Molecular Testing for Long-term Rejection Surveillance in Heart Transplant Recipients: Design of the Invasive Monitoring Attenuation Through Gene Expression (IMAGE) Trial

Applying Genomics to Unravel Health Disparities in Organ Transplantation: Paul I. Terasaki State-of-the-art Lecture; American Transplant Congress 2021

An extensive body of research about team science provides empirical evidence that diverse teams outperform homogenous teams in creating more innovative solutions to complex problems. At the core of diverse and inclusive teams is a rich diversity of perspectives, experiences, and backgrounds that invite new questions and broaden the scope of research. Diverse perspectives are especially relevant for biomedicine, which seeks to find solutions for challenging problems affecting the human condition. It is essential that diversity and inclusion in biomedicine is prioritized as a key driver of innovation, both through the people who conduct the research and the science itself. Key questions have been articulated as important drivers for funding research: (1) Who is doing the science and who is building the tools? (2) What science and technology is being done and how? and (3) Who has access to the knowledge and benefits of scientific innovation? I will briefly review the empirical evidence supporting diversity as a powerful enhancer of the quality and outputs of research and clinical care. I offer my own research as a case study of incorporating a framework of diversity, equity, and inclusion into research that uses new emerging genomic tools for earlier and more precise diagnosis of organ transplant rejection. I will demonstrate how these same tools hold great promise for accelerating the discovery of hitherto unexplored mechanisms that drive the poor outcomes for African ancestry organ transplant recipients, which in turn will identify new diagnostics and therapeutic targets that benefit transplant recipients across all ancestries.

Biomarker-Based Assessment for Infectious Risk Before and After Heart Transplantation

Purpose of Review

Survival outcomes for heart transplant recipients have improved in recent decades, but infection remains a significant cause of morbidity and mortality. In this review, we discuss several biological markers, or biomarkers, that may be used to monitor immunologic status in this patient population.

Recent Findings

While modest, data on the utility of immune biomarkers in heart transplant recipients suggest correlation between low level of immune response and increased infection risk. More novel assays, such as the detection of circulating levels of pathogen cell-free DNA in plasma and the use of Torque teno virus load as a surrogate for net state of immunosuppression, have potential to be additional important biomarkers.

Summary

Biomarker approaches to individualize immunosuppression therapy among heart transplant recipients is a promising area of medicine. However, additional studies are needed to inform the optimal protocol in which to incorporate these biomarkers into clinical practice.

The evolution of patient-specific precision biomarkers to guide personalized heart-transplant care

Introduction

In parallel to the clinical maturation of heart transplantation over the last 50 years, rejection testing has been revolutionized within the systems biology paradigm triggered by the Human Genome Project.

Areas Covered

We have co-developed the first FDA-cleared diagnostic and prognostic leukocyte gene expression profiling biomarker test in transplantation medicine that gained international evidence-based medicine guideline acceptance to rule out moderate/severe acute cellular cardiac allograft rejection without invasive endomyocardial biopsies. This work prompted molecular re-classification of intragraft biology, culminating in the identification of a pattern of intragraft myocyte injury, in addition to acute cellular rejection and antibody-mediated rejection. This insight stimulated research into non-invasive detection of myocardial allograft injury. The addition of a donor-organ specific myocardial injury marker based on donor-derived cell-free DNA further strengthens the non-invasive monitoring concept, combining the clinical use of two complementary non-invasive blood-based measures, host immune activity-related risk of acute rejection as well as cardiac allograft injury.

Expert Opinion

This novel complementary non-invasive heart transplant monitoring strategy based on leukocyte gene expression profiling and donor-derived cell-free DNA that incorporates longitudinal variability measures provides an exciting novel algorithm of heart transplant allograft monitoring. This algorithm's clinical utility will need to be tested in an appropriately designed randomized clinical trial which is in preparation.

Pediatric heart transplantation: how to manage problems affecting long-term outcomes?

