Novel insights into lung transplant rejection by microarray analysis

Molecular monitoring of lung allograft health: is it ready for routine clinical use?

Maintenance of long-term lung allograft health in lung transplant recipients (LTRs) requires a fine balancing act between providing sufficient immunosuppression to reduce the risk of rejection whilst at the same time not over-immunosuppressing individuals and exposing them to the myriad of immunosuppressant drug side-effects that can cause morbidity and mortality. At present, lung transplant physicians only have limited and rather blunt tools available to assist them with this task. Although therapeutic drug monitoring provides clinically useful information about single time point and longitudinal exposure of LTRs to immunosuppressants, it lacks precision in determining the functional level of immunosuppression that an individual is experiencing. There is a significant gap in our ability to monitor lung allograft health and therefore tailor optimal personalised immunosuppression regimens. Molecular diagnostics performed on blood, bronchoalveolar lavage or lung tissue that can detect early signs of subclinical allograft injury, differentiate rejection from infection or distinguish cellular from humoral rejection could offer clinicians powerful tools in protecting lung allograft health. In this review, we look at the current evidence behind molecular monitoring in lung transplantation and ask if it is ready for routine clinical use. Although donor-derived cell-free DNA and tissue transcriptomics appear to be the techniques with the most immediate clinical potential, more robust data are required on their performance and additional clinical value beyond standard of care.

Corticotropin releasing hormone as an identifier of bronchiolitis obliterans syndrome

Lung transplantion (LTx) recipients have low long-term survival and a high incidence of bronchiolitis obliterans syndrome (BOS), an inflammation of the small airways in chronic rejection of a lung allograft. There is great clinical need for a minimally invasive biomarker of BOS. Here, 644 different proteins were analyzed to detect biomarkers that distinguish BOS grade 0 from grades 1–3. The plasma of 46 double lung transplant patients was analyzed for proteins using a high-component, multiplex immunoassay that enables analysis of protein biomarkers. Proximity Extension Assay (PEA) consists of antibody probe pairs which bind to targets. The resulting polymerase chain reaction (PCR) reporter sequence can be quantified by real-time PCR. Samples were collected at baseline and 1-year post transplantation. Enzyme-linked immunosorbent assay (ELISA) was used to validate the findings of the PEA analysis across both time points and microarray datasets from other lung transplantation centers demonstrated the same findings. Significant decreases in the plasma protein levels of CRH, FERC2, IL-20RA, TNFB, and IGSF3 and an increase in MMP-9 and CTSL1 were seen in patients who developed BOS compared to those who did not. In this study, CRH is presented as a novel potential biomarker in the progression of disease because of its decreased levels in patients across all BOS grades. Additionally, biomarkers involving the remodeling of the extracellular matrix (ECM), such as MMP-9 and CTSL1, were increased in BOS patients.

Acute Rejection in the Modern Lung Transplant Era

Acute cellular rejection (ACR) remains a common complication after lung transplantation. Mortality directly related to ACR is low and most patients respond to first-line immunosuppressive treatment. However, a subset of patients may develop refractory or recurrent ACR leading to an accelerated lung function decline and ultimately chronic lung allograft dysfunction. Infectious complications associated with the intensification of immunosuppression can also negatively impact long-term survival. In this review, we summarize the most recent evidence on the mechanisms, risk factors, diagnosis, treatment, and prognosis of ACR. We specifically focus on novel, promising biomarkers which are under investigation for their potential to improve the diagnostic performance of transbronchial biopsies. Finally, for each topic, we highlight current gaps in knowledge and areas for future research.

Single-cell Transcriptomics and Solid Organ Transplantation

Single-cell RNA sequencing (scRNA-seq) allows the measurement of transcriptomes from individual cells providing new insights into complex biological systems. scRNA-seq has enabled the identification of rare cell types, new cell states, and intercellular communication networks that may be masked by traditional bulk transcriptional profiling. Researchers are increasingly using scRNA-seq to comprehensively characterize complex organs in health and disease. The diversity of immune cell types, some present at low frequency, in a transplanted organ undergoing rejection makes scRNA-seq ideally suited to characterize transplant pathologies because it can quantify subtle transcriptional differences between rare cell types. In this review, we discuss single-cell sequencing methods and their application in transplantation to date, current challenges, and future directions. We believe that the remarkably rapid pace of technological development in this field makes it likely that single-cell technologies such as scRNA-seq will have an impact on clinical transplantation within a decade.

