WO2005057217A1 - Methods for distinguishing immunoreactive t lymphocytes - Google Patents

Abstract

The invention provides in part methods for distinguishing subsets of immunoreactive T lymphocytes by contacting a sample including a heterogeneous population of T lymphocytes with an isolated cell membrane fragment comprising a major histocompatibility complex molecule, the isolated cell membrane fragment and the major histocompatibility complex molecule being derived from the same or different subject, in combination with an antigen derived from the same or different subject, and distinguishing a subset of T lymphocytes in the sample that binds to the major histocompatibility complex.

Description

METHODS FOR DISTINGUISHING IMMUNOREACTIVE T LYMPHOCYTES FIELD OF THE INVENTION The invention is in the field of immunology. More specifically, the invention relates to methods for distinguishing subsets of immunoreactive T lymphocytes.

BACKGROUND OF THE INVENTION Organ transplantation has made important advances in the last two decades, and is now the therapy of choice for many patients with end-stage vital organ failure. In order to prevent rejection of the transplanted organ, however, immunosuppressive therapy is used to suppress a patient's immune system. Current immunosuppressive therapies include an array of new agents that selectively inhibit discrete steps in the molecular process of lymphocyte activation [2], and often employ a combination of agents targeting specific steps in the immune response. For example, monoclonal antibodies that bind to the α-chain of the interleukin-2 (IL-2) receptor (CD25), which is expressed on proliferating CD45R0+ T cells, inhibit T cell activation throughout the first two months post-transplant [3]. Cyclosporine and tacrolimus (FK506) act through a common molecular pathway to inhibit calcineurin dependent T cell activation [4, 5]. Mycophenolate mofetil (MMF) acts more broadly in both T- and B- cells by selectively inhibiting purine synthesis, and sirolimus and everolimus inhibit a later stage in the immune cascade by blocking the downstream effects of the IL-2 receptor signal [6]. Despite these therapeutic advances, acute rejection, chronic graft failure, viral infection and other complications remain important barriers to success and are often etiologically linked. The graft course may be divided conceptually into three periods. The first, typically occurring during the first three months post-transplant, reflects the early allo-recognition of the donor MHC and other minor histocompatibility antigens, and leads to the generation of antibody and cellular responses directed at graft antigens expressed on the endothelium and other formed elements of the organ. Despite the potency of current immunosuppression, acute graft rejection occurs in 15-40% of kidney, heart and liver graft recipients and remains the most important cause of early morbidity and graft injury [1-3]. Pharmacokinetic studies indicate that the probability of acute rejection is closely related to the effective pharmacological concentration of the immunosuppressive drugs in vitro, and may be four times more common in those with low drug concentrations during the first week post-transplant. While acute rejection normally responds to an increase in immunosuppression, it presages the occurrence of chronic rejection, and graft half-life is markedly reduced in these subjects [5, 7-11]. The subsequent period of clinical and immunological quiescence may last for months or years, and is typified by stable graft function without evidence of acute or chronic tissue injury. The state of accommodation however is not identical for all graft types. For example, the removal of immunosuppression following renal or heart transplantation is often followed by acute or chronic graft rejection, while several studies have suggested that many liver graft recipients develop a state of partial tolerance to the graft which can persist in the absence of external immunosuppression. Additional studies have suggested the existence of a special class of antigen specific, regulatory T cells (Tr) which suppress immune activation in an antigen-specific manner. Chronic and progressive graft injury generally begins within months or years after transplantation, and may be triggered by an acute rejection episode in an otherwise stable recipient. Although the pathophysiology of chronic rejection is not fully understood, progressive vasculopathy and interstitial fibrosis are consistent findings [12]. These changes are generally accompanied by the increased deposition of normal basement membrane components including collagen type IV, laminin heparan sulphate and decorin [12]. Non-immunologic factors such as older donor organs, inadequate functional capacity of the donor organ to meet the metabolic demands of the recipient, preservation injury, donor atherosclerosis, and drug toxicity also contribute to the development of chronic graft injury, however, immune factors appear to play a key inciting role. Continuing endothelial injury by low titre anti-HLA antibody, or promotion of endothelial proliferation and interstitial fibrosis under the influence of TGF-beta and other cytokines released in excess, accelerates the normal physiological processes of graft senescence resulting in progressive loss of function (reviewed in [12]). The incidence of chronic graft injury increases with time after transplantation and eventually affects a majority of solid organ allografts, involving up to 80% of lung allografts, 30%- 40% of heart and kidney allografts and about 5% of liver grafts by 5 years post transplant. Many cells contribute to graft rejection, including T cells. In a graft recipient,

T cells recognize alloantigen throug the direct pathway in the context of donor major histocompatibility complex (MHC) or through the indirect pathway where donor alloantigens are cross-presented by the recipient's antigen presenting cells (APCs). Direct recognition may be the major mechanism (>90%) responsible for acute rejection [33-37] and may contribute to the onset of chronic rejection [40]. T cells have a vast variety of roles depending on their class/subset and may either promote or suppress graft destruction. For example, CD3⁺ T cells may be involved in initiating graft rejection, and are regulators and effectors of this process while the CD4⁺ T regulatory (Tr) cells are thought to protect against graft rejection [23]. To date, tissue biopsy has been the diagnostic method of choice for acute rejection in heart, liver and kidney recipients. Endomyocardial biopsy serves as a tool for surveillance of cardiac rejection and is an effective but invasive strategy. Examination of graft infiltrating cells by graft biopsy has suggested that acute rejection in animal models or human patients may be associated with up-regulation of genes associated with activation of alloreactive effector T cells [29, 39-45]. Non- invasive surveillance methods for heart rejection have focused on measurement of cardiac function, intragraft electrical events, and tissue properties as determined by a laser, peripheral protein markers of graft micronecrosis, and immune activation, as well as non-immune accompaniments of rejection [13-21] with variable success. Physiological measures have also been used to monitor organ function in vital organ transplantation with variable success. Similar issues apply to the diagnosis of chronic graft injury. Vasculopathy and interstitial fibrosis are non-specific changes associated with chronic kidney graft injury, and a decrease in the number of bile ducts is visible upon biopsy in chronic liver rejection. However, substantial organ damage has occurred by the time this diagnosis is made. Endomyocardial biopsy has limited value as a tool for diagnosis of chronic heart rejection since damage is typically only evident in the graft arterial tree [22] and endomyocardial biopsies do not generally sample affected vessels. DNA microarray analyses of kidney and cardiac biopsies have been performed [29-32] in attempts to identify genes associated with graft rejection, and changes in the expression of genes in peripheral blood mononuclear cells, including increases in TNF-α, IL-8 and decreases in TIRC7, perform, granzyme B and IFN-γ mRNA levels [16], as well as up-regulation of genes such as perform, granzyme B and FasL, which are associated with cytotoxic effector T cells, have been implicated with episodes of graft rejection [47, 48]. The presence of activated "memory" type T cells, as detected by flow cytometry, was used in conjunction with graft biopsies to distinguish between immune-mediated acute rejection and other types (eg, toxicity, arteriopathy) of rejection in renal human transplant recipients [46]. Analyses of peripheral blood however may be limited by the heterogeneity of haematopoietic cells and the paucity of T cells that are specifically involved in the allo-response to donor antigens. Potential changes in gene expression within the alloreactive T cell population may be masked by the large background of non- alloreactive cells. Approaches to detecting alloreactive T cells in a mixed population have included culturing the cells with alloantigen in the form of irradiated donor derived APCs and measuring biological endpoints such as proliferation, cytokine production, target cell killing and suppression of heterologous T cell growth [24-27].

