Dr. Daniel R. Salomon is a Professor and Director of the Laboratory for Functional Genomics at The Scripps Research Institute. He has been studying the biology of kidney transplantation for most of his career. The focus of his laboratory is the integrated study of transplantation immunology using the latest tools of functional genomics and molecular immunology including microarrays, next-generation sequencing and mass spectrometry. At the recent Ion World Tour in San Diego, he spoke about his research projects; including this work to, in the future, develop molecular diagnostics which may be used for individual patient management in the future and a new view into the role of the urinary microbiome in organ rejection.
First, a bit of background into kidney transplantation in the U.S. There are over 250,000 Americans with kidney transplants living today and about 17,000 new transplants done each year. According to the National Institutes of Health, diabetes is the most common cause of end stage kidney disease (https://www.nlm.nih.gov/medlineplus/ency/article/003005.htm) though other diseases, such as hypertension and glomerulonephritis, contribute to the need for transplantation. While the 10 year survival rate has increased from 25% in 1980 to nearly 45% in 2009 (http://www.niddk.nih.gov/health-information/health-statistics/Pages/kidney-disease-statistics-united-states.aspx#14), it means that the majority of patients will lose their transplant within 10 years, return to dialysis, require a new transplant at a time of a pressing organ shortage or die of end stage organ failure. Unfortunately, these survival statistics have not changed significantly in the last decade and that defines a significant unmet medical need to understand the causes and design a new generation of therapy.
Dr. Salomon and his laboratory are searching for biomarkers that may be used in the future to define which subjects are at risk for rejection. Success in this effort may potentially create a set of novel laboratory tests to optimize the efficacy of immunosuppressive therapy. The hope is that effective therapy will translate to better graft survival, a premise that is well founded in three decades of transplant history but will need to be proven. Moreover, a suite of tests that accurately reflect the efficacy of immunosuppressive therapy may create future opportunities to test the next generation of new drugs.
In this context, Dr. Salomon presented his most recent efforts to analyze archived samples in the hopes of finding biomarkers that will one day be used to develop a test for subclinical acute rejection. This is a state of active immune rejection and tissue injury that occurs in about 20-25% of all transplant patients in the first year. The frustrating fact is that it is completely invisible because there is no change in kidney function as measured by current tests until the destructive process has destroyed 50% of the kidney. In fact, it was only identified when a number of transplant centers, perplexed by the failure to improve long term survival rates began doing serial monitoring biopsies at fixed times in the first year after transplantation. The initial search for subclinical biomarkers has been performed on 69 sets of archived blood and biopsy samples and then duplicated in an additional 123 sample pairs. The initial work was done on commercial microarrays and replicated using Ion Torrent™ sequencing by an RNA-seq. Over 500 differentially expressed genes have been discovered between the sample types of ‘clinical acute rejection’, ‘subclinical acute rejection’ and ‘transplant excellent’ controls. Work in the lab continues to refine these expression profiles.
A more recent research study came about as they were investigating the role of antibody-producing B cells in archived samples with chronic rejection. Chronic rejection is the natural evolution of an uncontrolled immune process: subclinical to clinical acute rejection and then chronic rejection. After sequencing VDJ libraries of B cells obtained from such samples, they discovered that 2 germline sequences, IGHV1-69 and IGHV3-23, were over-expressed and clonal. After expression of these sequences in a baculovirus library, they demonstrated no reaction to the critical antigens of traditional transplant immunity, the HLA antigens. What was their target? As it turned out, these VDJ sequences were common to a number of known antibodies to microbial and viral targets. So Dr. Salomon decided to investigate the microbiome of these samples using the Ion 16S™ Metagenomics Solution. It will come as no surprise that E. coli is the most commonly found microbe. But what is surprising is the difference in the microbial populations of the cohorts. The ‘chronic rejection’ samples had a much more diverse population of bacteria than the ‘transplant excellent’ samples, with some of them being potentially pathogenic. In addition, there were unique differences in the microbial species present in male vs female samples with chronic rejection. The intriguing question now is whether early identification of changes in an individual urinary sample’s microbiome using RNA-seq metagenomics might be able to guide a new approach involving microbial replacement therapy to prevent of chronic rejection. It’s still very early days in this area of research, but you can keep informed of the progress on these projects at Dr. Salomon’s laboratory website.
For Research Use Only. Not for use in diagnostic procedures.