Precision medicine: integration of genetics and functional genomics in prediction of bronchiolitis obliterans after lung transplantation

PURPOSE OF REVIEW

Lung transplantation (LTx) can be a life saving treatment in end-stage pulmonary diseases, but survival after transplantation is still limited. Posttransplant development of chronic lung allograft dysfunction with bronchiolits obliterans syndrome (BOS) as the major subphenotype, is the main cause of morbidity and mortality. Early identification of high-risk patients for BOS is a large unmet clinical need. In this review, we discuss gene polymorphisms and gene expression related to the development of BOS.

RECENT FINDINGS

Candidate gene studies showed that donor and recipient gene polymorphisms affect transplant outcome and BOS-free survival after LTx. Both selective and nonselective gene expression studies revealed differentially expressed fibrosis and apoptosis-related genes in BOS compared with non-BOS patients. Significantly, recent microarray expression analysis of blood and broncho-alveolar lavage suggest a role for B-cell and T-cell responses prior to the development of BOS. Furthermore, 6 months prior to the development of BOS differentially expressed genes were identified in peripheral blood cells.

SUMMARY

Genetic polymorphisms and gene expression changes are associated with the development of BOS. Future genome wide studies are needed to identify easily accessible biomarkers for prediction of BOS toward precision medicine.

Transcriptomic studies in tolerance: Lessons learned and the path forward

Immunosuppression after solid organ transplantation is a delicate balance of the immune response and is a complex phenomenon with many factors involved. Despite advances in the care of patients receiving organ transplants the adverse effects associated with immunosuppressive agents and the risks of long-term immunosuppression present a series of challenges and the need to weigh the risks and benefits of either over or under-immunosuppression. Ideally, if all transplant recipients could develop donor-specific immunological tolerance, it could drastically improve long-term graft survival without the need for immunosuppressive agents. In the absence of this ideal situation, the next best approach would be to develop tools to determine the adequacy of immunosuppression in each patient, in a manner that would individualize or personalize therapy. Despite current genomics-based studies of tolerance biomarkers in transplantation there are currently, no clinically validated tools to safely increase or decrease the level of IS that is beneficial to the patient. However, the successful identification of biomarkers and/or mechanisms of tolerance that have implications on long-term graft survival and outcomes depend on proper integration of study design, experimental protocols, and data-driven hypotheses. The objective of this article is to first, discuss the progress made on genomic biomarkers of immunological tolerance and the future avenues for the development of such biomarkers specifically in kidney transplantation. Secondly, we provide a set of guiding principles and identify the pitfalls, advantages, and drawbacks of studies that generate genomic data aimed at understanding transplant tolerance that is applicable to all solid transplants.

MicroRNAs Implicated in Dysregulation of Gene Expression Following Human Lung Transplantation

Background

Lung transplantation remains the only viable treatment option for the majority of patients with advanced lung diseases. However, 5-year post-transplant survival rates remain low primarily secondary to chronic rejection. Novel insights from global gene expression profiles may provide molecular phenotypes and therapeutic targets to improve outcomes after lung transplantation.

Methods

Whole-genome gene expression profiling was performed in a cohort of patients that underwent lung transplantation as well as healthy controls using the Affymetrix Human Exon 1.0ST Array. To explore the potential roles of microRNAs (miRNAs) in regulating lung transplantation-associated gene dysregulation, miRNA expression levels were also profiled in the same samples using the Exiqon miRCURY LNA Array.

Results

In a cohort of 18 lung transplant patients, 364 dysregulated genes were identified in Caucasian patients relative to normal individuals without pulmonary disorders. Pathway enrichment analysis of the dysregulated genes pointed to Gene Ontology biological processes such as “defense response”, “immune response” and “response to wounding”. We then compared the expression profiles of potential regulating miRNAs, suggesting that dysregulation of a number of lung transplantation-associated genes (e.g., ATR, FUT8, LRRC8B, NFKBIA) may be attributed to the dysregulation of their respective regulating miRNAs.

Conclusions

Following human lung transplantation, a substantial proportion of genes, particularly those genes involved in certain biological processes like immune response, were dysregulated in patients relative to their healthy counterparts. This exploratory analysis of the relationships between miRNAs and their gene targets in the context of lung transplantation warrants further investigation and may serve as novel therapeutic targets in lung transplant complications.