SUMMARY OF THE INVENTION The invention provides, in part, methods for specific discrimination of subsets of immunoreactive T cells. In one aspect, the invention provides a method for distinguishing a subset of immunoreactive T lymphocytes by contacting a sample including a heterogeneous population of lymphocytes derived from a first subject with an isolated cell membrane fragment including a major histocompatibility complex molecule, the isolated cell membrane fragment and the major histocompatibility complex molecule being derived from a second subject; and distinguishing a subset of T lymphocytes in the sample that binds to the major histocompatibility complex, where the subset of T lymphocytes that bind to the major histocompatibility complex are immunoreactive T lymphocytes. In another aspect, the invention provides a method for distinguishing a subset of immunoreactive T lymphocytes by contacting a sample including a heterogeneous population of lymphocytes derived from a first subject with an isolated cell membrane fragment including a major histocompatibility complex molecule, the isolated cell membrane fragment and the major histocompatibility complex molecule being derived from the first subject, in combination with an antigen derived from a second subject; and distinguishing a subset of T lymphocytes in the sample that binds to the major histocompatibility complex, where the subset of T lymphocytes that bind to the major histocompatibility complex are immunoreactive T lymphocytes. In another aspect, the invention provides a method for distinguishing a subset of immunoreactive T lymphocytes by contacting a sample including a heterogeneous population of lymphocytes derived from a subject with an isolated cell membrane fragment including a major histocompatibility complex molecule, the isolated cell membrane fragment and the major histocompatibility complex molecule being derived from the subject; and distinguishing a subset of T lymphocytes in the sample that binds to the major histocompatibility complex, where the subset of T lymphocytes that bind to the major histocompatibility complex are immunoreactive T lymphocytes. In various embodiments of the aspects of the invention, distinguishing the subset of T lymphocytes in the sample may be performed by quantifying the subset of T lymphocytes in the sample that bind to the major histocompatibility complex; or by isolating the subset of T lymphocytes in the sample that bind to the major histocompatibility complex; or both. The immunoreactive T lymphocyte may be a CD3+ T lymphocyte and/or an alloreactive T lymphocyte. In various embodiments, the isolated cell membrane fragment may be: coated on a solid support (e.g., a microbead); detectably labeled; and/or oriented using a cell membrane orientation reagent (e.g., a CD45 antibody that specifically binds the intracellular domain of CD45). In various embodiments, the first subject may be a transplant recipient and/or the second subject may be a transplant donor. In various embodiments, the methods may be used for monitoring the progression of transplantation rejection; prognosing transplantation rejection; selecting a subject for an anti-transplantation rejection therapy; monitoring the efficacy of an anti-transplantation rejection therapy; screening a candidate compound for treating transplantation rejection; for monitoring the progression of an immune response against a foreign pathogen; for monitoring an autoimmune response; for monitoring an anti-tumour response; for monitoring efficacy of a vaccine; for monitoring efficacy of an anti-autoimmune disease therapy; for prognosing an autoimmune disease; for prognosing an infectious disease; for prognosing cancer immunity; for identification and isolation of a subset of T cells (e.g., antigen specific regulatory T cells, cytotoxic T cells, helper T cells, and memory T cells); for screening a candidate compound for treating an autoimmune disease; for screening a candidate compound for treating an infectious disease; for isolating an anti-tumour specific T cell; isolating an antigen specific T cell; depleting an alloreactive T cell; depleting an antigen specific T cell; and/or depleting a regulatory T cell. An "antigen" is any molecule that elicits an immune response, e.g., a humoral or cell-mediated immune response. An antigen is capable of specifically reacting with products of the elicited immune response, such as the antibody generated in response to the antigen, and/or a specifically activated T cell. An "allo-antigen" can provoke an immune response in a genetically distinct individual from the same species. A "xeno- antigen" is found in more than one species and can provoke an immune reponse in an individual from a different species. A "self-antigen" or "auto- antigen" can provoke an immune response in the same individual and can result in for example, an autoimmune disease. A "lymphocyte" is an agranulocytic leukocyte derived from lymphoid stem cells. Lymphocytes include T lymphocytes or "T cells" and B lymphocytes or "B cells." T cells may be subdivided into different classes (e.g., helper T cells, cytotoxic T-cells, suppressor T cells, regulatory T cells, etc.) and are responsible for cell- mediated immunity and for stimulating B -cells. Activated B cells produce antibody to specific antigens. An "immunoreactive" lymphocyte is a lymphocyte (e.g., T cell or B cell) that is activated in response to an antigen. For example, an alloreactive T cell is activated in response to an allo-antigen; a xenoreactive T cell is activated in response to a xeno- antigen; an autoreactive T cell is activated in response to an autoantigen. Alloreactive cells are very heterogeneous. Immunoreactive T cells may also be reactive to pathogens or cancerous cells or tissues. A "major histocompatibility complex molecule" or "MHC molecule" is a cell surface glycoprotein that is involved in mediating the immune response in mammals by presenting an antigenic peptide to a specific T cell receptor. In mammals, major histocompatibility complex molecules can be class I or class II molecules. Class I MHC molecules "present" endogenous (protein made in the cell) or exogenous (protein acquired from outside the cell) peptides to a specific T cell receptor for recognition by the T cell, and in the case of an autoimmune response, present self- peptides to the T cell receptor. Class I MHC molecules include HLA-A, B and C molecules in humans, H2-D and K in mice, RLA in rabbits, RT 1 in rats, DLA in dogs, SLA in pigs, etc. Common HLA molecules in humans include HLA*0201, HLA-A* 11, A*03, HLA-B*08, B*07, B*35. Common H2 molecules in inbred laboratory mice include H2-Kd, H-2Kb, H2-Dd, H2-Db. An antigen can be provided "in combination with a major histocompatibility molecule" if the antigen is present in a sample containing a MHC molecule, or is present in a sample containing an antigen presenting cell, or is present in an isolated cell membrane fragment, or is bound (e.g., in the antigen binding site) to a MHC molecule in an isolated cell membrane fragment. A MHC molecule can be in a multimer, for example, a tetramer, form. An "antigen presenting cell" or "APC" is any cell that carries antigen, bound to a major histocompatibility class I molecule, on its cell surface and presents the antigen in this context to a T cell. An antigen presenting cell can include, without limitation, an endothelial cell, a dendritic cell, a spleen cell, a macrophage, or any cell line, such as RMAS-Kd or P815. Antigen presenting cells are generally incubated with a peptide, (usually a nonapeptide, although peptides in the range of eight to ten amino acids can be used), that enables direct binding of the peptide to the MHC molecule of the APC. An antigen presenting cell can exogenously acquire a compound by being incubated in the presence of the compound. Larger molecules, such as larger peptides or nucleic acid molecules encoding larger peptides, can be introduced into an APC (by transfection, electroporation, liposome fusion, osmotic shock, etc.), such that they are processed endogenously and peptides of the appropriate size are