Transplantomics and biomarkers in organ transplantation: a report from the first international conference

Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation

Omics data address key issues in liver transplantation (LT) as the most effective therapeutic means for end-stage liver disease. The purpose of this study was to review the current application and future direction for omics in LT. We reviewed the use of multiomics to elucidate the pathogenesis leading to LT and prognostication. Future directions with respect to the use of omics in LT are also described based on perspectives of surgeons with experience in omics. Significant molecules were identified and summarized based on omics, with a focus on post-transplant liver fibrosis, early allograft dysfunction, tumor recurrence, and graft failure. We emphasized the importance omics for clinicians who perform LTs and prioritized the directions that should be established. We also outlined the ideal workflow for omics in LT. In step with advances in technology, the quality of omics data can be guaranteed using an improved algorithm at a lower price. Concerns should be addressed on the translational value of omics for better therapeutic effects in patients undergoing LT.

Surfing the Big Data Wave: Omics Data Challenges in Transplantation

In both research and care, patients, caregivers, and researchers are facing a leap forward in the quantity of data that are available for analysis and interpretation, marking the daunting "big data era." In the biomedical field, this quantitative shift refers mostly to the -omics that permit measuring and analyzing biological features of the same type as a whole. Omics studies have greatly impacted transplantation research and highlighted their potential to better understand transplant outcomes. Some studies have emphasized the contribution of omics in developing personalized therapies to avoid graft loss. However, integrating omics data remains challenging in terms of analytical processes. These data come from multiple sources. Consequently, they may contain biases and systematic errors that can be mistaken for relevant biological information. Normalization methods and batch effects have been developed to tackle issues related to data quality and homogeneity. In addition, imputation methods handle data missingness. Importantly, the transplantation field represents a unique analytical context as the biological statistical unit is the donor-recipient pair, which brings additional complexity to the omics analyses. Strategies such as combined risk scores between 2 genomes taking into account genetic ancestry are emerging to better understand graft mechanisms and refine biological interpretations. The future omics will be based on integrative biology, considering the analysis of the system as a whole and no longer the study of a single characteristic. In this review, we summarize omics studies advances in transplantation and address the most challenging analytical issues regarding these approaches.

Biomarkers in Solid Organ Transplantation

After more than 6 decades of clinical practice, the transplant community continues to research noninvasive biomarkers of solid organ injury to help improve patient care. In this review, we discuss the clinical usefulness of selective biomarkers and how they are processed at the laboratory. In addition, we organize these biomarkers based on specific aims and introduce innovative markers currently under investigation.

Biomarkers of immune tolerance in liver transplantation

The liver exhibits intrinsic immune tolerogenic properties that contribute to a unique propensity toward spontaneous acceptance when transplanted, both in animal models and in humans. Thus, in contrast to what happens after transplantation of other solid organs, several years following liver transplantation a significant subset of patients are capable of maintaining normal allograft function with histological integrity in the absence of immunosuppressive drug treatment. Significant efforts have been put into identifying sensitive and specific biomarkers of tolerance in order to stratify liver transplant recipients according to their need for immunosuppressive medication and their likelihood of being able to completely discontinue it. These biomarkers are currently being validated in prospective clinical trials of immunosuppression withdrawal both in Europe and in the United States. These studies have the potential to transform the clinical management of liver transplant recipients by mitigating, at least in part, the burden of lifelong immunosuppression.

Personalized treatment in heart transplantation

PURPOSE OF REVIEW

We are entering the era of personalized medicine, in which pharmacogenomics and biomarker-based assays can be used to tailor diagnostic tests and drug therapies to individual patients. This new approach to patient-specific care offers the potential to maximize the efficacy of available medical treatments while reducing the incidence of adverse side effects. Here, we present approaches to personalize the care of heart transplant recipients.

RECENT FINDINGS

Four strategies for personalized posttransplant care are described, including use of pharmacogenomic data to individualize the use of immunosuppressive drugs, immune monitoring to prevent acute rejection while reducing the long-term consequences of over immunosuppression, noninvasive surveillance for acute rejection, and targeted prophylaxis against opportunistic infections.

SUMMARY

The long-term survival of heart transplant recipients is limited by side effects of immunosuppressive drugs, including infectious complications, renal dysfunction, and malignancy. We discuss strategies to maximize the benefits of immunosuppressive and prophylactic therapies while minimizing their long-term toxicities.

Transplantomics: Toward Precision Medicine in Transplantation Research

Precision medicine is an emerging integrative approach for disease prevention, early detection, and treatment which takes into account individual variability in genetic and other molecular measurements, medical history, environmental exposures, and lifestyle. The development and availability of genomic and other molecular profiling technologies provide an unprecedented opportunity to apply precision medicine strategies in transplantation research. Developing integrative computational methods to analyze these diverse types of data provides new opportunities to impact diagnostics and therapeutics. In this article, we discuss ways we can leverage molecular data sets to develop new hypotheses for disease mechanisms, identify new disease biomarkers, and reposition drugs for diseases with unmet needs. We specifically discuss computational methods that can be applied to achieve these goals in the context of organ transplant.

