Identification of gene expression profile in tolerizing murine cardiac allograft by costimulatory blockade

Array-based methods for diagnosis and prevention of transplant rejection

DNA microarray is a microhybridization-based assay that is used to simultaneously study the expression of thousands of genes, thus providing a global view of gene expression in a tissue sample. This powerful technique has been adopted by many biomedical disciplines and will likely have a profound impact on the diagnosis, treatment and prognosis of human diseases. This review article presents an overview of the application of microarray technology to the field of solid-organ transplantation.

An effective immune-monitoring protocol based on gene expression profiles in the peripheral T-cell fraction reactive to graft antigens

BACKGROUND

The ability to induce tolerance, or at least minimize the need for immunosuppressive therapy, is a high priority in organ transplantation. Accomplishing this goal requires a novel method for determining when a patient has become tolerant to or is rejecting their graft. Here, we sought to develop an efficient monitoring protocol based on gene expression profiles of recipient T cells in murine skin and islet allograft models.

METHODS

Unlike previous studies, here, gene expression analysis was focused on donor antigen-reactive T cells, which were prepared by collecting CD69(+) T cells from cocultures of recipient peripheral T cells and donor antigen-presenting cells. Candidate tolerance and rejection biomarker genes were selected from a CD69(+) T-cell microarray analysis, and their expression levels were measured in the recipient CD69(+) T-cell fraction using quantitative reverse transcription polymerase chain reaction.

RESULTS

Our new monitoring protocol was capable of precisely detecting the immune status of recipients relative to their graft regardless of the organ received, whether they were taking immunosuppressive drugs, or different strains of origin.

CONCLUSIONS

Gene expression analysis focusing on recipient CD69(+) T cells as the donor antigen-reactive T-cell population could be used as an effective and sensitive method for monitoring transplant patients.

Gene expression profiling in organ transplantation

Aim of Review. Huge effort is being made among the transplant community investigating novel biomarkers that enable transplant clinicians to identify patients at risk for allograft rejection or those who will develop tolerance so that immunosuppression could be safely minimized or even ideally withdrawn. Despite the important advances achieved in the identification of several potential biomarkers of tolerance, rejection, or both, validation and demonstration of their clinical utility still needs to be tested, which will need international cooperative networks. It is important to note that the reproducibility of differently expressed genes might be affected by many factors such as gene ranking and selection methods, inherent differences between types, and the choice of thresholds. However, because microarray analyses are expensive and time consuming and their statistical evaluation is often very difficult, gene expression analysis using the RTPCR method is nowadays recommended. Conclusions. In the field of organ transplantation, gene-expression-based decision might help in improving patient and graft outcome and there are a multitude of studies showing that gene-expression profiling is feasible.

Graft-infiltrating cells expressing a CD200 transgene prolong allogeneic skin graft survival in association with local increases in Foxp3(+)Treg and mast cells

Expression of the molecule CD200 has been reported to increase allograft survival by suppression of inflammation and acquired immunity. In previous studies we have shown that increased skin and cardiac allograft survival in transgenic mice over-expressing CD200 (CD200(tg)) occurs in association with increased intra-graft expression of mRNAs for genes associated with altered T cell subset differentiation. We investigated changes in graft-infiltrating cells, Treg and mast cells in skin grafts post transplantation into control or CD200(tg) mice, using focused gene array and real-time PCR to assess altered gene expression, and FACS, immunohistology and MLC to determine numbers/function of those cells. Graft-infiltrating cells isolated from CD200(tg) recipients suppressed induction of CTL from control lymph node cells in vitro, and contained increased numbers of infiltrating, non-degranulating, mast cells and Foxp3(+)Treg. Mast cells were also evident in graft tissue of control animals, but there these cells showed evidence for degranulation, and fewer Foxp3(+)Treg were present than was the case of CD200(tg) mice. The infusion of a competitive inhibitor of CD200:CD200R interactions, CD200(tr), at high concentrations (50μg/mouse iv) caused rapid rejection of grafts in CD200(tg) mice, mast cell degranulation within graft tissue, and a decrease in Treg infiltrates. These effects were attenuated by simultaneous infusion of the mast cell stabilizer, sodium cromoglycate. We conclude that CD200 expression contributes to graft prolongation through local suppression of mast cell degranulation, attraction/expansion of Treg, and attenuation of T cell effector activation.