expressed on the cell surface of the APC. By "distinguishing" or "discriminating" is meant detecting, quantifying, and/or isolating a subset of immunoreactive cells e.g., T cells or B cells, from a population of heterogeneous cells which may include T cells, B cells, or any other cell. Distinguishing a subset of immunoreactive cells includes detecting, quantifying, and/or isolating cells that bind to a specific class of antigens, such as alloantigens, and distinguishing such cells from cells that bind to other classes of antigens, such as pathogens, autoantigens, etc. Quantifying a subset of immunoreactive cells includes measuring a change of any value between 3% and 100%, inclusive, or over 100%, when compared to a control, such as a syngeneic control when quantifying alloreactive cells. Isolating a subset of immunoreactive cells includes substantially purifying the immunoreactive cells from any other cells in the sample, such that over 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, or 85%, or over 90%, 95%, or 99% of the cells in the isolated subset are immunoreactive cells. By "cell membrane" or "plasma membrane" is meant a cellular structure that encloses the cytoplasm of a cell and provides a selective barrier. An "isolated cell membrane fragment" is a cell membrane preparation that has been separated from the other components of a cell, e.g., cellular organelles such as the nucleus, cytoplasm, golgi, etc. that are naturally present in an intact cell. An "isolated cell membrane fragment" includes lipids normally found in the cell membrane and includes proteins and other molecules normally associated with the cell membrane, such as integral membrane proteins, transmembrane proteins, proteins associated with the inner surface of the cell membrane in vivo, proteins capable of binding inner cell membrane proteins, etc. By "detectably labeled" is meant any means for marking and identifying the presence of a molecule, e.g., a molecule in an isolated cell membrane fragment. Methods for detectably-labelling a molecule are well known in the art and include, without limitation, radioactive labelling (e.g., with an isotope such as ³²P or ³⁵S) and nonradioactive labelling such as, enzymatic labelling (for example, using horseradish peroxidase or alkaline phosphatase), chemiluminescent labeling, fluorescent labeling (for example, using fluorescein), bioluminescent labeling, or antibody detection of a ligand attached to the probe. Also included in this definition is a molecule that is detectably labeled by an indirect means, for example, a molecule that is bound with a first moiety (such as biotin) that is, in turn, bound to a second moiety that may be observed or assayed (such as fluorescein-labeled streptavidin). Labels also include digoxigenin, luciferases, and aequorin. A "sample" can be any organ, tissue, cell, or cell extract derived or isolated from a subject. For example, a sample can include, without limitation, cells or tissue (e.g., from a biopsy or autopsy, amputated tissue, surgically excised tissue) from bone, brain, breast, colon, muscle, nerve, ovary, prostate, retina, skin, skeletal muscle, intestine, testes, heart, liver, kidney, stomach, pancreas, uterus, adrenal gland, tonsil, spleen, soft tissue, peripheral blood or fractions thereof (e.g., peripheral blood mononuclear cells), whole blood, red cell concentrates, platelet concentrates, leukocyte concentrates, blood cell proteins, blood plasma, platelet-rich plasma, a plasma concentrate, a precipitate from any fractionation of the plasma, a supernatant from any fractionation of the plasma, blood plasma protein fractions, purified or partially purified blood proteins or other components, serum, semen, mammalian colostrum, milk, urine, stool, saliva, placental extracts, amniotic fluid, a cryoprecipitate, a cryosupernatant, a cell lysate, mammalian cell culture or culture medium, products of fermentation, ascitic fluid, proteins present in blood cells, solid tumors, isolated from a mammal, or any other specimen, or any extract thereof, obtained from a patient (human or animal), test subject, or experimental animal. In some embodiments, sample may also include, without limitation, products produced in cell culture by normal or transformed cells (e.g., via recombinant DNA or monoclonal antibody technology), or be a cell or cell line created under experimental conditions, that is not directly isolated from a subject or be cell-free, artificially derived or synthesised. In some embodiments, sample may exclude products produced in cell culture by normal or transformed cells (e.g., via recombinant DNA or monoclonal antibody technology), or exclude a cell or cell line created under experimental conditions that is not directly isolated from a subject, or exclude a cell- free, artificially derived or synthesised sample. In some embodiments, a sample includes a "heterogeneous population" of lymphocytes if it includes different classes of T cells (e.g., helper T cells, cytotoxic T- cells, suppressor T cells, regulatory T cells, etc.) and B cells. In some embodiments, a sample includes a "heterogeneous population" of lymphocytes if it includes lymphocytes that are capable of binding to a variety of antigens such as autoantigens, alloantigens, xenoantigens, etc. In some embodiments, it may be desirable to separate lymphocytic cells, e.g., T cells or B cells, from non-lymphocytic cells, e.g., non-T or non-B cells in a sample. In some embodiments, it may be desirable to separate a specific class of T cells, such as helper T cells, cytotoxic T-cells, suppressor T cells, regulatory T cells, etc., or to separate T cells based on specific surface determinants, such as CD3+ cells, CD4+ cells, CD8+ cells, or lack of specific surface determinants, etc., — such a specific class of cells may also be a heterogeneous population of lymphocytes. In general, a T cell line that is maintained in culture and activated in response to a specific antigen e.g., a known antigen, is not a sample that includes a heterogeneous population of lymphocytes. In some embodiments, a sample may be derived from a normal (healthy) subject; a recipient of a transplanted organ, tissue, or cell; a donor of a transplanted organ, tissue, or cell; a subject having or at risk for an aberrant immune response, etc. As used herein, a "subject" may be any organism capable of launching an immune response against an antigen i.e., an organism naturally having lymphocytes and MHC molecules, e.g., a human, non-human primate, rodent (e.g., rat, mouse, hamster, guinea pig, etc.) cow, horse, pig, sheep, goat, dog, cat, etc. The subject may be a clinical patient, a clinical trial volunteer, an experimental animal, etc. The subject may have or may be at risk for: an aberrant or uncontrolled immune response e.g, an autoimmune disease; a cancer; or infection by a pathogenic organism e.g., virus, bacterium, etc. The subject may be a transplant recipient or donor. The subject may be living or dead. The subject may be of any age, e.g., an adult, an infant, etc. A "first" subject may be of the same species as the "second" subject, or may be of a different species. A "solid support" may be any surface suitable for binding a cell membrane. A solid support may include materials made of nylon, glass, ceramic, plastic, silica, aluminosilicates, borosilicates, metal oxides such as aluminum and nickel oxide, various clays, polystyrene, latex, nitrocellulose, etc. A solid support may be a sheet or a microparticle, e.g., a microbead. A microparticle may be made of a wide variety of suitable materials, such as polystyrene beads available from Spherotech Inc., or dextran-coated beads from Miltenyi Biotec or StemCell Technologies, Inc. The microparticles may be of any size suitable for analysis by flow cytometry with diameters ranging from any value between 50 nm to 15 μm, inclusive, e.g, 50nm, 2-3 μm, etc. Additionally or alternatively, the microparticles may be about one-tenth to one-twentieth the size of an immunoreactive cell. The microparticles may be fluorescently labelled, or may be paramagnetic in nature, or a combination thereof.