Transplant genetics and genomics

Ever since the discovery of the major histocompatibility complex, scientific and clinical understanding in the field of transplantation has been advanced through genetic and genomic studies. Candidate-gene approaches and recent genome-wide association studies (GWAS) have enabled a deeper understanding of the complex interplay of the donor-recipient interactions that lead to transplant tolerance or rejection. Genetic analysis in transplantation, when linked to demographic and clinical outcomes, has the potential to drive personalized medicine by enabling individualized risk stratification and immunosuppression through the identification of variants associated with immune-mediated complications, post-transplant disease or alterations in drug-metabolizing genes.

Emergent Transcriptomic Technologies and Their Role in the Discovery of Biomarkers of Liver Transplant Tolerance

Liver transplantation offers a unique window into transplant immunology due, in part, to the considerable proportion of recipients who develop immunological tolerance to their allograft. Biomarkers are able to identify and predict such a state of tolerance, and thereby able to establish suitable candidates for the minimization of hazardous immunosuppressive therapies, are not only of great potential clinical benefit but might also shed light on the immunological mechanisms underlying tolerance and rejection. Here, we review the emergent transcriptomic technologies serving as drivers of biomarker discovery, we appraise efforts to identify a molecular signature of liver allograft tolerance, and we consider the implications of this work on the mechanistic understanding of immunological tolerance.

Proteomics in transplantation

Proteomics and biochemical profiling have emerged as exciting and powerful tools in clinical biomarker research. In the field of transplantation, proteomics aims not only at developing noninvasive means for immune monitoring but also to gain mechanistic insights into the pathophysiology of the alloimmune response and hence defining new therapeutic targets. This chapter provides an overview of proteomic biomarker-driven approaches and its underlying concepts and discusses the advantages, clinical implications, challenges, and limitations of this novel modality as it relates to solid organ transplantation.

Transplantation genetics: current status and prospects

Over the last decade, advances in genetic technologies have accelerated our understanding of the genetic diversity across individuals and populations. Case-control and population-based studies have led to several thousand genetic associations across a range of phenotypes and traits being unveiled. Despite widespread and successful use of organ transplantation as a curative therapy for organ failure, genetic research has yet to make a major impact on transplantation practice aside from HLA matching. New studies indicate that non-HLA loci, termed minor histocompatibility antigens (mHAs), may play an important role in graft rejection. With several million common and rare polymorphisms observed between any two unrelated individuals, a number of these polymorphisms represent mHAs, and may underpin transplantation rejection. Genetic variation is also recognized as contributing to clinical outcomes including response to immunosuppressants, introducing the possibility of genotype-guided prescribing in the very near future. This review summarizes existing knowledge of the impact of genetics on transplantation outcomes and therapeutic responses, and highlights the translational potential that new genomic knowledge may bring to this field.

What are the key challenges we face in kidney transplantation today?

Transplantation is more predictable than it was 20 to 30 years ago and innovation over the last 20 years has been rapid, delivering substantial short-term and medium-term improvements. The challenges ahead are to deliver improved results globally in the context of also preventing chronic disease and reducing the costs of treatment. Countries achieving the best rates of transplantation combine deceased and living donors and can transplant more than 50 people per annum per million population, so why can this not be achieved everywhere? The mortality rates have dropped, but they are still up to 10-fold worse than age- and sex-matched controls, such that transplantation ages individuals by 30 years in terms of mortality risk. Cardiovascular disease, infection and malignancy remain the targets if mortality is to normalize. Graft survival rates will not change until the multiple injuries constituting chronic allograft dysfunction and the problems of recurrent disease can be brought to heel. Biomarkers may provide the next innovation to advance outcomes, but early experimental tolerance protocols implemented in clinical practice in at least three centers may deliver results more quickly.

Advances in lung preservation

After a brief review of conventional lung preservation, this article discusses the rationale behind ex vivo lung perfusion and how it has shifted the paradigm of organ preservation from conventional static cold ischemia to the utilization of functional normothermia, restoring the lung's own metabolism and its reparative processes. Technical aspects and previous clinical experience as well as opportunities to address specific donor organ injuries in a personalized medicine approach are also reviewed.

Immunologic monitoring in transplantation revisited

PURPOSE OF REVIEW

Tailoring immunosuppressive drugs to an individual's needs is crucial to improve long-term outcomes of organ transplant patients. The purpose of this review is to summarize the data on promising biomarkers able to detect the risk of acute or chronic rejection and to discuss the potential issues for their implementation in the clinic.

RECENT FINDINGS

Multiple publications have indicated that circulating antibodies targeting human leukocyte antigen (HLA) and non-HLA antigens as well as donor-specific memory T cells are associated with accelerated graft failure. Other studies published within the year show that specific genomic and proteomic signatures obtained from urine, blood, and graft tissue correlate with acute rejection in kidney and heart transplant patients.