Alternatively Expressed Genes Identified in the CD4+ T Cells of Allograft Rejection Mice

Allograft rejection is a leading cause for the failure of allotransplantation. CD4+ T cells play critical roles in this process. The identification of genes that alternatively expressed in CD4+ T cells during allograft rejection will provide critical information for studying the mechanism of allograft rejection, finding specific gene markers for monitoring, predicting allograft rejection, and opening new ways to regulate and prevent allograft rejection. Here, we established allograft and isograft transplantation models by adoptively transferring wild-type BALB/c mouse CD4+ T cells into severe combined immunodeficient (SCID) mice with a C57BL/6 or BALB/c mouse skin graft. Using the whole transcriptome sequencing-based serial analysis of gene expression (SAGE) technology, we identified 97 increasingly and 88 decreasingly expressed genes that may play important roles in allograft rejection and tolerance. Functional classification of these genes shows that apoptosis, transcription regulation, cell growth and maintenance, and signal transduction are among the frequently changed functional groups. This study provides a genome-wide view for the candidate genes of CD4+ T cells related to allotransplantation, and this report is a good resource for further microarray studies and for identifying the specific markers that are associated with clinical organ transplantations.

Expression of a CD200 transgene is necessary for induction but not maintenance of tolerance to cardiac and skin allografts

CD200, a type 2 transmembrane molecule of the Ig supergene family, can induce immunosuppression in a number of biological systems, as well as promote increased graft acceptance, following binding to its receptors (CD200Rs). Skin and cardiac allograft acceptance are readily induced in transgenic mice overexpressing CD200 under control of a doxycycline-inducible promoter, both of which are associated with increased intragraft expression of mRNAs for a number of genes associated with altered T cell subset differentiation, including GATA-3, type 2 cytokines (IL-4, IL-13), GITR, and Foxp3. Interestingly, some 12-15 days after grafting, induction of transgenic CD200 expression can be stopped (by doxycycline withdrawal), without obvious significant effect on graft survival. However, neutralization of all CD200 expression (including endogenous CD200 expression) by anti-CD200 mAb caused graft loss, as did introduction of an acute inflammatory stimulus (LPS, 10 microg/mouse, delivered by i.p. injection). We conclude that even with apparently stably accepted tissue allografts, disruption of the immunoregulatory balance by an intense inflammatory stimulus can cause graft loss.

Dextran sulfate facilitates anti-CD4 mAb-induced long-term rat cardiac allograft survival after prolonged cold ischemia

Ischemia/reperfusion injury leads to activation of graft endothelial cells (EC), boosting antigraft immunity and impeding tolerance induction. We hypothesized that the complement inhibitor and EC-protectant dextran sulfate (DXS, MW 5000) facilitates long-term graft survival induced by non-depleting anti-CD4 mAb (RIB 5/2). Hearts from DA donor rats were heterotopically transplanted into Lewis recipients treated with RIB 5/2 (20 mg/kg, days-1,0,1,2,3; i.p.) with or without DXS (grafts perfused with 25 mg, recipients treated i.v. with 25 mg/kg on days 1,3 and 12.5 mg/kg on days 5,7,9,11,13,15). Cold graft ischemia time was 20 min or 12 h. Median survival time (MST) was comparable between RIB 5/2 and RIB 5/2+DXS-treated recipients in the 20-min group with >175-day graft survival. In the 12-h group RIB 5/2 only led to chronic rejection (MST = 49.5 days) with elevated alloantibody response, whereas RIB 5/2+DXS induced long-term survival (MST >100 days, p < 0.05) with upregulation of genes related to transplantation tolerance. Analysis of the 12-h group treated with RIB 5/2+DXS at 1-day posttransplantation revealed reduced EC activation, complement deposition and inflammatory cell infiltration. In summary, DXS attenuates I/R-induced acute graft injury and facilitates long-term survival in this clinically relevant transplant model.

Intragraft gene expression profile associated with the induction of tolerance

Background

Xenotransplantation holds the promise of providing an unlimited supply of donor organs for terminal patients with organ failure. Pre-existing natural antibodies to the Galα1,3Galβ1,4GlcNac-R (αGal) carbohydrate xenoantigen, however, bind rapidly to the graft endothelium and initiate hyperacute rejection of wild type pig grafts in humans. Experimental procedures designed to prevent xenoantibody-mediated rejection have been tested in gal knockout mice. These mice produce anti-gal xenoantibodies and are widely used as small animal models for xenotransplantation research. In this model, chimerism for cells expressing the gal carbohydrate can be achieved by transplantation of mixed cells or by transduction of bone marrow cells with viral vectors expressing a functional α1,3 galactosyltransferase gene. Chimerism induces tolerance to heart grafts expressing αGal. The mechanisms by which tolerance is achieved include systemic changes such as clonal deletion and/or anergy. Intragraft changes that occur during the early stages of tolerance induction have not been characterized.