Electronic supplementary material

The online version of this article (doi:10.1186/2213-0802-1-12) contains supplementary material, which is available to authorized users.

Fractal circuit sensors enable rapid quantification of biomarkers for donor lung assessment for transplantation

Biomarker profiling is being rapidly incorporated in many areas of modern medical practice to improve the precision of clinical decision-making. This potential improvement, however, has not been transferred to the practice of organ assessment and transplantation because previously developed gene-profiling techniques require an extended period of time to perform, making them unsuitable in the time-sensitive organ assessment process. We sought to develop a novel class of chip-based sensors that would enable rapid analysis of tissue levels of preimplantation mRNA markers that correlate with the development of primary graft dysfunction (PGD) in recipients after transplant. Using fractal circuit sensors (FraCS), three-dimensional metal structures with large surface areas, we were able to rapidly (<20 min) and reproducibly quantify small differences in the expression of interleukin-6 (IL-6), IL-10, and ATP11B mRNA in donor lung biopsies. A proof-of-concept study using 52 human donor lungs was performed to develop a model that was used to predict, with excellent sensitivity (74%) and specificity (91%), the incidence of PGD for a donor lung. Thus, the FraCS-based approach delivers a key predictive value test that could be applied to enhance transplant patient outcomes. This work provides an important step toward bringing rapid diagnostic mRNA profiling to clinical application in lung transplantation.

The regulatory T cell effector molecule fibrinogen-like protein 2 is necessary for the development of rapamycin-induced tolerance to fully MHC-mismatched murine cardiac allografts

Therapies that promote tolerance in solid organ transplantation will improve patient outcomes by eliminating the need for long-term immunosuppression. To investigate mechanisms of rapamycin-induced tolerance, C3H/HeJ mice were heterotopically transplanted with MHC-mismatched hearts from BALB/cJ mice and were monitored for rejection after a short course of rapamycin treatment. Mice that had received rapamycin developed tolerance with indefinite graft survival, whereas untreated mice all rejected their grafts within 9 days. In vitro, splenic mononuclear cells from tolerant mice maintained primary CD4(+) and CD8(+) immune responses to donor antigens consistent with a mechanism that involves active suppression of immune responses. Furthermore, infection with lymphocytic choriomeningitis virus strain WE led to loss of tolerance suggesting that tolerance could be overcome by infection. Rapamycin-induced, donor-specific tolerance was associated with an expansion of regulatory T (Treg) cells in both the spleen and allograft and elevated plasma levels of fibrinogen-like protein 2 (FGL2). Depletion of Treg cells with anti-CD25 (PC61) and treatment with anti-FGL2 antibody both prevented tolerance induction. Tolerant allografts were populated with Treg cells that co-expressed FGL2 and FoxP3, whereas rejecting allografts and syngeneic grafts were nearly devoid of dual-staining cells. We examined the utility of an immunoregulatory gene panel to discriminate between tolerance and rejection. We observed that Treg-associated genes (foxp3, lag3, tgf-β and fgl2) had increased expression and pro-inflammatory genes (ifn-γ and gzmb) had decreased expression in tolerant compared with rejecting allografts. Taken together, these data strongly suggest that Treg cells expressing FGL2 mediate rapamycin-induced tolerance. Furthermore, a gene biomarker panel that includes fgl2 can distinguish between rejecting and tolerant grafts.

Automatic event detection in lung transplant recipients based on home monitoring of spirometry and symptoms

OBJECTIVE

The goal of this study was to develop, implement, and test an automated decision system to provide early detection of clinically important bronchopulmonary events in a population of lung transplant recipients following a home monitoring protocol.

SUBJECTS AND METHODS

Spirometry and other clinical data were collected daily at home by lung transplant recipients and transmitted weekly to the study data center. Decision rules were developed using wavelet analysis of declines in spirometry and increases in respiratory symptoms from a learning set of patient home data and validated with an independent patient set.

RESULTS

Using forced expiratory volume in 1 s or symptoms, the detection captured the majority of events (sensitivity, 80-90%) at an acceptable level of false alarms. On average, detections occurred 6.6-10.8 days earlier than the known event records.

CONCLUSIONS

This approach is useful for early discovery of pulmonary events and has the potential to decrease the time required for humans to review large amount of home monitoring data to discover relatively infrequent but clinically important events.

