NO: 3) 
               
               
                 TAKRCCQDGVTRLPMMRSCEQRAARVQQPDCREPFLSCCQFAESL 
               
               
                   
               
               
                 Complement C4 Anaphylatoxin 
               
               
                 (5191 Da, C4 alpha 702-746; SEQ ID NO: 2) 
               
               
                 CCQDGVTRLPMMRSCEQRAARVQQPDCREPFLSCCQFAESLRKKS 
               
               
                   
               
               
                 Serum Amyloid A-4 
               
               
                 (11694 Da, SAA4 21-122; SEQ ID NO: 14) 
               
               
                 WRSFFKEALQGVGDMGRAYWDIMISNHQNSNRYLYARGNYDAAQRGPGG 
               
               
                 VWAAKLISRSRVYLQGLIDCYLFGNSSTVLEDSKSNEKAEEWGRSGKDP 
               
               
                 DRFR 
               
               
                   
               
               
                 C-reactive protein 
               
               
                 (19409 Da, CRP 10-185; SEQ ID NO: 15) 
               
               
                 VFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKR 
               
               
                 QDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIV 
               
               
                 EFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDI 
               
               
                 GNVNMWDFVLSPDEINTIYLGGPFSPNVL 
               
               
                   
               
               
                 Apolipoprotein A1 
               
               
                 (28077 Da, Apo A1 56-267; SEQ ID NO: 6) 
               
               
                 DEPPQSPWDR VKDLATVYVDVLKDSGRDYVSQFEGSALGKQLNLKLLD 
               
               
                 NWDSVTSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKV 
               
               
                 QPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGE 
               
               
                 EMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAK 
               
               
                 ATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ 
               
               
                   
               
               
                 Apolipoprotein E 
               
               
                 (36747 Da, Apo 19-317, Glycosylated; SEQ ID NO: 16) 
               
               
                 KVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQTLSEQVQE 
               
               
                 ELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQ 
               
               
                 AAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKR 
               
               
                 LLRDADDLQKRLAVYQAGAREGAERGLSAIRERLGPLVEQGRVRAATVG 
               
               
                 SLAGQPLQERAQAWGERLRARMEEMGSRTRDRLDEVKEQVAEVRAKLEE 
               
               
                 QAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEKVQAAVGTSAAPV 
               
               
                 PSDNH 
               
               
                   
               
             
          
         
       
     
         [0142]    Throughout this application various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to describe more fully the state of the art to which this invention pertains. 
         [0143]    From the foregoing it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the invention. Accordingly, the invention is not limited except as by the appended claims.