Results

Cytoprotective genes heme oxygenase-1 (HO-1), Bcl2, and A20 that have been reported to contribute to long-term graft survival in various models of accommodation were not expressed at high levels in tolerant heart grafts. Intragraft gene expression at both early (Day 10) and late (>2 month) time points after heart transplant were examined by real-time PCR and microarray analysis was used to identify changes associated with the induction of tolerance. Intragraft gene expression profiling using microarray analysis demonstrated that genes identified in the functional categories of stress and immunity and signal transduction were significantly up-regulated in early tolerant grafts compared with syngeneic control grafts. Biological process classification showed lower binomial p-values in the categories of "response to biotic stimulus, defense response, and immune response" suggesting that up-regulated genes identified in these grafts promote survival in the presence of an immune response. The expression of the incompatible carbohydrate antigen (αGal) was reduced by 2 months post-transplant when compared with the expression of this gene at Day 10 post-transplant. These results suggest that the gal carbohydrate antigen is downmodulated over time in grafts that demonstrate tolerance.

Conclusion

Our study suggests that tolerance is associated with intragraft gene expression changes that render the heart resistant to immune-mediated rejection. Genes associated with stress and immunity are up-regulated, however cytoprotective genes HO-1, Bcl2 and A20 were not up-regulated. The expression of the gal carbohydrate, the key target initiating an immune response in this model, is down-regulated in the post-transplant period.

Identification of gene markers for the prediction of allograft rejection or permanent acceptance

The clinical success of new treatment strategies aiming on inducing permanent graft acceptance will rely on the ability to determine whether specific unresponsiveness to donor alloantigens has developed and for how long it is maintained. To identify markers for such posttransplant monitoring, genes differentially expressed by graft infiltrating leukocytes during tolerance induction or rejection after kidney transplantation in rats were compared. A subsequently performed full kinetic analysis in two different transplant models, kidney and heart, in two species, rat and mouse identified two markers (TOAG-1, alpha-1,2-mannosidase) with high specificity and reproducibility, which are highly expressed during induction and maintenance of acceptance, and downregulated during rejection. Expression level of these markers showed a strong positive correlation with graft function. In addition, expression of both genes was downregulated in the peripheral blood and the graft prior to rejection, suggesting that these markers may be useful for monitoring in clinical transplantation where peripheral blood is the most easily accessible patient sample. Interestingly, downregulation of TOAG-1 and alpha-1,2-mannosidase expression occurred in graft infiltrating cells and expression of both genes was also downregulated after T-cell activation in vitro.

Expression changes in tolerant murine cardiac allografts after gene therapy with a lentiviral vector expressing alpha1,3 galactosyltransferase

Comparison of intragraft gene expression changes in tolerant cardiac allograft models may provide the basis for identifying pathways involved in graft survival. Our laboratory has previously demonstrated that tolerance to the gal alpha1,3 gal epitope, the major target of rejection of wild-type pig hearts in human cardiac transplantation, can be achieved after transplantation with bone marrow transduced with a lentiviral vector expressing alpha1,3 galactosyltransferase. We now present intracardiac gene expression changes associated with long-term tolerance in this model. Biotin-labeled cRNA was hybridized to Affymetrix GeneChip 430 2.0 Mouse Genome Arrays. Data were subjected to functional annotation analysis to identify genes of known function in which expression was increased or decreased by at least 2-fold (t-test, P < .05) in tolerant gal+/+ wild-type hearts as compared to transplanted syngeneic controls. Tolerant hearts demonstrated increased expression of genes associated with the stress response, modulation of immune function and cell survival (HSPa9a, CD56, and Akt1s1), and decreased expression of several immunoregulatory genes (CD209, CD26, and PDE4b). These data suggest that tolerance may be associated with activation of immunomodulatory and survival pathways.