Review of the early diagnoses and assessment of rejection in vascularized composite allotransplantation

The emerging field of vascular composite allotransplantation (VCA) has become a clinical reality. Building upon cutting edge understandings of transplant surgery and immunology, complex grafts such as hands and faces can now be transplanted with success. Many of the challenges that have historically been limiting factors in transplantation, such as rejection and the morbidity of immunosuppression, remain challenges in VCA. Because of the accessibility of most VCA grafts, and the highly immunogenic nature of the skin in particular, VCA has become the focal point for cross-disciplinary approaches to developing novel approaches for some of the most challenging immunological problems in transplantation, particularly the early diagnoses and assessment of rejection. This paper provides a historically oriented introduction to the field of organ transplantation and the evolution of VCA.

Intragraft transcriptome level of CXCL9 as biomarker of acute cellular rejection after liver transplantation

BACKGROUND

Liver transplantation has been a life-saving and well-established treatment for acute liver failure and various end-stage liver diseases. However, acute cellular rejection (ACR) is one of the key factors that determine long-term graft function and survival after liver transplantation, and there are still no specific biomarkers available to monitor the alloimmune response. The aim of the present study was to identify molecular biomarkers for ACR in liver allograft.

METHODS

We analyzed the gene expression profile using an oligonucleotide microarray covering 44,000 human probes in 35 liver biopsy samples after living donor liver transplant, which consisted of 13 samples with ACR (ACR group; moderate/mild, 6/7), 13 samples with other dysfunctions (non-ACR group; recurrent hepatitis C / ischemia/reperfusion injury (IRI)/ nonspecific inflammation / small-for-size syndrome, 5/4/3/1), and 9 samples without liver dysfunction (protocol group). We selected 113 informative genes based on microarray results and adopted the network analysis to visualize key modulators in ACR. We selected 6 modulators (CXCL9, GZMB, CCL19, GBP2, LAIR1, and CDC25A) and confirmed the reproducibility in 23 independent biopsy samples and investigated the response to the rejection treatment in sequential samples.

RESULTS

Network analysis revealed the top three subnetworks, which had NF-κB, MAPK, and IFNG as central hubs. Among selected modulators, intragraft expression levels of CXCL9 mRNA was most upregulated and sensitive to alloimmune status.

CONCLUSION

Intragraft CXCL9 mRNA has a functionally important role in T-cell activation in liver allograft and serves as biomarker for ACR.

Characterization of the transcriptome in isolated and transplanted mouse pancreatic islets: associations with engraftment and dysfunction

The transplantation of pancreatic islets is an option for therapeutic management of hypoglycemia unawareness in select patients with type 1 diabetes mellitus. Characteristics of the transcriptome of freshly isolated islets, islet allografts, and islet isograft are reported in the literature. However, no single experiment has undertaken a comparison of the islet allograft to isograft. Potential implications of the latter are the use in diagnosis of rejection and to discover the molecular pathways in islet allograft dysfunction after transplant. Here, the mouse model of islet transplant is used to characterize the transcriptome of freshly isolated islets and compare islet graft in an isogeneic vs. allogeneic host using an Affymetrix GeneChip® Array assay. A set of islet associated transcripts (IAT) was developed, and subsequently shown to have high level of expression in islet allografts and isografts harvested either five- or ten-days after transplant. Furthermore, specific analysis of transcriptome differences between islet isografts and pre-rejection allografts (ten-day), reveal a series of islet rejection associated transcripts (IRAT). Nearly half of IRAT show overlap with previously described pathogenesis based transcript sets identified in the setting of mouse kidney allograft rejection. The novel transcripts identified to be associated with islet rejection include those involved in chemotaxis or lymphocyte function. Although use of biopsy based monitoring of humans islet transplants remains difficult at the present time, this study provides proof of principle for a transcriptome based technique for islet graft rejection monitoring and describes the transcripts associated with islet graft dysfunction.