BRIEF DESCRIPTION OF THE DRAWINGS Figures 1A-D. Flow cytometry data showing: A. Staining of Balb/C CD3-+ T cells with fluorescent beads coated with CD45 labeled plasma membranes derived from Balb/C (syngeneic) or C57BL/6 (allogeneic) splenocytes. B. Staining of C57BL/6 CD3+ T cells with CD45 labeled plasma membranes derived from C57BL/6 (syngeneic) or Balb/C (allogeneic) splenocytes. C. Staining of C57BL/6 splenocytes with paramagnetic fluorescent beads coated with plasma membranes derived from C57BL/6 (syngeneic) or Balb/C (allogeneic) splenocytes using EDC chemistry. E . Staining of C57BL/6 CD3+ T cells with paramagnetic fluorescent beads coated with plasma membranes derived from C57BL/6 (syngeneic) or Balb/C (allogeneic) splenocytes using EDC chemistry. (CD3-CyChrome gated cells). Figure 2. Bar graph showing detection of CD69 antigen in a mouse skin transplant model, n = 4 in each group P < 0.016. Figure 3. Bar graph showing detection of the development of an alloreactive (anti-graft response) in a mouse skin transplant model. Figure 4. Flow cytometry data showing analysis of alloreactive T cells in humans.

DETAILED DESCRIPTION OF THE INVENTION The invention provides, in general, methods for specific discrimination of subsets of immunoreactive T cells. Thus, for example, the methods may be used to specifically assay alloantigen-specific, xeno-antigen specific, or self-antigen specific T cells. In some embodiments, the methods are relatively non-invasive, for example when compared to tissue biopsy. In some embodiments, the methods permit discrimination between different immune responses, such as anti-graft responses and responses to other stimuli (e.g., infections). In some embodiments, the methods of the invention allow for specific discrimination of immunoreactive T cells where some of the antigenic peptides have not been identified. This may be useful, for example, in graft rejection, where the heterogeneity and undefined nature of the relevant allo-antigens, which include highly heterogeneous donor MHC and other graft-derived proteins, may otherwise make identification of allo-specific immunoreactive T cells difficult. In some embodiments, the methods of the invention provide for direct detection and quantification of immunoreactive T cells. Such direct techniques reduce or eliminate the requirement for in vitro culture of T cells, and are desirable since ex vivo expansion of such cells can change the relative ratios of the different subset of T cells present and the activation state of the cell. For example, T regulatory (Tr) cells, which appear to suppress graft destruction and are thought to be indicative of tolerance, grow poorly in culture [28]. Furthermore, in vitro culture may change the phenotype (e.g., gene expression profile) of the cell so the properties of the native activation state of the original cell may be difficult to determine in the absence of direct discrimination methods. In some embodiments, the methods of the invention may further permit isolation of immunoreactive T cells and determination of their effector function e.g., determination of whether the immunoreactive T cells fall into harmful or protective subsets, and/or identification and characterization of biological markers that can reflect the status of the specific immune response. Immunoreactive T cells distinguished according to the methods described herein are relatively less heterogeneous than the general population of cells in a sample, e.g., haematopoietic or lymphocytic cells, and are enriched for example in subsets of T cells that are specifically involved in the allo-response to donor antigens. Thus, biological markers identified from such immunoreactive T cells may be diagnostic of graft rejection, and may be diagnostic of different stages of graft rejection, e.g., acute or chronic. Immunoreactive lymphocytes isolated using the methods of the invention may be analyzed for expression of genes or proteins, or specific activity states or post- translational modifications of the proteins. In alternative aspects, specific gene or protein expression levels, or specific post translational modifications may be identified as specific markers of the immune health of a transplant recipient patient using the methods of the invention. Immunoreactive T-cells may be quantified and correlated with the organ function and overall immune health of the patient. This correlation may be used to modify immunosuppressive therapy in the transplant patient, and for future monitoring of the health of the graft or transplanted tissue or organ. Thus, in some embodiments, the methods of the invention may permit the use of genomic and proteomic approaches to identify diagnostic and predictive biological markers for rejection and accommodation using for example immunoreactive T cells isolated from for example peripheral blood lymphocytes, serum or urine. Such biological markers may discriminate between different immune responses, such as anti-graft responses and responses to other stimuli (e.g., infections), when compared to for example biological markers identified from total peripheral blood. Furthermore, the methods of the invention may identify potential changes in gene expression within the alloreactive T cell population which may otherwise be masked by the background of non-alloreactive cells. Biological markers may be identified, for example by defining genomic and/or proteomic expression profiles in blood or other tissues that correspond to allograft rejection or immune accommodation of transplanted tissues. For example, by comparing the gene expression profile of the alloreactive T cell population in liver, heart and kidney transplant recipients, gene signatures indicating the presence of alloantigen specific Tr cells in liver transplant recipients can be identified, and conditions favoring their development may be determined. Conversely, development of a harmful effector T cell response against the graft may be detected. Thus this assay provides the ability to monitor the characteristics of the alloreactive T cell population in liver recipients and systematically manage the dose of immunosuppression and facilitate the careful withdrawal of these drugs in appropriate patients and adjust therapy to prevent graft injury or avoid toxicity. Thus, immunosuppressive therapy can be tailored to suit the requirements of the individual patient. Identification of biological markers may also provide an approach toward the induction of graft tolerance, achieving specific immunological unresponsiveness to the transplanted graft while maintaining normal immune function in the absence of antirejection drugs. In some aspects, the methods of the invention provide sensitive, accurate and non-invasive assays that reflect the status of the immune response for example in graft rejection. In some embodiments, the methods of the invention provide the ability to detect an early immune response, for example, rejection prior to graft injury and to recognize periods of accommodation when immunosuppression may be safely reduced. In addition, reliable predictors or indicators of these states may allow clinicians to individualize immunosuppression and maximize treatment benefit. Immunosuppressive drugs are routinely administered at maximum tolerable doses on an empirical basis to all patients to minimize the risk of immunological injury leading to acute and/or chronic rejection. A refined approach based upon accurate monitoring of immune status would enable knowledgeable adjustment of immunosuppressive therapy, improving short- and long-term survival by abrogating graft injury and reducing the deleterious side effects of immunosuppression such as infection, malignancy, hypertension, hyperlipidemia, diabetes mellitus, renal failure, and bone loss. While the methods of the invention are described herein with respect to transplantation rejection, in alternative aspects the methods may be used to distinguish subsets of immunoreactive T cells involved in other immune responses, such as Graft versus Host disease, infections, cancer, autoimmune diseases, etc. Various alternative embodiments and examples of the invention are described herein. These embodiments and examples are illustrative and should not be construed as limiting the scope of the invention.

Cell Membranes Cell membranes may be obtained from any suitable source. For example, to detect immunoreactive T cells that recognize allo- or xeno-antigen in transplantation rejection, cell membranes may be obtained from donor-derived splenocytes (e.g., from cadavers) or peripheral blood mononuclear cells (e.g., living donors) to assess the direct pathway, and from host-derived dendritic cells (DCs) loaded with donor antigen to assess the indirect pathway. For example, membranes can be derived from APCs, such as dendritic cells or macrophages, from a subject, which have been loaded with self or foreign antigens by culturing with protein antigens, bacterial or viral proteins or by gene transduction. A sustained long-term source of donor-derived cells may involve for example Epstein Barr virus immortalization of splenic or peripheral blood B cells. For example, for distinguishing alloreactive T cells recognizing alloantigen through the indirect pathway, membranes can be isolated from DCs generated from recipient peripheral blood mononuclear cells by culture in GM-CSF and IL-4 for 6 days and loaded with apoptotic donor cells [49]. Murine CDllc+ DCs may be isolated from spleen and loaded with osmotically shocked splenocytes [50] to generate DCs that are able to cross present cellular antigens to both CD4+ and CD8+ T cells. Isolated cell membrane fragments may be prepared using any method, for example hypotonic lysis, described herein or known in the art. Examples of such methods include, but are not limited to, those found in Current Protocols in Cell