Since the initial International Society of Heart Lung Transplantation registry was published in 1982, the number of pediatric heart transplantations has increased markedly, reaching a steady state of 500-550 transplantation annually and occupying up to 10% of total heart transplantations. Heart transplantation is considered an established therapeutic option for patients with end-stage heart disease. The long-term outcomes of pediatric heart transplantations were comparable to those of adults. Issues affecting long-term outcomes include acute cellular rejection, antibody-mediated rejection, cardiac allograft vasculopathy, infection, prolonged renal dysfunction, and malignancies such as posttransplant lymphoproliferative disorder. This article focuses on medical issues before pediatric heart transplantation, according to the Korean Network of Organ Sharing registry and as well as major problems such as graft rejection and cardiac allograft vasculopathy. To reduce graft failure rate and improve long-term outcomes, meticulous monitoring for rejection and medication compliance are also important, especially in adolescents.

Heart Transplant Immunosuppression Strategies at Cedars-Sinai Medical Center

Heart transplant is the optimal treatment for selected patients with end-stage heart failure. Immunosuppression after heart transplantation has significantly reduced the incidence of rejection and improved patient outcomes with the routine use of calcineurin inhibitors. Antimetabolites and proliferation signal inhibitors add to the improvement in patient outcomes as well. The goal of induction therapy is to provide intense immunosuppression when the risk of allograft rejection is highest. Most maintenance immunosuppressive protocols employ a 3-drug regimen consisting of a calcineurin inhibitor, an antimetabolite agent and glucocorticoids. The management of rejection proceeds in a stepwise fashion based on the severity of rejection detected on biopsy and the patient's clinical presentation. This review will cover induction, maintenance, rejection therapy and some special considerations including sensitization, renal sparing protocol, and corticosteroid weaning. It will end in consideration of potential future directions in immunosuppressive strategies to promote patient and graft survival.

Methods for the evaluation of biomarkers in patients with kidney and liver diseases: multicentre research programme including ELUCIDATE RCT

Background

Protein biomarkers with associations with the activity and outcomes of diseases are being identified by modern proteomic technologies. They may be simple, accessible, cheap and safe tests that can inform diagnosis, prognosis, treatment selection, monitoring of disease activity and therapy and may substitute for complex, invasive and expensive tests. However, their potential is not yet being realised.

Design and methods

The study consisted of three workstreams to create a framework for research: workstream 1, methodology – to define current practice and explore methodology innovations for biomarkers for monitoring disease; workstream 2, clinical translation – to create a framework of research practice, high-quality samples and related clinical data to evaluate the validity and clinical utility of protein biomarkers; and workstream 3, the ELF to Uncover Cirrhosis as an Indication for Diagnosis and Action for Treatable Event (ELUCIDATE) randomised controlled trial (RCT) – an exemplar RCT of an established test, the ADVIA Centaur® Enhanced Liver Fibrosis (ELF) test (Siemens Healthcare Diagnostics Ltd, Camberley, UK) [consisting of a panel of three markers – (1) serum hyaluronic acid, (2) amino-terminal propeptide of type III procollagen and (3) tissue inhibitor of metalloproteinase 1], for liver cirrhosis to determine its impact on diagnostic timing and the management of cirrhosis and the process of care and improving outcomes.

Results

The methodology workstream evaluated the quality of recommendations for using prostate-specific antigen to monitor patients, systematically reviewed RCTs of monitoring strategies and reviewed the monitoring biomarker literature and how monitoring can have an impact on outcomes. Simulation studies were conducted to evaluate monitoring and improve the merits of health care. The monitoring biomarker literature is modest and robust conclusions are infrequent. We recommend improvements in research practice. Patients strongly endorsed the need for robust and conclusive research in this area. The clinical translation workstream focused on analytical and clinical validity. Cohorts were established for renal cell carcinoma (RCC) and renal transplantation (RT), with samples and patient data from multiple centres, as a rapid-access resource to evaluate the validity of biomarkers. Candidate biomarkers for RCC and RT were identified from the literature and their quality was evaluated and selected biomarkers were prioritised. The duration of follow-up was a limitation but biomarkers were identified that may be taken forward for clinical utility. In the third workstream, the ELUCIDATE trial registered 1303 patients and randomised 878 patients out of a target of 1000. The trial started late and recruited slowly initially but ultimately recruited with good statistical power to answer the key questions. ELF monitoring altered the patient process of care and may show benefits from the early introduction of interventions with further follow-up. The ELUCIDATE trial was an ‘exemplar’ trial that has demonstrated the challenges of evaluating biomarker strategies in ‘end-to-end’ RCTs and will inform future study designs.