Novel insights into lung transplant rejection by microarray analysis

Gene expression microarrays can estimate the prevalence of mRNA for thousands of genes in a small sample of cells or tissue. Organ transplant researchers are increasingly using microarrays to identify specific patterns of gene expression that predict and characterize acute and chronic rejection, and to improve our understanding of the mechanisms underlying organ allograft dysfunction. We used microarrays to assess gene expression in bronchoalveolar lavage cell samples from lung transplant recipients with and without acute rejection on simultaneous lung biopsies. These studies showed increased expression during acute rejection of genes involved in inflammation, apoptosis, and T-cell activation and proliferation. We also studied gene expression during the evolution of airway obliteration in a murine heterotopic tracheal transplant model of chronic rejection. These studies demonstrated specific patterns of gene expression at defined time points after transplantation in allografts, whereas gene expression in isografts reverted back to that of native tracheas within 2 wk after transplantation. These studies demonstrate the potential power of microarrays to identify biomarkers of acute and chronic lung rejection. The application of new genetic, genomic, and proteomic technologies is in its infancy, and the microarray-based studies described here are clearly only the beginning of their application to lung transplantation. The massive amount of data generated per tissue or cell sample has spawned an outpouring of invention in the bioinformatics field, which is developing methodologies to turn data into meaningful and reproducible clinical and mechanistic inferences.

Microarrays: a monitoring tool for transplant patients?

Microarray technology holds a distinct advantage over traditional genomic methods, with the unique capability to rapidly generate multiple global gene expression profiles in parallel. This technology is quickly gaining widespread use in many areas of science and medicine because it can be easily adapted to study many experimental questions, particularly relating to disease heterogeneity. Microarray experiments have begun to advance our understanding of the underlying molecular processes in solid organ transplantation; however, several obstacles must be overcome before this technology is ready for application in the clinical setting. This article will review the current applications of microarray technology in the field of transplantation, and discuss the potential impact of this technology on monitoring of solid organ transplant recipients.

New evidence for a role of allograft accommodation in long-term tolerance

BACKGROUND

Progressively better therapies have largely prevented or at least effectively treated acute allograft rejection. Consequently, the long-term survival of solid organ transplants has increasingly become limited primarily by the development of chronic allograft rejection. The mechanisms of chronic rejection remain largely unknown and the induction of specific tolerance would be the ultimate achievement in transplant immunology. We previously demonstrated, in a fully major histocompatibility complex (MHC)-mismatched rat cardiac allograft combination, that a 20-day treatment with a deoxyspergualin (DSG) analogue, LF15-0195, induces allograft tolerance with the development of potent CD4CD25 regulatory T cells. In order to better characterize the mechanisms involved in allograft tolerance, we compared long-term tolerated allografts with allografts exhibiting signs of chronic rejection induced by donor-specific blood transfusion.

METHODS

We analyzed both types of allografts for infiltration, alloantibody production and gene expression by histology, exhaustive microarray and quantitative reverse-transcriptase polymerase chain reaction.

RESULTS

Interestingly, we observed in tolerated allografts an infiltrate as dense as the one observed in chronically rejected allografts and alloantibody deposits on graft endothelial cells. Prominent gene expression of many putative proinflammatory cytokines and genes related to cell activation or cytotoxicity were observed in tolerated allografts. However, we observed a specific upregulation of cytoprotective genes such as nitric oxide synthase, BclXL, and indoleamine 2,3 dioxygenase, and a poor in situ expression of immunoglobulin chain gene.

CONCLUSIONS

This study demonstrates a state of accommodation of tolerated allografts and suggests the importance of early control of humoral immunity for the prevention of chronic rejection and the maintenance of long-term tolerance.

Frontiers of immunological tolerance

Herein, we succinctly review mechanisms underlying self-tolerance and the roles of dendritic leukocytes (DCs) in T-cell tolerance to self and foreign antigens. We also consider the properties of naturally arising and other populations of regulatory T cells (Treg), together with growing evidence that interplay between DCs and Treg cells can sustain antigen-specific tolerance. B-cell tolerance and the role of hematopoietic cell chimerism in the induction and maintenance of tolerance are also discussed, as is the impact of cosignaling pathway manipulation on tolerance induction. This overview also surveys prospects for technological advances in the monitoring and prediction of tolerance and the application of genomic and proteomic analysis. In addition, we consider potential novel therapeutic targets for promotion of tolerance induction.