Biology [51] or Jacobson and Branton [59]. For example, total cell membranes may be prepared by hypotonic lysis from donor cells and labeled using an orienting molecule (e.g., an antibody recognizing the intracellular domain of CD45). The membrane fragments may be coated onto a solid surface such as a microparticle or may be used in solution. A cell membrane orientation molecule may be bound to the inner surface of the cell membrane fragment. For example, membrane-coated microparticles may be prepared using EDC chemistry. EDC (1- Ethyl-3-(3-dimethylaminopropyl)-carbodiimide) is a water-soluble carbodiimide that can catalyze the formation of amide bonds between carboxylic acids or phosphates and amines by activating carboxyl or phosphate to form an O-urea derivative. EDC may be reacted with the carbonyl group of a polystyrene bead using standard techniques. The activated beads may be subsequently incubated with cell membranes to attach the membranes to the bead. Alternatively, membrane-coated microparticles may be prepared using microparticles (e.g., fluorescent and/or paramagnetic beads available from vendors such as Spherotech or Miltenyi) and coating isolated membrane fragments on the microparticles according to the manufacturer's instructions. A cell membrane orientation reagent may be used to orient the outer surface of the cell membrane away from the surface of the bead, thus making the cell membrane surface proteins accessible to immunoreactive cells. Membranes may be coupled with the microparticles at various concentrations e.g, any value between 0.1 to 1 ug/ul, 1-5 ug/ul, 5-10 ug/ul, or 1-10 mg/ml. Unbound sites on the microparticles may be blocked with FACS buffer. Membrane coated microparticles may be stored in FACS buffer or in glycerol containing buffer at -20°C or -80°C. Alternatively, membranes can be stored frozen, thawed and bounds to microparticles just prior to use. The membrane preparations may be substantially pure.

Membrane Orientation Reagents Any reagent or molecule (e.g., an antibody or a protein) capable of recognizing the intracellular domain of a cell surface transmembrane protein (e.g, CD antigens, MHC molecules, transporter proteins, adhesion molecules) or a protein associated with the inner surface of the cell membrane (e.g., spectrin, profilin) can be used to orient isolated membrane fragments on a surface such as a microbead or in solution. A reagent (e.g., an antibody or a protein) such as annexin V capable of binding a lipid expressed predominantly on the inner surface of the cell membrane (e.g., phosphatidylserine) can be used, or a protein capable of binding a inner cell membrane protein. A membrane orientation reagent recognizes molecules (e.g., proteins or lipids) on the inner or cytoplasmic surface of a cell membrane. Examples of such reagents include without limitation the following commercially available reagents: Annexin V (Sigma), Annexin V-FITC (BD Biosciences), Annexin V-beads (Miltenyi); antibodies against proteins associated with cytoplasmic side of plasma membrane e.g., antibodies against vinculin (Nova Castra Laboratories), spectrin (Abeam); antibodies against the intracellular domains of transmembrane proteins e.g., antibodies against CD45 intracellular domain (BD Biosciences), FAS receptor (Abeam), IL-10R (Santa Cruz), IL-21 intracellular domain (Sigma), CD20 (Diagnostic Biosystems), phosphotyrosine (BD Biosciences); proteins that bind to membrane associated proteins such as: SH2 or PTB containing proteins, She, Grb2, IRS-1,-2,-3, -4 that bind to phosphotyrosines; FADD, TRADD /

etc which contain death effector domains that bind to intracellular domains of Fas, or TNF receptor, proteins which specifically bind to membrane proteins such as the integrin-linked kinase which binds to the intracellular portion of the integrin receptor; pleckstrin homology domain containing proteins like Akt, PDK1, ILK, TAPPI, TAPP2, PEPP-3 , CKJP- 1 , FAPP- 1 which bind to inositol phospholipids, phosphatidylethanolamine binding proteins such as PEBP, RKTP which bind phosphatidylethanolamine which are found in the inner leaflet of the plasma membrane

T Cell Markers Various Cluster of Differentiation (CD) antigens and other surface molecules have been described to be expressed in a regulated manner in resting vs activated T cells (Table 1). The surface expression level of these molecules can be used to assess the activation state of the immunoreactive T cell population and quantify the antigen specific immune response in vivo. Many other surface expressed and intracellular proteins can also be used to assess T cell activation state by measuring expression levels (Tables 2 and 3; [52]). Transcriptome and proteome expression analyses of activated CD4+ and CD8+ T cells have identified genes/proteins whose expression levels are up or down regulated following T cell activation [67-78]. The expression level of surface molecules can be measured for example by standard surface staining with antibodies, while the expression level of intracellular molecules can be measured for example by intracellular staining techniques, measurement of RNA levels, or by any other method.

Assays A variety of assays may be performed to distinguish a subset of immunoreactive cells from a sample containing a heterogeneous population of cells. In some embodiments, any assay capable of directly distinguishing a subset of immunoreactive cells, i.e., without the necessity for first culturing the immunoreactive cells, is suitable. For example, in transplantation rejection, plasma membrane fragments prepared from either donor APC (to address the direct pathway) or from host APC pulsed with donor alloantigen (to address the indirect pathway) may be used to specifically interact with alloreactive recipient T cells through cognate T cell receptor: MHC interactions without a priori knowledge of the relevant alloantigen. Recipient T cells may be incubated with membranes, that may be labeled and/or bound to beads, for 60 min at 4°C in fluorescence activated cell sorting (FACS) buffer (phosphate buffered saline, or Hank's balanced salt solution containing 3% fetal bovine serum) and washed 3X with FACS buffer. Protein-A conjugated to a fluorochrome or to a fluorescent (or fluorescent and paramagnetic) microbead may then be added (lOμg/mL) for 30 min at 4°C. Cells may be washed again and analyzed by flow cytometry. Immunoreactive cells may be physically isolated or separated from the remainder of the population for example by FACS or by magnetic bead separation. Allospecificity of the T cells recognized by the isolated membrane fragments in solution or bound to beads may be assayed. The relative ability of the positive, negative, and unseparated populations to respond to stimulation by allogeneic APC can be assessed by for example a one-way mixed lymphocyte reaction (MLR). Any assay capable of physically isolating the immunoreactive cells may be used. If desired, the assays may further included assessing the activation state of immunoreactive cells by co-staining with antibodies specific for T cell activation markers such as those described herein or known in the art. Cells may be simultaneously stained with membrane coated beads and antibodies to T cell specific markers. The expression level of the RNAs encoding the T cell marker molecules may be analysed. Membrane fragment coated bead bound immunoreactive cells or membrane bound immunoreactive cells can be co-stained with antibodies to cell surface markers to allow immunophenotyping of the immunoreactive cells. This may allow determination of the activation status of the cell (e.g., CD69 cells) as well as the class (e.g., CD4+ vs CD8+) and/or subset (Thl, Th2, Tr) of the immunoreactive T cells. For example, Tim-3 [53] may be used to identify immunoreactive Thl cells; ST2L [54] may be used to identify immunoreactive Th2 cells; EL-15R may be used to identify immunoreactive Trl cells; GITR and/or CTLA-4 [55] may be used to identify immunoreactive CD25+ Tr cells; FoxP3 [65] may be used to identify immunoreactive CD25+, CD4+ Tr cells. Where appropriate, the assays may include intracellular staining of membrane coated bead bound immunoreactive cells or membrane bound immunoreactive cells e.g., for FoxP3 staining. For example, T cells may be first stained with membrane fragment coated beads or isolated membrane fragments and cross-linked with formaldehyde which both cross-links the bead to the cells and fixes the cell prior to saponin permeabilization for staining of intracellular proteins. To generate cells of the required phenotype for testing, in vitro MLRs may be set up under conditions favoring generation of each cell type. For example, for basal alloreactive T cells (-1% in an unchallenged animal [55]), syngeneic stimulators may be used, and the cells may be co-stained for CD4 or CD8; for elevated expression of alloreactive T cells, allogeneic stimulators may be used, and the cells may be co-stained for CD4 or CD8; to enhance the proportion of Thl alloreactive T cells, IL-12 may be added, and the cells may be co-stained for Tim-3; to enhance the proportion of Th2 alloreactive T cells, IL-4 may be added, and the cells may be co-stained for ST2L; to enhance the proportion of Trl alloreactive T cells, IL-10 may be added, and the cells may be co- stained for IL-15R; to enhance the proportion of CD25+ Tr cells, culture may be initiated with purified CD25+CD4+ cells, and the cells may be co-stained for one or more of GITR, FoxP3, CTLA-4. Expression analysis of mRNA levels of the T cell markers described herein or known in the art may be used. Alternatively or additionally, the numbers or percentages of immunoreactive cells present in a heterogeneous population of cells may be quantified.