MicroRNA signature of intestinal acute cellular rejection in formalin-fixed paraffin-embedded mucosal biopsies

Despite continuous improvement of immunosuppression, small bowel transplantation (SBT) is plagued by a high incidence of acute cellular rejection (ACR) that is frequently intractable. Therefore, there is a need to uncover novel insights that will lead to strategies to achieve better control of ACR. We hypothesized that particular miRNAs provide critical regulation of the intragraft immune response. The aim of our study was to identify miRNAs involved in intestinal ACR. We examined 26 small intestinal mucosal biopsies (AR/NR group; 15/11) obtained from recipients after SBT or multivisceral transplantation. We investigated the expression of 384 mature human miRNAs and 280 mRNAs associated with immune, inflammation and apoptosis processes. We identified differentially expressed 28 miRNAs and 58 mRNAs that characterized intestinal ACR. We found a strong positive correlation between the intragraft expression levels of three miRNAs (miR-142-3p, miR-886-3p and miR-132) and 17 mRNAs including CTLA4 and GZMB. We visualized these miRNAs within cells expressing CD3 and CD14 proteins in explanted intestinal allografts with severe ACR. Our data suggested that miRNAs have a critical role in the activation of infiltrating cells during intestinal ACR. These differences in miRNA expression patterns can be used to identify novel biomarkers and therapeutic targets for immunosuppressive agents.

Gene expression profiling in acute allograft rejection: challenging the immunologic constant of rejection hypothesis

In humans, the role and relationship between molecular pathways that lead to tissue destruction during acute allograft rejection are not fully understood. Based on studies conducted in humans, we recently hypothesized that different immune-mediated tissue destruction processes (i.e. cancer, infection, autoimmunity) share common convergent final mechanisms. We called this phenomenon the "Immunologic Constant of Rejection (ICR)." The elements of the ICR include molecular pathways that are consistently described through different immune-mediated tissue destruction processes and demonstrate the activation of interferon-stimulated genes (ISGs), the recruitment of cytotoxic immune cells (primarily through CXCR3/CCR5 ligand pathways), and the activation of immune effector function genes (IEF genes; granzymes A/B, perforin, etc.). Here, we challenge the ICR hypothesis by using a meta-analytical approach and systematically reviewing microarray studies evaluating gene expression on tissue biopsies during acute allograft rejection. We found the pillars of the ICR consistently present among the studies reviewed, despite implicit heterogeneity. Additionally, we provide a descriptive mechanistic overview of acute allograft rejection by describing those molecular pathways most frequently encountered and thereby thought to be most significant. The biological role of the following molecular pathways is described: IFN-γ, CXCR3/CCR5 ligand, IEF genes, TNF-α, IL-10, IRF-1/STAT-1, and complement pathways. The role of NK cell, B cell and T-regulatory cell signatures are also addressed.

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.

The immunosuppressive pipeline: meeting unmet needs in liver transplantation

Liver transplantation is now recognized as the treatment of choice for end-stage liver failure. Its success can be attributed largely to the generation of selective immunosuppressive agents, which have resulted in a dramatic reduction in the incidence of acute rejection and improvements in the short- and long-term outcomes of patients. However, the unresolved limitation of current immunosuppressive agents is long-term toxicity, which results in increases in the incidence and severity of cardiovascular, neurological, and renal diseases. Our recent understanding of the pathways of cell activation has resulted in the development of a new generation of immunosuppressive agents that may address the challenges facing transplantation today and allow the minimization or substitution of existing agents. Furthermore, advances in our understanding of the mechanisms of tolerance and the identification of biomarker signatures hold the promise that in some patients transplantation may be able to be performed without the need for long-term immunosuppression (tolerance).

Feasibility of diagnosing renal allograft dysfunction by oligonucleotide array: Gene expression profile correlates with histopathology

BACKGROUND

Effective non-invasive monitoring method to tell histopathology is a big challenge in renal transplantation.

METHODS

We used 70-mer long oligonucleotide array with 449 immune related genes to determine gene expression profiles of peripheral blood mononuclear cells (PBMCs) under different immune status including stable renal function (TX), acute tubular necrosis (ATN), biopsy conformed acute rejection (AR), clinical rejection with pathology of borderline changes (BL), clinical rejection without biopsy proven/presumed rejection (PR) and renal dysfunction without rejection (NR).

RESULTS

Distinct molecular expression signatures in each group were found to correlate with histopathology. And we concluded that B cell chemokine CXCL13 and mast cell may play a role in renal allograft rejection through significant difference analysis and functional pathway analysis.

CONCLUSIONS

It provides a potential non-invasive method for monitoring renal allograft function and immune status of renal transplant recipients.