Molecular signature of mice T lymphocytes following tolerance induction by allogeneic BMT and CD40-CD40L costimulation blockade

Tolerance induction by mixed chimerism and costimulation blockade is a promising approach to avoid immunosuppression, but the molecular basis of tolerant T lymphocytes remains elusive. We investigated the genome-wide gene expression profile of murine T lymphocytes after tolerance induction by allogeneic bone marrow transplantation (BMT) and costimulatory blockade using the anti-CD40L antibody MR1. Molecular functions, biological processes, cellular locations, and coregulation of identified genes were determined. A total of 113 unique genes exhibited a significant differential expression between the lymphocytes of MR1-treated Tolerance (TOL) and untreated recipients Control (CTRL). The majority of genes upregulated in the TOL group are involved in several signal transduction cascades such as members of the MAPKKK cascade (IL6, Tob2, Stk39, and Dusp24). Other genes involved in lymphocyte differentiation and highly expressed in the TOL group are lymphotactin, the estrogen receptors (ERs) and the suppressor of cytokine signaling 7. Common transcription factors such as ER 1 alpha, GATA-binding protein 1, insulin promoter factor 1, and paired-related homeobox 2 could be identified in the promoter regions of upregulated genes in the TOL group. These data suggest that T lymphoctes of tolerant mice exhibit a distinct molecular expression profile, which needs to be evaluated in other experimental tolerance models to determine whether it is a universal signature of tolerance.

The promise of protein-based and gene-based clinical markers in heart transplantation: from bench to bedside

Advances in immunosuppression, guided by invasive endomyocardial biopsy for the assessment of graft rejection, have ushered heart transplantation into the clinical arena by the demonstration of acceptable 1-year outcomes. Further decreases in the risk of malignancy and cardiac allograft vasculopathy that improve long-term outcomes, are, however, still desired. Attention has become directed towards the use of markers that can be detected noninvasively to provide insight into underlying molecular and cellular events associated with the immune response and graft function. Various candidate, protein-based markers have been identified: those of alloimmune activation; those of microvascular injury, such as cardiac-specific troponins; those of inflammation, including C-reactive protein; and surrogate markers of cardiac function, including natriuretic peptides such as brain natriuretic peptide. In the realm of genomics, it is becoming increasingly clear that a single molecular marker is unlikely to prove to be useful, but rather that multiple genes from a number of pathways are needed to capture biological complexity and overcome variability in the general population. Thus, the field of protein-based and gene-based biomarkers is advancing rapidly to define its place in clinical therapeutics and to guide immunosuppression according to molecular mechanisms of disease. We discuss here the main findings for the more-successful protein markers identified so far, and the genomic molecular approaches being used to improve heart transplant outcomes.

[Appliance of microarray technology to clinical organ transplantation]

Although recent advances in immunosuppressive therapy have dramatically enhanced the early survival of solid organ transplant recipients, acute rejection still occurs in some recipients. Long-term immunosuppressive drug administration, furthermore, entails a number of potentially significant problems such as infection, spontaneous neoplasm and drug toxicity. Alloantigen specific tolerance induction is the ultimate goal in transplant immunology, and can be induced in a rodent model; however, the precise mechanism by which specific tolerance is affected are not clearly understood, and the current immunosuppression regimens have all failed to achieve this goal in a clinical setting. DNA microarray technology has made it possible to analyze the expression of a large number of genes and revolutionized many areas of biology and medicine. This new technology can provide non-biased, global expressions of tens of thousands of genes simultaneously. Recent studies on gene expression profiles in various diseases, including allograft rejection, have successfully provided important information and new insights into the biological mechanisms of these diseases. In this article, we reviewed these insights, especially with the viewpoint of appliance of microarray technology to clinical solid organ transplantation.

Arraying the orchestration of allograft pathology

Microarrays, or gene chips, are exciting investigative tools for analyzing expression changes across thousands of genes in concert in tissues and cells of interest. Despite the relatively recent application of microarrays to transplant research, they hold great promise for unraveling the staging of rejection, stratifying patients towards more individualized treatment regimes, and discovering noninvasive biomarkers for monitoring of intragraft events. Bioinformatics tools are being developed to sift through the large data sets generated as "genomic fingerprints" of the underlying biologic pathways. Gene clustering and class prediction tools allow discovery of diagnostic and prognostic molecular signatures of health and disease. Oligonucleotide-based microarrays also have utility in genotyping polymorphic markers. This report reviews the current literature of microarray use in transplantation research, compares currently available array platforms, and discusses future application of this technology to clinical organ transplantation.