Designer genes: Filling the gap in transplantation

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.

Deconvoluting the 'omics' for organ transplantation

PURPOSE OF REVIEW

The desire for biomarkers for diagnosis and prognosis of diseases has never been greater. With the availability of genome data and an increased availability of proteome data, the discovery of biomarkers has become increasingly feasible. This article reviews some recent applications of the many evolving 'omic technologies to organ transplantation.

RECENT FINDINGS

With the advancement of many high-throughput 'omic techniques such as genomics, metabolomics, antibiomics, peptidomics, and proteomics, efforts have been made to understand potential mechanisms of specific graft injuries and develop novel biomarkers for acute rejection, chronic rejection, and operational tolerance.

SUMMARY

The translation of potential biomarkers from the laboratory bench to the clinical bedside is not an easy task and will require the concerted effort of the immunologists, molecular biologists, transplantation specialists, geneticists, and experts in bioinformatics. Rigorous prospective validation studies will be needed using large sets of independent patient samples. The appropriate and timely exploitation of evolving 'omic technologies will lay the cornerstone for a new age of translational research for organ transplant monitoring.

Biomarkers to discern transplantation tolerance after allogeneic hematopoietic cell transplantation

Although it is commonly accepted that allogeneic hematopoietic cell transplant (HCT) recipients develop transplantation tolerance and can quickly discontinue all immunosuppressive drugs, existing data does not support this concept. Most patients will require a prolonged duration of immunosuppression, lasting commonly several years. This has even greater importance, as the majority of transplants are now performed utilizing peripheral blood mobilized stem cells, which are associated with an increased risk of chronic graft-versus-host disease (cGVHD) and prolonged duration of immunosuppression. Despite these challenges, the approach to liberation from immunosuppression after HCT is empiric, and biomarkers of operational tolerance after HCT are lacking. Conversely, investigators in solid organ allografting have begun to examine tolerance associated gene expression in renal and hepatic allograft recipients. Significant challenges in the design and interpretation of these studies potentially limit comparisons. However, a relatively unified model is beginning to emerge, which largely recapitulates previously established mechanisms of immune tolerance. This evidence supports a state of immune quiescence with reduced expression of costimulation and immune response genes, and upregulation of cell cycle control genes. Data indirectly supports the importance of tumor growth factor (TGF)-beta, supports the role of CD4(+)CD25(+) regulatory T cells, and offers new insights into the role of natural killer (NK) cells. Distinct in hepatic allograft tolerance, emerging evidence highlights the importance of gammadeltaT cells, and selection of the Vgammadelta1+ subtype among the gammadeltaT cell population. The deficiencies in the current understanding of transplantation tolerance after HCT, as well as the inadequacies evident in the current empiric approach to immunosuppressive medication (IS) management after HCT make clear the rationale for investigation aimed at elucidating tolerance associated biomarkers after HCT.

The proteogenomic path towards biomarker discovery

The desire for biomarkers for diagnosis and prognosis of diseases has never been greater. With the availability of genome data and an increased availability of proteome data, the discovery of biomarkers has become increasingly feasible. However, the task is daunting and requires collaborations among researchers working in the fields of transplantation, immunology, genetics, molecular biology, biostatistics and bioinformatics. With the advancement of high throughput omic techniques such as genomics and proteomics (collectively known as proteogenomics), efforts have been made to develop diagnostic tools from new and to-be discovered biomarkers. Yet biomarker validation, particularly in organ transplantation, remains challenging because of the lack of a true gold standard for diagnostic categories and analytical bottlenecks that face high-throughput data deconvolution. Even though microarray technique is relatively mature, proteomics is still growing with regards to data normalization and analysis methods. Study design, sample selection and rigorous data analysis are the critical issues for biomarker discovery using high-throughput proteogenomic technologies that combine the use and strengths of both genomics and proteomics. In this review, we look into the current status and latest developments in the field of biomarker discovery using genomics and proteomics related to organ transplantation, with an emphasis on the evolution of proteomic technologies.

Noninvasive prediction of organ graft rejection and outcome using gene expression patterns

Development of predictive, diagnostic, and prognostic biomarkers of allograft status and outcome is important and challenging, and may be rewarded with individualized therapy for the organ graft recipient. Herein, we summarize noninvasive messenger RNA profiling studies for ascertaining allograft status and outcome. Nucleic acid-based biomarkers of allograft status have been developed by several laboratories, but the studies have primarily been single center investigations. Ongoing multicenter trials including the Clinical Trials in Organ Transplantation (https://www.ctotstudies.org) should help further to define the clinical utility of noninvasively developed messenger RNA profiles as biomarkers of allograft status and outcome.