Update on the clinical pharmacogenomics of organ transplantation

Organ transplantation suffers from a static graft and patient survival rate, and a high incidence of serious adverse drug effects. The pharmacogenomics of organ transplantation has emerged only recently and is complementary to the immunogenetic information that has accumulated over the past decade. Gene polymorphism studies have focused on the genes that interact across the group of immunosuppressants, including ciclosporin, tacrolimus, sirolimus and corticosteroids. The polymorphisms that hold the most potential for use in a drug selection algorithm are in genes CYP3A5, ABCB1, IMPDH1 and IMPDH2, and cytokines and growth factors. Gene-expression arrays have led to gene-expression testing, such as the use of AlloMap((R)) with heart transplant patients. The expanded use of gene-expression assays, proteomics and drug selection algorithms in organ transplantation will progress slowly and may be outpaced by drug test co-development programs for new transplant drugs. In the future, clinical pharmacogenomics will be a routine part of patient care for organ transplant patients.

Mechanisms behind local immunosuppression using inhaled tacrolimus in preclinical models of lung transplantation

Inhaled immunosuppression with tacrolimus (TAC) is a novel strategy after lung transplantation. Here we investigate the feasibility of tacrolimus delivery via aerosol, assess its immunosuppressive efficacy, reveal possible mechanisms of action, and evaluate its airway toxicity. Rats received 4 mg/kg TAC via oral or inhaled (AER) administration. Pharmacokinetic properties were compared, and in vivo airway toxicity was assessed. Full-thickness human airway epithelium (AE) was grown in vitro at an air-liquid interface. Equal TAC doses (10-1,000 ng) were either added to the bottom chamber (MED) or aerosolized for gas-phase exposure (AER). Airway epithelium TAC absorption, cell toxicity, and interactions of TAC with NFκB activation were studied. Single-photon emission computed tomography demonstrated a linear tracer accumulation within the lungs during TAC inhalation. The AER TAC generated higher lung-tissue concentrations, but blood concentrations that were 11 times lower. Airway histology and gene expression did not reveal drug toxicity after 3 weeks of treatment. In vitro AE exposed to TAC at 10-1,000 ng, orally or AER, maintained its pseudostratified morphology, did not show cell toxicity, and maintained its epithelial integrity, with tight junction formation. The TAC AER-treated AE absorbed the drug from the apical surface and generated lower-chamber TAC concentrations sufficient to suppress activated lymphocytes. Tacrolimus AER was superior to TAC MED at preventing AE IFN-γ, IL-10, IL-13, monocyte chemoattractant protein-1 chemokine (C-C motif) ligand 5 (RANTES) and TNF-α up-regulation. Tacrolimus inhibited airway epithelial cell NFκB activation. In conclusion, TAC can be delivered easily and effectively into the lungs without causing airway toxicity, decreases inflammatory AE cytokine production, and inhibits NFκB activation.

Using gene arrays in diagnosis of rejection

PURPOSE OF REVIEW

In the last decade, microarray technology has revolutionized biological research by allowing the screening of tens of thousands of genes simultaneously. This article reviews recent studies in organ transplantation using microarrays and highlights the issues that should be addressed in order to use microarrays in diagnosis of rejection.

RECENT FINDINGS

Microarrays have been useful in identifying potential biomarkers for chronic rejection in peripheral blood mononuclear cells, novel pathways for induction of tolerance, and genes involved in protecting the graft from the host immune system. Microarray analysis of peripheral blood mononuclear cells from chronic antibody-mediated rejection has identified potential noninvasive biomarkers. In a recent study, correlation of pathogenesis-based transcripts with histopathologic lesions is a promising step towards inclusion of microarrays in clinics for organ transplants.

SUMMARY

Despite promising results in diagnosis of histopathologic lesions using microarrays, the low dynamic range of microarrays and large measured expression changes within the probes for the same gene continue to cast doubts on their readiness for diagnosis of rejection. More studies must be performed to resolve these issues. Dominating expression of globin genes in whole blood poses another challenge for identification of noninvasive biomarkers. In addition, studies are also needed to demonstrate effects of different immunosuppression therapies and their outcomes.

Microarrays: monitoring for transplant tolerance and mechanistic insights

With recent advances in immunology and a growing understanding of transplantation biology, the development of reliable assays that may be used for identification and prediction of the current state of an immune response (rejection and tolerance) are urgently needed to allow us to predict the development of immunologic graft injury, individualize immunosuppression, rationally minimize immunosuppressive drug toxicity, promote a better understanding of the mechanisms underlying stable graft acceptance, and aid in the design of tolerance-inducing clinical transplantation trials. Microarrays can provide nonbiased, simultaneous global expression patterns for more than 40,000 human genes across different experiments. High throughput microarray technology offers a means to study disease-specific transcriptional changes in tissue biopsy, peripheral blood, and biofluids.