SUMMARY

The development of reliable biomarkers is crucial for individualizing therapy aimed at extending allograft survival and improving patient health. Emerging data indicate that monitoring assays, likely used in panels, have the potential to be diagnostic and possibly predictive of long-term outcome. In addition to ongoing discovery efforts, progress in the field will require multicenter validation, assay standardization, and commercialization so as to efficiently deliver reliable testing strategies to the practicing clinician.

The future of heart transplantation

The field of heart transplantation has seen significant progress in the past 40 years. However, the breakthroughs in long-term outcome have seen stagnation in the past decade. Through advances in genomics and transcriptomics, there is hope that an era of personalized transplant therapy lies in the future. To see where heart transplantation truly fits into the long term, searching for and understanding the alternative approaches for heart failure therapy is both important and inevitable. The application of mechanical circulatory support has contributed to the largest advancement in treatment of end stage heart failure. It has already been approved for destination therapy of heart failure, and greater portability and ease of use of the device will be the future trend. Although it is still not prime time for stem cell therapy, clinical experiences have already suggested its potential therapeutic effects. And finally, whole organ engineering is on the horizon as new techniques have opened the way for this to proceed. In the end, progress on alternative therapies largely depends on our deeper understanding of the mechanisms of heart failure and how to prevent it.

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.

Deceased-donor kidney perfusate and urine biomarkers for kidney allograft outcomes: a systematic review

BACKGROUND

Accurate and reliable assessment of kidney quality before transplantation is needed to predict recipient outcomes and to optimize management and allocation of the allograft. The aim of this study was to systematically review the published literature on biomarkers in two mediums (the perfusate from deceased-donor kidneys receiving machine perfusion and deceased-donor urine) that were evaluated for their possible association with outcomes after kidney transplantation.

METHODS

We searched the Ovid Medline and Scopus databases using broad keywords related to deceased-donor biomarkers in kidney transplantation (limited to humans and the English language). Studies were included if they involved deceased-donor kidneys, measured perfusate or urine biomarkers and studied a possible relationship between biomarker concentrations and kidney allograft outcomes. Each included article was assessed for methodological quality.

RESULTS

Of 1430 abstracts screened, 29 studies met the inclusion criteria. Of these, 23 were studies of perfusate (16 biomarkers examined) and 6 were studies of urine (18 biomarkers examined). Only 3 studies (two perfusate) met the criteria of 'good' quality and only 12 were published since 2000. Perfusate lactate dehydrogenase, glutathione-S-transferase (GST) and aspartate transaminase were all found to be significantly associated with delayed graft function in a majority of their respective studies (6/9, 4/6 and 2/2 studies, respectively). Urine neutrophil gelatinase-associated lipocalin, GST, Trolox-equivalent antioxidant capacity and kidney injury molecule-1 were found to be significantly associated with allograft outcomes in single studies that examined diverse end points.

CONCLUSION

Higher quality studies are needed to investigate modern kidney injury biomarkers, to validate novel biomarkers in larger donor populations and to determine the incremental predictive value of biomarkers over traditional clinical variables.

The coin toss of B cells in rejection and tolerance: danger versus defense

Transplantation is the preferred therapy for the end stage organ disease. Since the introduction of organ transplantation into medical practice in 1953 [1], significant progress has been achieved in patient and graft survival rates due to improvements in surgical techniques and more targeted immunosuppressive medications [2]. Nevertheless, current gaps in the management of the transplant patient stem from an incomplete understanding about the heterogeneity of the injury response in organ transplantation, at different rates and different time points after transplantation, as well as our inability to monitor the immunologic threshold of risk versus safety in each individual patient. Recent advances in immunology/transplantation biology with the advent of high throughput "omic" assays such as gene microarrays, proteomics, metabolomics, antibiomics, chemical genomics and functional imaging with nanoparticles, offers us unique methods to interrogate and decipher the variability and unpredictability of the immune response in organ transplantation (Fig. 1) [3]. Recent studies using these applications [3-8] have uncovered a critical and pivotal role for specific B cell lineages in organ injury [9] and organ acceptance [10,11] (Fig. 2). The availability of specific therapies against some of these defined B cell populations provides for an exciting new field of B cell targeted manipulation that can both abrogate the allospecific injury response, as well as promote allospecific graft accommodation and health.

Peripheral blood sampling for the detection of allograft rejection: biomarker identification and validation

Currently, acute allograft rejection can only be detected reliably by deterioration of graft function confirmed by allograft biopsy. A huge drawback of this method of diagnosis is that substantial organ damage has already taken place at the time that rejection is diagnosed. Discovering and validating noninvasive biomarkers that predict acute rejection, and chronic allograft dysfunction, is of great importance. Many studies have investigated changes in the peripheral blood in an attempt to find biomarkers that reflect changes in the graft directly or indirectly. Herein, we will review the promises and limitations of the peripheral blood biomarkers that have been described in the literature so far.