Objective
The project aims to establish novel cell free DNA and cell free RNA biomarkers present in the blood of islet transplant (IT) recipients that can predict IT outcomes/injury and help guide management of future islet transplant recipients. Under AIM 1: COH will send samples available before and after IT previously transplanted T1D to Romix Biosciences for cfRNA analysis and use Romix’s machine-learning outcome prediction with results obtained from City of Hope and actual clinical and other laboratory information already exist at COH. In parallel, COH will complete the measurement of demethylated insulin gene (qMSP) sample analysis and examine the results for potential complementarity with islet cfDNA. Under Aim 2: Samples from new participants in current and future IT protocols will be assessed by COH’s BiPAP and qMSP assays and shared with Romix’s for cfRNA analysis and machine-learning outcome prediction. This project will be complete over two years.
Background Rationale
This project builds upon unique cell genomic markers (cell free DNA and cell free RNA) developed by City of Hope (COH) and Romix Biosciences. COH has conducted islet transplantation (IT) in patients with Type 1 Diabetes for over 20 years and has hundreds of stored specimens and a large database to support analyses of these biomarkers under this project. COH developed two cfDNA assays. The first assay (BiPAP) detects donor cfDNA in the blood of IT recipients as a measure of donor-specific islet graft injury. When cells die they spill their DNA contents and these DNA pieces or snips (SNPs) can be detected in blood. COH have analyzed blood from patients before and after IT and found that donor cfDNA is present during the initial days after IT when some islet loss is expected, but reappears or persists in patients who experience islet rejection. COH has also developed another cfDNA assay (qMSP) for detecting specific injury to insulin-making beta cells by measuring demethylated (active) insulin gene, which exists only in the beta cells, while all other body cells have methylated (inactive) insulin gene.
While cfDNA is an excellent measure of cell death, it does not reveal why the cells died. Romix Biosciences has developed a cfRNA profiling assay and advanced machine learning analytics platform. They have processed thousands of samples and published on the predictive power of cfRNA in a range of clinical settings, including for other cell transplants and inflammatory diseases. They have found that cfRNA reflects real-time signals from cell therapy products, immune cells, and distant organ health that can help predict outcomes.
Together, these cfDNA and cfRNA biomarkers hold promise for monitoring islet graft health, understanding mechanisms of injury, and generating a unique and complementary biomarker panel to guide the care of future IT recipients.
Description of Project
Islet transplantation (IT) is capable of stabilizing blood glucose and permitting insulin independence in adults with type 1 diabetes (T1D). However, the degree and durability of graft function varies between patients. Assessment of IT outcomes has focused on improvement in blood sugar control with reduced insulin requirements. However, these changes may not appear until significant damage to the islets have already occurred. Interactions between the islets and the recipient can lead to immune rejection and cell stress/exhaustion, which remain poorly understood. Genomic assessments of recipient blood have potential to clarify these complex processes and allow early detection of injury. Cell-free DNA (cfDNA) can be used to detect donor/cell specific injury, while cell-free RNA (cfRNA) contains signals from cell therapy products, immune cells, and distant organs that influence IT success. City of Hope (COH) and Romix Biosciences have developed novel genomic analyses for measuring cell free DNA and RNA signals with compelling preliminary evidence supporting their potential to aid clinical monitoring and management of IT patients. This project will evaluate cfDNA and cfRNA signals in groups of prior islet transplant recipients and in new patients undergoing islet transplant to determine their ability to predict IT outcomes and injury.
Anticipated Outcome
Together, the islet donor cfDNA (to detect islet graft injury), demethylated insulin gene (to detect beta cell injury), and total cfRNA profiles (to detect graft and whole-body responses) will establish a first of its kind, complementary biomarker panel for monitoring islet graft health and understanding mechanisms of injury to guide the care of IT recipients. Positive findings in this initial study are expected to yield preliminary data needed to support future trials to support regulatory clearance and clinical application.
Relevance to T1D
This project is in direct alignment with Breakthrough T1D’s Project ACT, which is focused on accelerating cell therapies for people with T1D. Establishment of a novel and complementary biomarker panel using cfDNA to distinguish between different types of cell injury combined with cfRNA analysis to clarify the mechanisms underlying those injuries has the potential to transform the monitoring and success of islet transplantation in T1D. These approaches could also be useful for stem-cell derived islet transplant and immunotherapies for T1D.