Animal Models Any suitable animal model for studying immune function or for providing a model for a condition in which immune responses are involved may be used. Such conditions include cell, tissue, or organ transplantation, cancers, autoimmune diseases, pathogenic infections, etc. Animals, e.g., rodents (mice, rats, guinea pigs, etc.) or other non-human animals are available from a variety of commercial sources . suc as The Jackson Laboratories, Bar Harbor, ME, USA; Harlan, IN, USA, etc. Exemplary use of animal models include, for example in transplantation rejection, the introduction of an allograft in to a non-immunosuppressed animal stimulates the activation and proliferation of alloreactive T cells. This increase in alloreactive T cell numbers can be monitored using the methods of the invention. For example, a murine islet transplant model or a skin transplant model can be used for monitoring alloreactive T cells. In the islet transplant model, graft infiltrating cells can be recovered from the graft with relative ease, allowing comparison of alloreactive cells present for example in peripheral blood with the graft tissue. For example, transplantation of C57BL/6 (H-2b) islets into Balb/C (H-2d) recipients results in loss of the graft by -23 days [56]. Administration of the global immunosuppressive agent rapamycin at 0.3 mg/kg/day protects against graft rejection [57]. On the other hand, treatment with a combination of 1 alpha, 25- Dihydrozyvitamin D3 (l,25(0h)2D3) and mycophenolate mofetil (MMF) generates allospecific transplantation tolerance [58]. Tolerance can be transferred by adoptive transfer of CD25+CD4+ cells into naive mice which protects against islet allografts of the same donor (C57BL/6) but not from a third party donor. Thus, alloreactive cells which contribute to graft rejection (no drug: CD8+, CD4+ Thl, CD4+ Th2), inhibition of development of those cells (rapamycin), or graft tolerance ((l,25(0h)2D3 MMF: CD25+CD4+ Tr cells) may be detected and identified.

Applications and Uses Methods according to the invention may be used for monitoring the progression of transplantation rejection; prognosing transplantation rejection; selecting a subject for an anti-transplantation rejection therapy; monitoring the efficacy of an anti-transplantation rejection therapy; screening a candidate compound for treating transplantation rejection; for monitoring the progression of an immune response against a foreign pathogen; for monitoring an autoimmune response; for monitoring an anti-tumour response; for monitoring efficacy of a vaccine; for monitoring efficacy of an anti-autoimmune disease therapy; for prognosing an autoimmune disease; for prognosing an infectious disease; for prognosing cancer immunity; for identification and isolation of a subset of T cells (e.g., antigen specific regulatory T cells, cytotoxic T cells, helper T cells, and memory T cells); for screening a candidate compound for treating an autoimmune disease; for screening a candidate compound for treating an infectious disease; for isolating an anti-tumour specific T cell for expansion and transplantation for cancer therapy; isolating an antigen specific T cell for cellular transplantation therapy for treatment of infection diseases; depleting an alloreactive T cell for bone marrow transplantation; depleting an antigen specific T cell for autoimmune diseases; and/or depleting a regulatory T cell to enhance anti-tumour immunity. For example, for monitoring the progression of transplantation rejection or for prognosing transplantation rejection or for monitoring the efficacy of a transplantation therapy (e.g., immunosuppressive therapy), a sample (e.g., a peripheral blood sample) including a heterogeneous population of T lymphocytes derived from a transplant recipient may be contacted with an isolated cell membrane fragment (including a major histocompatibility complex molecule) derived from a transplant donor, at multiple time points after transplantation and determining whether there is any change in the number, characteristics, or proportions of alloreactive or xenoreactive T lymphocytes over a period of time, where an increase in the number of the reactive T lymphocytes may indicate transplantation rejection, or a poor prognosis, or an inefficacious therapy, and a decrease in the number of reactive T lymphocytes may indicate accomodation, a good prognosis, or an efficacious therapy. Similarly, a change in the number, characteristics, or proportions of alloreactive or xenoreactive T lymphocytes when compared to those from a syngeneic control, for example, may assist in selecting a subject for an anti-transplantation therapy, or for prognosing transplantation rejection. The methods of the invention may also be used for screening a candidate compound for treating transplantation rejection. For example, a transplant recipient (e.g., an experimental animal) may be administered a test compound and a sample including a heterogeneous population of T lymphocytes derived from the transplant recipient may be contacted with an isolated cell membrane fragment (including a major histocompatibility complex molecule) derived from the transplant donor, and any change in the number, characteristics, or proportions of alloreactive or xenoreactive T lymphocytes (depending on the type of transplantation) may be determined. The results may be compared to suitable controls, such as a transplant recipient that has not been administered the test compound and/or a non-transplant recipient that has been administered the test compound, and an increase in the number of the reactive T lymphocytes may indicate an inefficacious compound, and a decrease in the number of reactive T lymphocytes may indicate a candidate compound for transplantation rejection therapy. Similarly, the methods of the invention may be used in connection with other conditions that involve immune responses, such as autoimmune diseases. For example, for monitoring the progression of an autoimmune disease or for prognosing an autoimmune disease or for monitoring the efficacy of anti-autoimmune disease therapy, a sample (e.g., a peripheral blood sample) including a heterogeneous population of T lymphocytes derived from a patient suffering from an autoimmune disease or at risk for an autoimmune disease may be contacted with an isolated cell membrane fragment (including a major histocompatibility complex molecule) derived from the patient, at multiple time points and determining whether there is any change in the number, characteristics, or proportions of autoreactive T lymphocytes over a period of time, where an increase in the number of the autoreactive T lymphocytes may indicate autoimmune disease progression, or a poor prognosis, or an inefficacious therapy, and a decrease in the number of reactive T lymphocytes may indicate regression, or a good prognosis, or an efficacious therapy. Similarly, a change in the number, characteristics, or proportions of autoreactive T lymphocytes when compared to those from a control that does not have the autoimmune disease, for example, may assist in selecting a subject for an anti-autoimmune disease therapy, or for prognosing autoimmune disease. The methods of the invention may also be used for screening a candidate compound for treating autoimmune disease. For example, a subject with an autoimmune disease (e.g., an animal model for an autoimmune disease e.g. EAE) may be administered a test compound and a sample including a heterogeneous population of T lymphocytes derived from the subject may be contacted with an isolated cell membrane fragment (including a major histocompatibility complex molecule) also derived from the subject, and any change in the number, characteristics, or proportions of autoreactive T lymphocytes may be determined. The results may be compared to suitable controls, such as a subject that has not been administered the test compound and/or a non-autoimmune disease subject that has been administered the test compound, and an increase in the number of the reactive T lymphocytes may indicate an inefficacious compound, and a decrease in the number of reactive T lymphocytes may indicate a candidate compound for autoimmune disease therapy. Similarly, the methods of the invention may be used in connection with other conditions that involve immune responses, such as immune responses against foreign pathogens, or immune responses against tumors, or monitoring vaccination efficacy, or enhancing anti-tumor immunity. The choice of source of the sample including a heterogeneous population of T lymphocytes and of isolated cell membrane fragment (including a major histocompatibility complex molecule) and antigen may be determined depending upon the specific condition. EXAMPLES Example 1: CD3+ T Cells Are Bound By Fluorescent Beads Coated With Plasma Membranes Plasma membranes were prepared from mouse spleen cells by hypotonic lysis from red cell depleted splenocytes. Briefly,cells were resuspended in a hypotonic lysis buffer containing protease inhibitors, homogenized with a dounce homogenizer and passaged 3X through 26 ga needles. Unbroken cells and nuclei were pelleted by centrifugation at 600Xg. The supernatant was then layered over a 41% sucrose cushion and ultracentrifuged at lOOOOOXg for lhr. Plasma membranes were isolated from the top of the sucrose layer and concentrated by another high speed spin. Plasma membranes were then resuspended by pipetting into ice cold buffer. Membranes were covalently coupled onto fluorescent microspheres (Spherotech, Inc., Libertyville, IL, USA) (protein A modified, coated with anti-CD45 intracellular domain antibody for two hours at 4°C. Membrane-coated beads were then incubated (luL of a 20% slurry) with 300,000 purified CD3+ lymphocytes for 1 hr at 4'C. Cells were washed 3 times prior to analysis by flow cytometry. Beads coated with membranes prepared from Balb/C or C57BL/6 splenocytes were then tested for their interaction with Balb/C T cells. Results are representative of three separate membrane preparations and three independent T cells staining experiments. As shown in Figure 1 A, 7.7% of Balb/C T cells reacted with the allogeneic C57BL/6 membrane coated beads while only 0.15% of the Balb/C T cells were stained by the Balb/C membrane coated beads.