Conclusions

The limitations in the programme were principally that, during the collection and curation of the cohorts of patients with RCC and RT, the pace of discovery of new biomarkers in commercial and non-commercial research was slower than anticipated and so conclusive evaluations using the cohorts are few; however, access to the cohorts will be sustained for future new biomarkers. The ELUCIDATE trial was slow to start and recruit to, with a late surge of recruitment, and so final conclusions about the impact of the ELF test on long-term outcomes await further follow-up. The findings from the three workstreams were used to synthesise a strategy and framework for future biomarker evaluations incorporating innovations in study design, health economics and health informatics.

Trial registration

Current Controlled Trials ISRCTN74815110, UKCRN ID 9954 and UKCRN ID 11930.

Funding

This project was funded by the NIHR Programme Grants for Applied Research programme and will be published in full inProgramme Grants for Applied Research; Vol. 6, No. 3. See the NIHR Journals Library website for further project information.

Quantitative or qualitative transcriptional diagnostic signatures? A case study for colorectal cancer

Background

Due to experimental batch effects, the application of a quantitative transcriptional signature for disease diagnoses commonly requires inter-sample data normalization, which would be hardly applicable under common clinical settings. Many cancers might have qualitative differences with the non-cancer states in the gene expression pattern. Therefore, it is reasonable to explore the power of qualitative diagnostic signatures which are robust against experimental batch effects and other random factors.

Results

Firstly, using data of technical replicate samples from the MicroArray Quality Control (MAQC) project, we demonstrated that the low-throughput PCR-based technologies also exist large measurement variations for gene expression even when the samples were measured in the same test site. Then, we demonstrated the critical limitation of low stability for classifiers based on quantitative transcriptional signatures in applications to individual samples through a case study using a support vector machine and a naïve Bayesian classifier to discriminate colorectal cancer tissues from normal tissues. To address this problem, we identified a signature consisting of three gene pairs for discriminating colorectal cancer tissues from non-cancer (normal and inflammatory bowel disease) tissues based on within-sample relative expression orderings (REOs) of these gene pairs. The signature was well verified using 22 independent datasets measured by different microarray and RNA_seq platforms, obviating the need of inter-sample data normalization.

Conclusions

Subtle quantitative information of gene expression measurements tends to be unstable under current technical conditions, which will introduce uncertainty to clinical applications of the quantitative transcriptional diagnostic signatures. For diagnosis of disease states with qualitative transcriptional characteristics, the qualitative REO-based signatures could be robustly applied to individual samples measured by different platforms.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4446-y) contains supplementary material, which is available to authorized users.

Prognostic Utility of Right Ventricular Free Wall Strain in Low Risk Patients After Orthotopic Heart Transplantation

Global longitudinal strain (GLS) by speckle-tracking echocardiography is a sensitive measure of regional left and right ventricular (LV and RV) dysfunction, before onset of overt systolic dysfunction. We sought to evaluate the prognostic utility of measuring LV-GLS and RV free wall strain (FWS) in low risk patients at 1 year after orthotopic heart transplantation (OHT). We retrospectively studied 96 OHT recipients (age 52 ± 14 years, 64% men) free of antibody-mediated rejection or moderate to severe coronary allograft vasculopathy (CAV, grade 2 to 3) at 1 year after transplant. LV-GLS and RV-FWS were calculated using EchoPAC software. Cox models were developed after adjusting for the Index for Mortality Prediction After Cardiac Transplantation (IMPACT) score (post-transplant risk score), with the primary outcome of death, moderate to severe CAV, or treated rejection. At 1 year after transplant, LV ejection fraction and RV fractional area change (FAC) were 58 ± 7% and 42 ± 10%, respectively. LV-GLS was -17.0 ± 3.3% and RV-FWS -16.4 ± 4.5%. At an average follow-up of 4.5 years, 28 patients met the primary end point (10 death, 5 vasculopathy, 17 rejection). In sequential Cox models, markers of RV function were associated with the primary outcome (RV-FAC, p = 0.012; RV-FWS, p = 0.022), while LV ejection fraction and LV-GLS were not. We conclude that in low risk patients 1 year after OHT, markers of RV function (RV-FAC and RV-FWS) are independently associated with incident rejection, CAV, and death. Markers of RV dysfunction could potentially be incorporated into risk scores and future prospective studies to risk stratify patients after OHT.