Impact of human donor lung gene expression profiles on survival after lung transplantation: a case-control study

Primary graft dysfunction (PGD) continues to be a major cause of early death after lung transplantation. Moreover, there remains a lack of accurate pretransplant molecular markers for predicting PGD. To identify distinctive donor lung gene expression signatures associated with PGD, we profiled human donor lungs using microarray technology prior to implantation. The genomic profiles of 10 donor lung samples from patients who subsequently developed clinically defined severe PGD were compared with 16 case-matched donor lung samples from those who had a favorable outcome without PGD (development set, n = 26). Selected PCR validated predictive genes were tested by quantitative reverse transcription-polymerase chain reaction in an independent test set (n = 81). Our microarray analyses of the development set identified four significantly upregulated genes (ATP11B, FGFR2, EGLN1 and MCPH1) in the PGD samples. These genes were also significantly upregulated in donor samples of the test set of patients with poor outcomes when compared to those of patients with good outcomes after lung transplantation. This type of biological donor lung assessment shows significant promise for development of a more accurate diagnostic strategy to assess donor lungs prior to implantation.

Biomechanical aspects of the auto-digestion theory

Increasing evidence suggests that most cardiovascular diseases, tumors and other ailments are associated with an inflammatory cascade. The inflammation is accompanied by activation of cells in the circulation and fundamental changes in the mechanics of the microcirculation, expression of pro-inflammatory genes and downregulation of anti-inflammatory genes, attachment of leukocytes to the endothelium, elevated permeability of the endothelium, and many other events. The evidence has opened great opportunities for medicine to develop new anti-inflammatory interventions. But it also raises a fundamental question: What is the origin of inflammation? I will discuss a basic series of studies that was designed to explore trigger mechanisms for inflammation in shock and multi-organ failure, an important clinical problem associated with high mortality. We traced the source of the inflammatory mediators to the powerful digestive enzymes in the intestine. Synthesized in the pancreas as part of normal digestion, they have the ability to degrade almost all biological tissues and molecules. In the lumen of the intestine, digestive enzymes are fully activated and self-digestion of the intestine is prevented by compartmentalization in the lumen of the intestine facilitated by the mucosal epithelial barrier. Under conditions of intestinal ischemia, however, the mucosal barrier becomes permeable to pancreatic enzymes allowing their entry into the wall of the intestine. The process leads to auto-digestion of the intestinal wall and production of inflammatory mediators. The hypothesis that multi-organ failure in shock may be due an auto-digestion process by pancreatic enzymes is ready to be tested in a variety of shock conditions.

Integrating genomic and clinical medicine: searching for susceptibility genes in complex lung diseases

The integration of molecular, genomic, and clinical medicine in the post-genome era provides the promise of novel information on genetic variation and pathophysiologic cascades. The current challenge is to translate these discoveries rapidly into viable biomarkers that identify susceptible populations and into the development of precisely targeted therapies. In this article, we describe the application of comparative genomics, microarray platforms, genetic epidemiology, statistical genetics, and bioinformatic approaches within examples of complex pulmonary pathobiology. Our search for candidate genes, which are gene variations that drive susceptibility to and severity of enigmatic acute and chronic lung disorders, provides a logical framework to understand better the evolution of genomic medicine. The dissection of the genetic basis of complex diseases and the development of highly individualized therapies remain lofty but achievable goals.

Applying genomics to organ transplantation medicine in both discovery and validation of biomarkers

The field of biomarker discovery made a significant leap over the past few decades. As we enter the Era of the Human Genome, thousands of biomarkers can be identified in a relatively high-throughput fashion. While such magnitude and diversity of biomarkers can be seen as a challenge by itself, the field is being moved forward by new advances in bioinformatics and Systems Biology. Because of the life and death nature of end stage organ failure that transplantation treats, the severe donor organ shortage, and the powerful and toxic drug therapies required for the lifetimes of transplant patients, we envision a future for biomarkers as tools to diagnose disease in its early stages, predict prognosis, suggest treatment options and then assist in the implementation of therapies. By harnessing the power of multiple technologies in parallel makes it possible to discover and then validate the next generation of biomarkers for transplantation. We see the road ahead diverge into two paths: one from biomarkers to diagnosis and therapy and the other to a new level of insight into the complex molecular networks that determine when a healthy state becomes diseased and dysfunctional.