Example 2: CD3+ T Cells Are Bound By Fluorescent Plasma Membranes Total cell membranes were prepared by hypotonic lysis from donor cells and labeled using an orienting antibody (e.g, an antibody recognizing the intracellular domain of CD45). Recipient T cells were then incubated with labeled membranes for 60 min at 4°C in FACS buffer (phosphate buffered saline, or Hank's balanced salt solution containing 3% fetal bovine serum) and washed 3X with FACS buffer. Protein-A conjugated to a fluorochrome (Protein- A-FITC, Sigma) was then added (lOμg/mL) for 30 min at 4°C. Cells were washed again and analyzed by flow cytometry. Membranes from C57BL/6 (syngeneic) and Balb/C (allogeneic) splenocytes were labeled with an antibody directed against the intracellular domain of CD45 as described herein. CD3+ T cells from C57BL/6 mice were stained with either syngeneic or allogeneic membranes and the percentage of alloreactive cells were detected using protein A-FITC and flow cytometry (Figure IB). The results indicated that more T cells bound allogeneic membranes when compared to syngeneic membranes.

Example 3: C57BL/6 Splenocytes and CD3+ T cells Are Bound By Paramagnetic Fluorescent Beads Coated With Plasma Membranes Membranes were prepared by hypotonic lysis from red cell depleted C57BL/6 or Balb/C splenocytes and covalently coupled onto paramagnetic fluorescent microspheres (Spherotech) using EDC chemistry. Membrane-coated beads were then incubated with C57BL/6 splenocytes or purified CD3+ T lymphocytes. CD3+ T lymphocytes were purified using the StemSep™ Mouse CD3 negative selection kit (StemCell Technologies). Cells were washed prior to analysis by flow cytometry. Beads coated with membranes prepared from Balb/C or C57BL/6 splenocytes were then tested for their interaction with C57BL/6 splenocytes (Figure 1C) or purified CD3+ T lymphocytes (Figure ID). The results indicated that under these conditions the EDC prepared beads provided better discrimination between allogeneic and syngeneic membranes when purified CD3+ T lymphocytes were used.

Example 4: Detection of a T cell activation marker in alloreactive T cells in a mouse skin transplant model C57BL/6 mice were used as skin graft recipients of Balb/C (allogeneic) or

C57BL/6 (syngeneic) donor skin grafts. Allogeneic (Balb/C) membrane coated beads were made using a CD45 antibody as described herein. At day 5 after transplant, T cells (CD3+ cells) were isolated from the donor C57BL/6 mice (using the StemSep™ Mouse CD3 negative selection kit (StemCell

Technologies) and the activation status of the alloreactive population was assessed by co-staining with the allogeneic membrane coated beads and an antibody to CD69 (an activation marker of T cells; CD69-PE, BD Biosciences). The results indicated that the percentage of CD69 positive cells in the allogeneic membrane coated bead population was significantly higher in the mice receiving the allogeneic transplant compared to the mice receiving the syngeneic transplant (Figure 2). Thus, alloreactive cells express more CD69 antigen in mice exposed to alloantigen and measuring the activation state of the alloreactive T cell population enables monitoring the anti-graft immune status of the recipient at an early stage, since at day 5, no visible graft damage had yet occurred (this generally happens at days 9-10) [66] but the developing anti-graft immune response was detectable.

Example 5: Detection of the development of an alloreactive (anti-graft response) in a mouse skin transplant model Skin was harvested from the tails of Balb/C mice and grafted onto the dorsal upper thorax of recipient C57BL/6 mice using standard procedures and the mice allowed to recover for 6 or 10 days. T cells were then isolated from the spleens of Balb/C, untransplanted C57BL/6 mice, or from C57BL/6 mice transplanted with Balb/C skin grafts 6 or 10 days earlier using the StemSep™ Mouse CD3 negative selection kit (StemCell Technologies). The percentage of alloreactive T cells in the population was then determined by assessing the number of T cells which bound to Balb/C (alloantigen) derived membrane bound-beads.

Balb/C derived membrane coated beads bound to 3% of T cells isolated from naive C57BL/6 mice and this alloreactive T cell population increased in number in mice transplanted with Balb/C skin grafts (Figure 3). Alloreactive T cells composed 5% of the population 6 days after transplantation and rose further to 8% 10 days after transplantation (Figure 3). Thus, the introduction of an allograft into a non- immunosuppressed animal stimulated the activation and proliferation of alloreactive T cells. This increase in alloreactive T cell numbers could be monitored.

Example 6: Discrimination of Alloreactive T cells in Humans Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll density centrifugation from donor A and donor B. CD4+ T cells obtained using the EasySep™ Human CD4 negative selection kit (StemCell Technologies) were also isolated from donor A for analysis using membrane coated beads generated from either donor A (control membrane coated beads) or donor B (allogeneic membrane coated beads). Beads were prepared using the CD45 antibody based orientating method and fluorescent microbeads as described herein. Alloreactive membrane coated beads reacted with a greater number of T cells than control (syngeneic) membrane coated beads as determined by flow cytometry (Figure 4).