Gene expression profiling to study racial differences after heart transplantation

Background

The basis for increased mortality after heart transplantation in African Americans and other non-Caucasian racial groups is poorly defined. We hypothesized that increased risk of adverse events is driven by biological factors. To test this hypothesis in the IMAGE study, we determined whether the event rate of the primary outcome of acute rejection, graft dysfunction, death, or re-transplantation varied by race as a function of calcineurin inhibitor levels and gene expression profile (GEP) scores.

Methods

We determined the event rate of the primary outcome, comparing racial groups, stratified by time post-transplant. Logistic regression was used to compute the relative risk across racial groups and linear modeling was used to measure the dependence of CNI levels and GEP score on race.

Results

In 580 patients followed for a median of 19 months, the incidence of the primary endpoint in African Americans, other non-Caucasians, and Caucasians was 18.3%, 22.2%, and 8.5%, respectively (p<0.001). There were small but significant correlations of race and tacrolimus trough levels to GEP score. Tacrolimus levels were similar between races. Of patients receiving tacrolimus, other non-Caucasians had higher GEP scores than the other racial groups. African American recipients demonstrated a unique decrease in expression of the FLT3 gene in response to higher tacrolimus levels.

Conclusions

African Americans and other non-Caucasian heart transplant recipients were 2.5–3 times more likely than Caucasians to experience outcome events in IMAGE. The increased risk of adverse outcomes may be partly due to the biology of the alloimmune response, which is less effectively inhibited at similar tacrolimus levels in minority racial groups.

Immunosuppression following heart transplantation: prospects and challenges

Immunosuppression after heart transplantation has significantly reduced the incidence of cellular rejection and improved patient outcomes with the routine use of calcineurin inhibitors. Antimetabolites and proliferation signal inhibitors add to the improvement in patient outcomes, particularly with respect to the reduced burden of cardiac allograft vasculopathy. Patients with antibody sensitization are potentially at higher risk of postoperative complications. Sensitized patients are undergoing heart transplantation with increased frequency, in part due to the emergence of ventricular assist device use as a bridge to heart transplantation. Despite improvements in immunosuppressive therapies, many challenges face physicians and patients, which will further refine and improve care of the post-heart transplant patient.

Gene expression analysis in RA: towards personalized medicine

Gene expression has recently been at the forefront of advance in personalized medicine, notably in the field of cancer and transplantation, providing a rational for a similar approach in rheumatoid arthritis (RA). RA is a prototypic inflammatory autoimmune disease with a poorly understood etiopathogenesis. Inflammation is the main feature of RA; however, many biological processes are involved at different stages of the disease. Gene expression signatures offer management tools to meet the current needs for personalization of RA patients' care. This review analyses currently available information with respect to RA diagnostic, prognostic and prediction of response to therapy with a view to highlight the abundance of data, whose comparison is often inconclusive due to the mixed use of material source, experimental methodologies and analysis tools, reinforcing the need for harmonization if gene expression signatures are to become a useful clinical tool in personalized medicine for RA patients.

Challenges and solutions in the development of genomic biomarker panels: a systematic phased approach

In the post-genome era, high throughput gene expression profiling has been successfully used to develop genomic biomarker panels (GBP) that can be integrated into clinical decision making. The development of GBPs in the context of personalized medicine is a scientifically challenging and resource-intense process. It needs to be accomplished in a systematic phased approach to address biological variation related to a clinical phenotype (e.g. disease etiology, gender, etc.) and minimize technical variation (noise). Here we present the methodological aspects of GBP development based on the experience of the Cardiac Allograft Rejection Gene Expression Observation (CARGO) study, a study that lead to the development of a molecular classifier for rejection screening in heart transplant patients.

Genetic and genomic approaches to the detection of heart transplant rejection

Since Christiaan Barnard performed the first heart transplant in 1967, over 100,000 heart transplants have been performed worldwide. As was true then, rejection remains the major threat to the function and survival of the allograft. The development of the endomyocardial biopsy as a means to monitor for rejection has allowed heart transplantation to thrive as a therapy for patients with end-stage heart disease. The need for a noninvasive method of rejection surveillance led to the development of the first genetic test for allograft rejection, the AlloMap^®. In this article, after presenting the pathological and clinical features of cardiac allograft rejection, the authors discuss the development and application of gene-expression testing for the detection of cardiac allograft rejection. We then explore emerging 'omic' approaches that will be the rejection detection methods of the future.

Identification and classification of acute cardiac rejection by intragraft transcriptional profiling

BACKGROUND

Treatment of acute rejection (AR) in heart transplantation relies on histopathological grading of endomyocardial biopsies according to International Society for Heart and Lung Transplantation guidelines. Intragraft gene expression profiling may be a way to complement histological evaluation.

METHODS AND RESULTS

Transcriptional profiling was performed on 26 endomyocardial biopsies, and expression patterns were compared with the 1990 International Society for Heart and Lung Transplantation AR grades. Importantly, transcriptional profiles from settings with an equivalent AR grade appeared the same. In addition, grade 0 profiles could not be distinguished from 1A profiles, and grade 3A profiles could not be distinguished from 3B profiles. Comparing the AR groupings (0+1A, 1B, and 3A+3B), 0+1A showed more striking differences from 1B than from 3A+3B. When these findings were extrapolated to the 2005 revised guidelines, the combination of 1A and 1B into a single category (1R) appears to have brought together endomyocardial biopsies with different underlying processes that are not evident from histological evaluation. Grade 1B was associated with upregulated immune response genes, as 1 categorical distinction from grade 1A. Although grade 1B was distinct from the clinically relevant AR grades 3A and 3B, all of these grades shared a small number of overlapping pathways consistent with common physiological underpinnings.

CONCLUSION

The gene expression similarities and differences identified here in different AR settings have the potential to revise the clinical perspective on acute graft rejection, pending the results of larger studies.

Gene expression profiling and cardiac allograft rejection monitoring: is IMAGE just a mirage?

The search for an effective non-invasive monitoring technique for cardiac allograft rejection eluded us until the discovery and validation of a commercially available gene-based peripheral blood bio-signature signal. The Invasive Monitoring Attenuation through Gene Expression (IMAGE) trial tested the hypothesis of cardiac biopsy minimization using this gene-based panel in stable, low-risk survivors, late after cardiac transplantation and demonstrated non-inferiority of this strategy. We present a clinician's critical perspective on this important effort and outline the key caveats and highlights for the potential way forward in using these results. Furthermore, we contend that it may not be necessary to replace an invasive cardiac biopsy strategy with anything other than better standardized clinical and functional allograft vigilance in low-risk survivors.

Gene-expression profiling for rejection surveillance after cardiac transplantation

BACKGROUND

Endomyocardial biopsy is the standard method of monitoring for rejection in recipients of a cardiac transplant. However, this procedure is uncomfortable, and there are risks associated with it. Gene-expression profiling of peripheral-blood specimens has been shown to correlate with the results of an endomyocardial biopsy.

METHODS

We randomly assigned 602 patients who had undergone cardiac transplantation 6 months to 5 years previously to be monitored for rejection with the use of gene-expression profiling or with the use of routine endomyocardial biopsies, in addition to clinical and echocardiographic assessment of graft function. We performed a noninferiority comparison of the two approaches with respect to the composite primary outcome of rejection with hemodynamic compromise, graft dysfunction due to other causes, death, or retransplantation.

RESULTS

During a median follow-up period of 19 months, patients who were monitored with gene-expression profiling and those who underwent routine biopsies had similar 2-year cumulative rates of the composite primary outcome (14.5% and 15.3%, respectively; hazard ratio with gene-expression profiling, 1.04; 95% confidence interval, 0.67 to 1.68). The 2-year rates of death from any cause were also similar in the two groups (6.3% and 5.5%, respectively; P=0.82). Patients who were monitored with the use of gene-expression profiling underwent fewer biopsies per person-year of follow-up than did patients who were monitored with the use of endomyocardial biopsies (0.5 vs. 3.0, P<0.001).