Example 7: Discrimination of Alloreactive T cells in a Mouse Islet Transplant Model Pancreatic islet cells are isolated from C57BL/6 mice [60] and transplanted under the kidney capsule of Balb/C recipients. Drug administration is begun peritransplant. Mice are monitored for a total of 10 weeks. Peripheral blood (150 ul) is drawn weekly from the saphenous vein. Weekly cohorts of mice have their islet allograft removed for histological examination of graft status and also to isolate graft infiltrating cells [61]. Peripheral blood mononuclear cells and graft infiltrating lymphocytes are subjected to staining with donor (C57BL/6) membrane coated beads. The nature of the alloreactive cells is determined by immunophenotyping or RNA expression analysis for T cell subset specific markers. Elevated levels (greater than the basal estimate of 7.7%) of alloreactive T cells i.e., CD8+, CD4+Thl, CD4+Th2 cells, are detected in the no drug treated group. These elevated levels are reduced by rapamycin treatment. To generate a graft rejection episode, drug is withdrawn from one group of rapamycin treated mice 4 weeks after transplantation to trigger rejection. Relative levels of alloreactive cells detected in peripheral blood vs. those isolated from the islet graft are compared and correlated with histological evaluation of graft destruction. The appearance of alloreactive T cells in the peripheral blood is used to predict graft immune injury. l,25(OH)2D3/MMF-treated mice develop long term alloantigen tolerance associated with expansion of the alloreactive CD25+CD4+ Tr population. Alloreactive T cells from peripheral blood and graft infiltrating cells are analyzed by immunophenotyping or RNA expression analysis for markers of CD25+CD4+ Tr cells (e.g., FoxP3, GITR). Example 8: Discrimination of Alloreactive T cells in Transplant Patients Membrane coated beads are used to monitor the nature of the alloreactive cells in the peripheral blood of liver transplant recipients [62,63]. A sample of donor spleen is removed at the time of liver organ retrieval. Alloreactive T cells of immunostimulatory phenotype associated with rejection episodes [64], as well as Tr cells, are detected. The presence of Tr cells may vary inversely with rejection, and may be present in limited numbers. If, in an individual patient, the number of immunostimulatory alloreactive T cells are below a certain threshold, immunosuppressive therapy may be adjusted.

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OTHER EMBODIMENTS Although various embodiments of the invention are disclosed herein, many adaptations and modifications may be made within the scope of the invention in accordance with the common general knowledge of those skilled in this art. Such modifications include the substitution of known equivalents for any aspect of the invention in order to achieve the same result in substantially the same way. Accession numbers, as used herein, refer to Accession numbers from multiple databases, including GenBank, the European Molecular Biology Laboratory (EMBL), the DNA Database of Japan (DDBJ), or the Genome Sequence Data Base (GSDB), for nucleotide sequences, and including the Protein Information Resource (PER), SWISSPROT, Protein Research Foundation (PRF), and Protein Data Bank (PDB) (sequences from solved structures), as well as from translations from annotated coding regions from nucleotide sequences in GenBank, EMBL, DDBJ, or RefSeq, for polypeptide sequences. Numeric ranges are inclusive of the numbers defining the range. In the specification, the word "comprising" is used as an open-ended term, substantially equivalent to the phrase "including, but not limited to", and the word "comprises" has a corresponding meaning. Citation of references herein shall not be construed as an admission that such references are prior art to the present invention. All publications are incorporated herein by reference as if each individual publication were specifically and individually indicated to be incorporated by reference herein and as though fully set forth herein. The invention includes all embodiments and variations substantially as hereinbefore described and with reference to the examples and drawings.

Claims

WHAT IS CLAIMED IS:

1. A method for distinguishing a subset of immunoreactive T lymphocytes comprising: contacting a sample comprising a heterogeneous population of lymphocytes derived from a first subject with an isolated cell membrane fragment comprising a major histocompatibility complex molecule, the isolated cell membrane fragment and the major histocompatibility complex molecule being derived from a second subject; and distinguishing a subset of T lymphocytes in the sample that binds to the major histocompatibility complex, wherein the subset of T lymphocytes that bind to the major histocompatibility complex are immunoreactive T lymphocytes.

2. A method for distinguishing a subset of immunoreactive T lymphocytes comprising: contacting a sample comprising a heterogeneous population of lymphocytes derived from a first subject with an isolated cell membrane fragment comprising a major histocompatibility complex molecule, the isolated cell membrane fragment and the major histocompatibility complex molecule being derived from the first subject, in combination with an antigen derived from a second subject; and distinguishing a subset of T lymphocytes in the sample that binds to the major histocompatibility complex, wherein the subset of T lymphocytes that bind to the major histocompatibility complex are immunoreactive T lymphocytes.

3. A method for distinguishing a subset of immunoreactive T lymphocytes comprising: contacting a sample comprising a heterogeneous population of lymphocytes derived from a subject with an isolated cell membrane fragment comprising a major histocompatibility complex molecule, the isolated cell membrane fragment and the major histocompatibility complex molecule being derived from the subject; and distinguishing a subset of T lymphocytes in the sample that binds to the major histocompatibility complex, wherein the subset of T lymphocytes that bind to the major histocompatibility complex are immunoreactive T lymphocytes.

4. The method of any one of claims 1 through 3 wherein the distinguishing comprises quantifying the subset of T lymphocytes in the sample that bind to the major histocompatibility complex.

5. The method of any one of claims 1 through 4 wherein the distinguishing comprises isolating the subset of T lymphocytes in the sample that bind to the major histocompatibility complex.

6. The method of any one of claims 1 through 5 wherein the immunoreactive T lymphocytes are CD3+ T lymphocytes.

7. The method of any one of claims 1 through 6 wherein the isolated cell membrane fragment is coated on a solid support.

8. The method of claim 7 wherein the solid support is a microbead.

9. The method of any one of claims 1 through 8 wherein the isolated cell membrane fragment is detectably labeled.

10. The method of any one of claims 1 through 9 wherein the isolated cell membrane fragment is oriented using a cell membrane orientation reagent.

11. The method of claim 10 wherein the cell membrane orientation reagent is a CD45 antibody that specifically binds the intracellular domain of CD45.

12. The method of any one of claims 1 through 11 wherein the first subject is a transplant recipient.

13. The method of any one of claims 1 through 12 wherein the second subject is a transplant donor.

14. The method of any one of claims 1 through 13 wherein the immunoreactive T lymphocyte is an alloreactive T lymphocyte.

15. Use of the method of any one of claims 1 through 14 for: monitoring the progression of transplantation rejection; prognosing transplantation rejection; selecting a subject for an anti- transplantation rejection therapy; monitoring the efficacy of an anti- transplantation rejection therapy; screening a candidate compound for treating transplantation rejection; for monitoring the progression of an immune response against a foreign pathogen; for monitoring an autoimmune response; for monitoring an anti-tumour response; for monitoring efficacy of a vaccine; for monitoring efficacy of an anti- autoimmune disease therapy; for prognosing an autoimmune disease; for prognosing an infectious disease; for prognosing cancer immunity; for identification and isolation of a subset of T cells; for screening a candidate compound for treating an autoimmune disease; for screening a candidate compound for treating an infectious disease; for isolating an anti-tumour specific T cell; isolating an antigen specific T cell; depleting an alloreactive T cell; depleting an antigen specific T cell; or depleting a regulatory T cell.

16. The use of claim 15 wherein the subset of T cells is selected from any one or more of the group consisting of antigen specific regulatory T cells, cytotoxic T cells, helper T cells, and memory T cells.