CONCLUSIONS

Among selected patients who had received a cardiac transplant more than 6 months previously and who were at a low risk for rejection, a strategy of monitoring for rejection that involved gene-expression profiling, as compared with routine biopsies, was not associated with an increased risk of serious adverse outcomes and resulted in the performance of significantly fewer biopsies. (ClinicalTrials.gov number, NCT00351559.)

Apollon/RNF41 myocardial messenger RNA diagnoses cardiac allograft apoptosis in rejection

BACKGROUND

Endomyocardial biopsy (EMB) remains the gold standard for acute cellular rejection (ACR) diagnosis in cardiac transplantation yet is subject to interobserver variability. A method that could avoid discordant EMB analysis would be desirable. The apoptosis rate in EMB correlates with ACR severity. Apollon inhibits apoptosis, and RNF41 catalyzes its degradation. Whether tissue Apollon/RNF41 could diagnose ACR is not known. This study addressed this issue.

METHODS

Apollon/RNF41 messenger RNA (mRNA) was measured by real time reverse-transcriptase polymerase chain reaction and apoptosis was quantified with TUNEL assays in EMBs of 268 transplant recipients. EMBs were obtained at 1, 2, 3, 4, 7, 12, 24, and 52 posttransplant weeks.

RESULTS

At all time points posttransplant, Apollon mRNA decreased significantly in EMBs with ACR grades 2R/3R combined (P<or=0.0010) compared with 0/1R combined, although RNF41 mRNA significantly increased in EMBs with ACR grade 1R (P<0.0001) or 2R/3R combined (P<0.0001) compared with 0. At the identified cut-off level of less than or equal to 168.2 arbitrary units, Apollon mRNA identified ACR grades 2R/3R with 100% sensitivity and 84% specificity, whereas RNF41 mRNA at the cut-off level of more than or equal to 51.8 identified ACR grades 1R-3R with 99% sensitivity and 95% specificity. Increased RNF41 (rs, 0.728; P<0.0001) and decreased Apollon (rs, -0.562; P<0.0001) expression correlated significantly with the degree of apoptosis in EMBs.

CONCLUSIONS

Combined Apollon/RNF41 mRNA quantitatively and specifically identifies ACR associated with apoptosis in cardiac allografts and could validate ACR grading variability associated with histologic EMB analysis.

Impact of animal strain on gene expression in a rat model of acute cardiac rejection

Background

The expression levels of many genes show wide natural variation among strains or populations. This study investigated the potential for animal strain-related genotypic differences to confound gene expression profiles in acute cellular rejection (ACR). Using a rat heart transplant model and 2 different rat strains (Dark Agouti, and Brown Norway), microarrays were performed on native hearts, transplanted hearts, and peripheral blood mononuclear cells (PBMC).

Results

In heart tissue, strain alone affected the expression of only 33 probesets while rejection affected the expression of 1368 probesets (FDR 10% and FC ≥ 3). Only 13 genes were affected by both strain and rejection, which was < 1% (13/1368) of all probesets differentially expressed in ACR. However, for PBMC, strain alone affected 265 probesets (FDR 10% and FC ≥ 3) and the addition of ACR had little further effect. Pathway analysis of these differentially expressed strain effect genes connected them with immune response, cell motility and cell death, functional themes that overlap with those related to ACR. After accounting for animal strain, additional analysis identified 30 PBMC candidate genes potentially associated with ACR.

Conclusion

In ACR, genetic background has a large impact on the transcriptome of immune cells, but not heart tissue. Gene expression studies of ACR should avoid study designs that require cross strain comparisons between leukocytes.

The changing face of heart transplantation

It has been 40 years since the first human-to-human heart transplant performed in South Africa by Christiaan Barnard in December 1967. This achievement did not come as a surprise to the medical community but was the result of many years of early pioneering experimental work by Alexis Carrel, Frank Mann, Norman Shumway, and Richard Lower. Since then, refinement of donor and recipient selection methods, better donor heart management, and advances in immunosuppression have significantly improved survival. In this article, we hope to give a perspective on the changing face of heart transplantation. Topics that will be covered in this review include the changing patient population as well as recent advances in transplantation immunology, organ preservation, allograft vasculopathy, and immune tolerance.